From outaleb at web.de  Mon Oct  1 07:46:08 2007
From: outaleb at web.de (issam outaleb)
Date: Mon, 01 Oct 2007 13:46:08 +0200
Subject: [Bioperl-l] help about Fasta file???
Message-ID: <2005673060@web.de>



hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;

all 



#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht m?glich zum ?ffnen!!" ;open (OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;        if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {        #print OUT $1."\n"; #print this IPIs in this file.


 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new file with the description


#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    


		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){


$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien  geschlossen, Kopiervorgang 


. 


	
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From shameer at ncbs.res.in  Mon Oct  1 12:57:15 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Mon, 1 Oct 2007 22:27:15 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>

Dear All,

Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
 My input file are in phylip  treefile format. Any Modules / codes in
Bio::Graphics / Phylogeny sections ?

Input file :
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);

-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in


From luciap at sas.upenn.edu  Mon Oct  1 14:03:00 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:03:00 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
Message-ID: <1191261780.47013654cb81b@webmail.sas.upenn.edu>

I think you'll have better luck using some of already available programs to do
that, you'll get better looking trees. If you just have one tree to draw I
recommend you use:
http://itol.embl.de/

Lucia


Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear All,
>
> Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
>  My input file are in phylip  treefile format. Any Modules / codes in
> Bio::Graphics / Phylogeny sections ?
>
> Input file :
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
> 
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
> 
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania

From shameer at ncbs.res.in  Mon Oct  1 14:39:05 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Tue, 2 Oct 2007 00:09:05 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191263834.47013e5a6af93@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
Message-ID: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>

Dear Lucia,

Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
methods. Some how missed this excellent HOWTO :
http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
tried that and it worked very nicely. I have to work around to beautify
the tree and I am just going to do that.

Thanks & Cheers,
Shameer

> OK
>
> you can use the implementations in Bio::TreeIO
>
> you can basically read the tree in newick format and out as an svg graph
> something like this:
>
> my $in = new Bio::TreeIO(-file => 'input',
>                          -format => 'newick');
> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>                           -format => 'svggraph');
> while( my $tree = $in->next_tree ) {
>     $out->write_tree($tree);
> }
>
> you can also use Bio::Tree::Draw
>
> hope that helps
>
> Lucia
>
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Hi,
>>
>> Thanks for your mail. I have to create these trees as a part of a
>> webserver. i need to generate them dynamically using users input
>> sequence.
>> I think ITOL is not the stuff best suited for my purpose.
>>
>> > I think you'll have better luck using some of already available
>> programs
>> > to do
>> > that, you'll get better looking trees. If you just have one tree to
>> draw I
>> > recommend you use:
>> > http://itol.embl.de/
>> >
>> > Lucia
>> >
>> >
>> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
>> >
>> >> Dear All,
>> >>
>> >> Is it possible to draw a phylogeny tree file in PNG format using
>> Bioperl
>> >> ?
>> >>  My input file are in phylip  treefile format. Any Modules / codes in
>> >> Bio::Graphics / Phylogeny sections ?
>> >>
>> >> Input file :
>> >>
>> >
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
>>  3.
>> >>
>> >
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>  5
>> >>
>> >
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>> >>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
>


-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in


From luciap at sas.upenn.edu  Mon Oct  1 14:48:51 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:48:51 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
Message-ID: <1191264531.47014113f2b54@webmail.sas.upenn.edu>

Yes,
that's the issue about those commands, trees are not pretty at all
that's why for a one tree only kind of thing I rather use ITOL
other thing to try is the tree drawer of the Mesquite package
glad I could help

Lucia

Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear Lucia,
>
> Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
> methods. Some how missed this excellent HOWTO :
> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
> tried that and it worked very nicely. I have to work around to beautify
> the tree and I am just going to do that.
>
> Thanks & Cheers,
> Shameer
>
> > OK
> >
> > you can use the implementations in Bio::TreeIO
> >
> > you can basically read the tree in newick format and out as an svg graph
> > something like this:
> >
> > my $in = new Bio::TreeIO(-file => 'input',
> >                          -format => 'newick');
> > my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >                           -format => 'svggraph');
> > while( my $tree = $in->next_tree ) {
> >     $out->write_tree($tree);
> > }
> >
> > you can also use Bio::Tree::Draw
> >
> > hope that helps
> >
> > Lucia
> >
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Hi,
> >>
> >> Thanks for your mail. I have to create these trees as a part of a
> >> webserver. i need to generate them dynamically using users input
> >> sequence.
> >> I think ITOL is not the stuff best suited for my purpose.
> >>
> >> > I think you'll have better luck using some of already available
> >> programs
> >> > to do
> >> > that, you'll get better looking trees. If you just have one tree to
> >> draw I
> >> > recommend you use:
> >> > http://itol.embl.de/
> >> >
> >> > Lucia
> >> >
> >> >
> >> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >> >
> >> >> Dear All,
> >> >>
> >> >> Is it possible to draw a phylogeny tree file in PNG format using
> >> Bioperl
> >> >> ?
> >> >>  My input file are in phylip  treefile format. Any Modules / codes in
> >> >> Bio::Graphics / Phylogeny sections ?
> >> >>
> >> >> Input file :
> >> >>
> >> >
> >>
> >
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
> >>  3.
> >> >>
> >> >
> >>
> >
>
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>  5
> >> >>
> >> >
> >>
> >
>
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
> >> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> >
>
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania

From jason at bioperl.org  Mon Oct  1 15:32:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 1 Oct 2007 12:32:38 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191264531.47014113f2b54@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
	<1191264531.47014113f2b54@webmail.sas.upenn.edu>
Message-ID: <F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>

I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
for prettier trees - you get postscript out but you can render this  
to png or jpg with unix tools.  If there is a better stand alone tree  
drawing engine we're happy to try and integrate it into bioperl - the  
modules here are native Perl only and you can use the bioperl-run  
modules that wrap DrawTree and DrawGram from EMBOSS to get other PS  
rendering output.

Mesquite, TreeView or other tools are usually much better but not  
always an option if you want to auto-render these images for a  
website, etc.

-jason


On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:

> Yes,
> that's the issue about those commands, trees are not pretty at all
> that's why for a one tree only kind of thing I rather use ITOL
> other thing to try is the tree drawer of the Mesquite package
> glad I could help
>
> Lucia
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Dear Lucia,
>>
>> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
>> Tree::Draw
>> methods. Some how missed this excellent HOWTO :
>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as  
>> well. I
>> tried that and it worked very nicely. I have to work around to  
>> beautify
>> the tree and I am just going to do that.
>>
>> Thanks & Cheers,
>> Shameer
>>
>>> OK
>>>
>>> you can use the implementations in Bio::TreeIO
>>>
>>> you can basically read the tree in newick format and out as an  
>>> svg graph
>>> something like this:
>>>
>>> my $in = new Bio::TreeIO(-file => 'input',
>>>                          -format => 'newick');
>>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>>>                           -format => 'svggraph');
>>> while( my $tree = $in->next_tree ) {
>>>     $out->write_tree($tree);
>>> }
>>>
>>> you can also use Bio::Tree::Draw
>>>
>>> hope that helps
>>>
>>> Lucia
>>>
>>>
>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>
>>>> Hi,
>>>>
>>>> Thanks for your mail. I have to create these trees as a part of a
>>>> webserver. i need to generate them dynamically using users input
>>>> sequence.
>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>
>>>>> I think you'll have better luck using some of already available
>>>> programs
>>>>> to do
>>>>> that, you'll get better looking trees. If you just have one  
>>>>> tree to
>>>> draw I
>>>>> recommend you use:
>>>>> http://itol.embl.de/
>>>>>
>>>>> Lucia
>>>>>
>>>>>
>>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>> Bioperl
>>>>>> ?
>>>>>>  My input file are in phylip  treefile format. Any Modules /  
>>>>>> codes in
>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>
>>>>>> Input file :
>>>>>>
>>>>>
>>>>
>>>
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> 1.51514,_H_255_263:6.20895):0.83877, 
> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> 0.92645,_H_520_534:7.97418):0.15279, 
> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> 1.52226,_H_463_464:5.42226):0.94093, 
> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> 1.64489,_L_336_343:8.00808):0.88402, 
> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> (((((_E_470_474:3.85000,_E_344_348:
>>>>  3.
>>>>>>
>>>>>
>>>>
>>>
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107, 
> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> 0.71112,_L_513_519:6.65273):0.67204, 
> ((_L_296_304:5.00000,_H_292_295:5.00000): 
> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> 1.08193,_H_229_243:7.93459):0.18730, 
> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> 0.07448,_L_120_122:7.07448):1.59389, 
> ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>>>  5
>>>>>>
>>>>>
>>>>
>>>
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> 0.88488,_E__40__48:5.79344):0.60814, 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> 1.25080):0.17461):6.94325);
>>>>>>
>>>>
>>>> --
>>>> Shameer Khadar
>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>> National Centre for Biological Sciences (TIFR)
>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>> T - 91-080-23666001 EXT - 6251
>>>> W - http://www.ncbs.res.in
>>>>
>>>
>>>
>>> Lucia Peixoto
>>> Department of Biology,SAS
>>> University of Pennsylvania
>>>
>>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From outaleb at web.de  Mon Oct  1 22:37:26 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 04:37:26 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
Message-ID: <4701AEE6.6070506@web.de>

Hi every body,
i have some AccNum in a file-> IPI67675
                                                 IPI98976.
                                                 ...

what i want is how can i look in the fasta file (db fasta) if there is 
some match
if yes then copy the entire entry into a new fasta file.
i tried with bioperl but cause i m noob:-(( i don t get it.
thx all


From ULNJUJERYDIX at spammotel.com  Tue Oct  2 02:21:31 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Tue, 2 Oct 2007 14:21:31 +0800
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
Message-ID: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>

Hi!
I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
sequence)
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in
bioperl.

I found similar solutions like
http://www.bio.davidson.edu/projects/DAB/DAB.html
divide and blast (but I need to specify coords)

there also this from the bioperl archives
http://bioinformatics.org/pipermail/bioclusters/2002-August/000375.html

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?

From n.haigh at sheffield.ac.uk  Tue Oct  2 03:56:57 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 08:56:57 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701AEE6.6070506@web.de>
References: <4701AEE6.6070506@web.de>
Message-ID: <4701F9C9.4050808@sheffield.ac.uk>

outaleb Issame wrote:
> Hi every body,
> i have some AccNum in a file-> IPI67675
>                                                  IPI98976.
>                                                  ...
>
> what i want is how can i look in the fasta file (db fasta) if there is 
> some match
> if yes then copy the entire entry into a new fasta file.
> i tried with bioperl but cause i m noob:-(( i don t get it.
> thx all
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   

Can you state clearly, what is in the "AccNum" file exactly, some sample
text from the actual file would be good. Is the FASTA file containing
the sequences in raw FASTA format or has it been processed using
somthing like formatdb from the BLAST software?

A few more details will help people understand and in turn help you with
a swift solution.

Cheers
Nath

From outaleb at web.de  Tue Oct  2 05:22:17 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 11:22:17 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701F9C9.4050808@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
Message-ID: <47020DC9.8040401@web.de>

hi,
with this file i mean, i picked out this Accession Number from IPI-Human 
Dbase,they come from a fasta file,
so they re under eachother like a i a table in separate file now.
what i want is how how can i check it in the fasta File (so in the 
IPI-Human FAsta File), i they re really there;
if yes please copy the entire entry of this Number (>....the sequence 
also)in new fasta file.so that i get at the end a new
FASTA file with jus this IPI Accession Number.
thx and hope was clearly.

Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>Hi every body,
>>i have some AccNum in a file-> IPI67675
>>                                                 IPI98976.
>>                                                 ...
>>
>>what i want is how can i look in the fasta file (db fasta) if there is 
>>some match
>>if yes then copy the entire entry into a new fasta file.
>>i tried with bioperl but cause i m noob:-(( i don t get it.
>>thx all
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>  
>>    
>>
>
>Can you state clearly, what is in the "AccNum" file exactly, some sample
>text from the actual file would be good. Is the FASTA file containing
>the sequences in raw FASTA format or has it been processed using
>somthing like formatdb from the BLAST software?
>
>A few more details will help people understand and in turn help you with
>a swift solution.
>
>Cheers
>Nath
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>


From n.haigh at sheffield.ac.uk  Tue Oct  2 05:56:49 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 10:56:49 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47020DC9.8040401@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de>
Message-ID: <470215E1.4080901@sheffield.ac.uk>

outaleb Issame wrote:
> hi,
> with this file i mean, i picked out this Accession Number from
> IPI-Human Dbase,they come from a fasta file,
> so they re under eachother like a i a table in separate file now.
> what i want is how how can i check it in the fasta File (so in the
> IPI-Human FAsta File), i they re really there;
> if yes please copy the entire entry of this Number (>....the sequence
> also)in new fasta file.so that i get at the end a new
> FASTA file with jus this IPI Accession Number.
> thx and hope was clearly.

Ok, first of all, I'd read the contents of your Accession numbers into a
hash, something like the following (this could be written in a shorter
form, but since you're a newbie I'll leave it in a longer form so you
can follow easier).

-- start script --
use strict;
use Bio::SeqIO;

# change the following three lines to point to the relevant paths
# of your list of accessions file, your fasta file and your output
# fasta file
my $acc_file = "/path/to/your/file";
my $fasta_file_in = "/path/to/your/fasta/file";
my $fasta_file_out = "/path/to/your/fasta/output/file";

# Use a hash to keep a record of accessions we want to find
my %hash_of_req_acc;

# read all the required accessions from the file into the hash as keys
open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
while (<ACC_FILE>) {
  my $line = $_;
  chomp $line;
  $hash_of_req_acc{$_} = 1;
}
close ACC_FILE;

my $seqio_object_in = Bio::SeqIO->new(
  -file => $fasta_file_in,
  -format => 'fasta'
);
my $seqio_object_out = Bio::SeqIO->new(
  -file => $fasta_file_out,
  -format => 'fasta'
);

# loop through all the sequences in the fasta file
while (my $seq_object = $seqio_object_in->next_seq) {
  # get the sequence accession for easy matching
  my $seq_acc = $seq_object->accession_number;

  # write the sequence object to the output fasta file if we have a
matching accession
  $seqio_object_out->write_seq($seq_object) if exists
$hash_of_req_acc{$seq_acc};
}
-- end script --

I haven't tested this, but it should at least get you started. Also, the
fasta description line in the output file may not be exactly as it was
in the input fasta file - if this really matters, you may need to get
back to us. Also, if the input fasta file is huge (many thousands of
sequences) it may be wise to create an index of the fasta file in order
to speed up retrieval.

You may find this page helpful:
http://www.bioperl.org/wiki/HOWTO:SeqIO

Anyway, hope this helps to get you started.
Nath



From outaleb at web.de  Tue Oct  2 06:50:32 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 12:50:32 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <470215E1.4080901@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk>
Message-ID: <47022278.7010700@web.de>

thx for the help, but i got a empty output file,
i think its problem with matching the acc number, my fasta file look like:

*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU...
 >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU..
 >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
MMMMM..*

and my i Accnum File look like:
*IPI00177321
IPI00453473

*i hopt it helps to understand.*
*.


Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>hi,
>>with this file i mean, i picked out this Accession Number from
>>IPI-Human Dbase,they come from a fasta file,
>>so they re under eachother like a i a table in separate file now.
>>what i want is how how can i check it in the fasta File (so in the
>>IPI-Human FAsta File), i they re really there;
>>if yes please copy the entire entry of this Number (>....the sequence
>>also)in new fasta file.so that i get at the end a new
>>FASTA file with jus this IPI Accession Number.
>>thx and hope was clearly.
>>    
>>
>
>Ok, first of all, I'd read the contents of your Accession numbers into a
>hash, something like the following (this could be written in a shorter
>form, but since you're a newbie I'll leave it in a longer form so you
>can follow easier).
>
>-- start script --
>use strict;
>use Bio::SeqIO;
>
># change the following three lines to point to the relevant paths
># of your list of accessions file, your fasta file and your output
># fasta file
>my $acc_file = "/path/to/your/file";
>my $fasta_file_in = "/path/to/your/fasta/file";
>my $fasta_file_out = "/path/to/your/fasta/output/file";
>
># Use a hash to keep a record of accessions we want to find
>my %hash_of_req_acc;
>
># read all the required accessions from the file into the hash as keys
>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>while (<ACC_FILE>) {
>  my $line = $_;
>  chomp $line;
>  $hash_of_req_acc{$_} = 1;
>}
>close ACC_FILE;
>
>my $seqio_object_in = Bio::SeqIO->new(
>  -file => $fasta_file_in,
>  -format => 'fasta'
>);
>my $seqio_object_out = Bio::SeqIO->new(
>  -file => $fasta_file_out,
>  -format => 'fasta'
>);
>
># loop through all the sequences in the fasta file
>while (my $seq_object = $seqio_object_in->next_seq) {
>  # get the sequence accession for easy matching
>  my $seq_acc = $seq_object->accession_number;
>
>  # write the sequence object to the output fasta file if we have a
>matching accession
>  $seqio_object_out->write_seq($seq_object) if exists
>$hash_of_req_acc{$seq_acc};
>}
>-- end script --
>
>I haven't tested this, but it should at least get you started. Also, the
>fasta description line in the output file may not be exactly as it was
>in the input fasta file - if this really matters, you may need to get
>back to us. Also, if the input fasta file is huge (many thousands of
>sequences) it may be wise to create an index of the fasta file in order
>to speed up retrieval.
>
>You may find this page helpful:
>http://www.bioperl.org/wiki/HOWTO:SeqIO
>
>Anyway, hope this helps to get you started.
>Nath
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>


From cjfields at uiuc.edu  Tue Oct  2 09:00:57 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 08:00:57 -0500
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
Message-ID: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>

There is a script that comes with the bioperl core distribution,  
bp_split_seq.pl, which does this.  Here's the CVS location:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
scripts/seq/?cvsroot=bioperl

chris

On Oct 2, 2007, at 1:21 AM, Kevin Lam wrote:

> Hi!
> I am trying to annotate a 200kb sequence by doing blastx to find  
> the protein
> seq location
> I need to split the sequence up so that I get the best hits for  
> each region
> (the top blast hits will mask the smaller proteins if i do it as a  
> whole
> sequence)
> if i were to do it manually i can set the subsequence in the web  
> gui for
> ncbi's blast.
> this way, the blast hits coords are based on the whole 200kb.
>
> but I can't find this option in blast or a straightforward way to  
> do it in
> bioperl.
>
> I found similar solutions like
> http://www.bio.davidson.edu/projects/DAB/DAB.html
> divide and blast (but I need to specify coords)
>
> there also this from the bioperl archives
> http://bioinformatics.org/pipermail/bioclusters/2002-August/ 
> 000375.html
>
> but isn't there an easier way like i can specify blast subsequence  
> 200-900
> of fasta file and it will return the blastx hits in coords in terms  
> of the
> whole 200kb?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From rrc22 at cam.ac.uk  Tue Oct  2 09:38:45 2007
From: rrc22 at cam.ac.uk (Roy Chaudhuri)
Date: Tue, 02 Oct 2007 14:38:45 +0100
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <470249E5.6050206@cam.ac.uk>

> but isn't there an easier way like i can specify blast subsequence 200-900
> of fasta file and it will return the blastx hits in coords in terms of the
> whole 200kb?

Once you have split up your sequence (as Chris suggested), and run your 
BLAST, then you can add the hits to each subsequence as features. The 
subsequences can then be re-assembled using the cat method from 
Bio::SeqUtils, which will adjust the coordinates of the features 
appropriately.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

From cjfields at uiuc.edu  Tue Oct  2 11:03:29 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 10:03:29 -0500
Subject: [Bioperl-l] exonerate
In-Reply-To: <29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
Message-ID: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>

One option is to try running $run->cleanup() after you finish  
parsing, which gets rid of the tempfiles on each run.

chris

On Sep 30, 2007, at 8:53 PM, alan wrote:

> Hi,
>
>
>>> I am calling exonerate.pm within my script while attempting to
>>> align cDNA  to multiple genomic fragments. After processing about
>>> 120+ genomic fragments my code crashes with the following error:
>>>
>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>> aborting...
>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>
>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>> routine yet I get the error message about "too many open files".
>>> Any suggestions on how I should be closing these files?
>>>
>>>
>>> Extract from my code that runs exonerate is listed below.
>>>
>>> foreach my $f(@files) {
>>>   next unless (-f  "$dir/$f");
>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>   my $query_obj = $q_in->next_seq();
>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>> format=>"Fasta");
>>>   my $target_obj = $target_in->next_seq();
>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>
>>>   [code for parsing the data.......]
>>>
>>>   $exonerate_io->close; #tried this line out of desperation but it
>>> did not help :-)
>>> }
>>>
>>> thanks
>>> alan



From outaleb at web.de  Tue Oct  2 10:51:05 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 16:51:05 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47022278.7010700@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de>
Message-ID: <47025AD9.1090105@web.de>

hi again,
i think i can resolve this problem with the method : id_parser();
how can i do that?
any suggestion .or experience??
ehx again



outaleb Issame wrote:

>thx for the help, but i got a empty output file,
>i think its problem with matching the acc number, my fasta file look like:
>
>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU...
> >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU..
> >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>MMMMM..*
>
>and my i Accnum File look like:
>*IPI00177321
>IPI00453473
>
>*i hopt it helps to understand.*
>*.
>
>
>Nathan S. Haigh wrote:
>
>  
>
>>outaleb Issame wrote:
>> 
>>
>>    
>>
>>>hi,
>>>with this file i mean, i picked out this Accession Number from
>>>IPI-Human Dbase,they come from a fasta file,
>>>so they re under eachother like a i a table in separate file now.
>>>what i want is how how can i check it in the fasta File (so in the
>>>IPI-Human FAsta File), i they re really there;
>>>if yes please copy the entire entry of this Number (>....the sequence
>>>also)in new fasta file.so that i get at the end a new
>>>FASTA file with jus this IPI Accession Number.
>>>thx and hope was clearly.
>>>   
>>>
>>>      
>>>
>>Ok, first of all, I'd read the contents of your Accession numbers into a
>>hash, something like the following (this could be written in a shorter
>>form, but since you're a newbie I'll leave it in a longer form so you
>>can follow easier).
>>
>>-- start script --
>>use strict;
>>use Bio::SeqIO;
>>
>># change the following three lines to point to the relevant paths
>># of your list of accessions file, your fasta file and your output
>># fasta file
>>my $acc_file = "/path/to/your/file";
>>my $fasta_file_in = "/path/to/your/fasta/file";
>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>
>># Use a hash to keep a record of accessions we want to find
>>my %hash_of_req_acc;
>>
>># read all the required accessions from the file into the hash as keys
>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>while (<ACC_FILE>) {
>> my $line = $_;
>> chomp $line;
>> $hash_of_req_acc{$_} = 1;
>>}
>>close ACC_FILE;
>>
>>my $seqio_object_in = Bio::SeqIO->new(
>> -file => $fasta_file_in,
>> -format => 'fasta'
>>);
>>my $seqio_object_out = Bio::SeqIO->new(
>> -file => $fasta_file_out,
>> -format => 'fasta'
>>);
>>
>># loop through all the sequences in the fasta file
>>while (my $seq_object = $seqio_object_in->next_seq) {
>> # get the sequence accession for easy matching
>> my $seq_acc = $seq_object->accession_number;
>>
>> # write the sequence object to the output fasta file if we have a
>>matching accession
>> $seqio_object_out->write_seq($seq_object) if exists
>>$hash_of_req_acc{$seq_acc};
>>}
>>-- end script --
>>
>>I haven't tested this, but it should at least get you started. Also, the
>>fasta description line in the output file may not be exactly as it was
>>in the input fasta file - if this really matters, you may need to get
>>back to us. Also, if the input fasta file is huge (many thousands of
>>sequences) it may be wise to create an index of the fasta file in order
>>to speed up retrieval.
>>
>>You may find this page helpful:
>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>
>>Anyway, hope this helps to get you started.
>>Nath
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> 
>>
>>    
>>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>


From rvos at interchange.ubc.ca  Tue Oct  2 13:00:36 2007
From: rvos at interchange.ubc.ca (rvos at interchange.ubc.ca)
Date: Tue, 02 Oct 2007 10:00:36 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <405453b66e.3b66e40545@interchange.ubc.ca>

An alternative is to explore the Bio::Phylo treedrawer:

http://search.cpan.org/~rvosa/Bio-Phylo-0.17_RC6/lib/Bio/Phylo/Treedrawer.pm

This is a separate install (in the interest of full disclosure: I'm the author).

Rutger

----- Original Message -----
From: Jason Stajich <jason at bioperl.org>
Date: Monday, October 1, 2007 12:32 pm
Subject: Re: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?

> I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
> for prettier trees - you get postscript out but you can render this 
> 
> to png or jpg with unix tools.  If there is a better stand alone 
> tree  
> drawing engine we're happy to try and integrate it into bioperl - 
> the  
> modules here are native Perl only and you can use the bioperl-run  
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS 
> 
> rendering output.
> 
> Mesquite, TreeView or other tools are usually much better but not  
> always an option if you want to auto-render these images for a  
> website, etc.
> 
> -jason
> 
> 
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
> 
> > Yes,
> > that's the issue about those commands, trees are not pretty at all
> > that's why for a one tree only kind of thing I rather use ITOL
> > other thing to try is the tree drawer of the Mesquite package
> > glad I could help
> >
> > Lucia
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Dear Lucia,
> >>
> >> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
> >> Tree::Draw
> >> methods. Some how missed this excellent HOWTO :
> >> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as 
> 
> >> well. I
> >> tried that and it worked very nicely. I have to work around to  
> >> beautify
> >> the tree and I am just going to do that.
> >>
> >> Thanks & Cheers,
> >> Shameer
> >>
> >>> OK
> >>>
> >>> you can use the implementations in Bio::TreeIO
> >>>
> >>> you can basically read the tree in newick format and out as an  
> >>> svg graph
> >>> something like this:
> >>>
> >>> my $in = new Bio::TreeIO(-file => 'input',
> >>>                          -format => 'newick');
> >>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >>>                           -format => 'svggraph');
> >>> while( my $tree = $in->next_tree ) {
> >>>     $out->write_tree($tree);
> >>> }
> >>>
> >>> you can also use Bio::Tree::Draw
> >>>
> >>> hope that helps
> >>>
> >>> Lucia
> >>>
> >>>
> >>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>
> >>>> Hi,
> >>>>
> >>>> Thanks for your mail. I have to create these trees as a part 
> of a
> >>>> webserver. i need to generate them dynamically using users input
> >>>> sequence.
> >>>> I think ITOL is not the stuff best suited for my purpose.
> >>>>
> >>>>> I think you'll have better luck using some of already available
> >>>> programs
> >>>>> to do
> >>>>> that, you'll get better looking trees. If you just have one  
> >>>>> tree to
> >>>> draw I
> >>>>> recommend you use:
> >>>>> http://itol.embl.de/
> >>>>>
> >>>>> Lucia
> >>>>>
> >>>>>
> >>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>>>
> >>>>>> Dear All,
> >>>>>>
> >>>>>> Is it possible to draw a phylogeny tree file in PNG format 
> using>>>> Bioperl
> >>>>>> ?
> >>>>>>  My input file are in phylip  treefile format. Any Modules / 
> 
> >>>>>> codes in
> >>>>>> Bio::Graphics / Phylogeny sections ?
> >>>>>>
> >>>>>> Input file :
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> > (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> > 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> > 1.51514,_H_255_263:6.20895):0.83877, 
> > (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> > 0.92645,_H_520_534:7.97418):0.15279, 
> > (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> > 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> > ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> > 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> > (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> > 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> > 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> > 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> > 1.52226,_H_463_464:5.42226):0.94093, 
> > (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> > 1.64489,_L_336_343:8.00808):0.88402, 
> > (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> > (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> > (((((_E_470_474:3.85000,_E_344_348:
> >>>>  3.
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 85000):0.89054,_L_475_478:4.74054):1.20107, 
> > (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> > 0.71112,_L_513_519:6.65273):0.67204, 
> > ((_L_296_304:5.00000,_H_292_295:5.00000): 
> > 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> > 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> > 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> > 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> > 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> > 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> > 1.08193,_H_229_243:7.93459):0.18730, 
> > (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> > ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> > 0.07448,_L_120_122:7.07448):1.59389, 
> > ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> > 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> > 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> > ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> > (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> > 0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>>>  5
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> > (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> > ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> > 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> > 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> > ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> > (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> > 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> > 0.88488,_E__40__48:5.79344):0.60814, 
> > 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> > 1.25080):0.17461):6.94325);
> >>>>>>
> >>>>
> >>>> --
> >>>> Shameer Khadar
> >>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >>>> National Centre for Biological Sciences (TIFR)
> >>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >>>> T - 91-080-23666001 EXT - 6251
> >>>> W - http://www.ncbs.res.in
> >>>>
> >>>
> >>>
> >>> Lucia Peixoto
> >>> Department of Biology,SAS
> >>> University of Pennsylvania
> >>>
> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From Russell.Smithies at agresearch.co.nz  Tue Oct  2 17:34:20 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 10:34:20 +1300
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>

I know this is the Bioperl list but how about just doing it with grep?

	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of outaleb Issame
> Sent: Wednesday, 3 October 2007 3:51 a.m.
> To: outaleb Issame
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> 
> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
> 
> 
> 
> outaleb Issame wrote:
> 
> >thx for the help, but i got a empty output file,
> >i think its problem with matching the acc number, my fasta file look
like:
> >
> >*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU...
> > >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU..
> > >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >MMMMM..*
> >
> >and my i Accnum File look like:
> >*IPI00177321
> >IPI00453473
> >
> >*i hopt it helps to understand.*
> >*.
> >
> >
> >Nathan S. Haigh wrote:
> >
> >
> >
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>
> >>>hi,
> >>>with this file i mean, i picked out this Accession Number from
> >>>IPI-Human Dbase,they come from a fasta file,
> >>>so they re under eachother like a i a table in separate file now.
> >>>what i want is how how can i check it in the fasta File (so in the
> >>>IPI-Human FAsta File), i they re really there;
> >>>if yes please copy the entire entry of this Number (>....the
sequence
> >>>also)in new fasta file.so that i get at the end a new
> >>>FASTA file with jus this IPI Accession Number.
> >>>thx and hope was clearly.
> >>>
> >>>
> >>>
> >>>
> >>Ok, first of all, I'd read the contents of your Accession numbers
into a
> >>hash, something like the following (this could be written in a
shorter
> >>form, but since you're a newbie I'll leave it in a longer form so
you
> >>can follow easier).
> >>
> >>-- start script --
> >>use strict;
> >>use Bio::SeqIO;
> >>
> >># change the following three lines to point to the relevant paths
> >># of your list of accessions file, your fasta file and your output
> >># fasta file
> >>my $acc_file = "/path/to/your/file";
> >>my $fasta_file_in = "/path/to/your/fasta/file";
> >>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>
> >># Use a hash to keep a record of accessions we want to find
> >>my %hash_of_req_acc;
> >>
> >># read all the required accessions from the file into the hash as
keys
> >>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>while (<ACC_FILE>) {
> >> my $line = $_;
> >> chomp $line;
> >> $hash_of_req_acc{$_} = 1;
> >>}
> >>close ACC_FILE;
> >>
> >>my $seqio_object_in = Bio::SeqIO->new(
> >> -file => $fasta_file_in,
> >> -format => 'fasta'
> >>);
> >>my $seqio_object_out = Bio::SeqIO->new(
> >> -file => $fasta_file_out,
> >> -format => 'fasta'
> >>);
> >>
> >># loop through all the sequences in the fasta file
> >>while (my $seq_object = $seqio_object_in->next_seq) {
> >> # get the sequence accession for easy matching
> >> my $seq_acc = $seq_object->accession_number;
> >>
> >> # write the sequence object to the output fasta file if we have a
> >>matching accession
> >> $seqio_object_out->write_seq($seq_object) if exists
> >>$hash_of_req_acc{$seq_acc};
> >>}
> >>-- end script --
> >>
> >>I haven't tested this, but it should at least get you started. Also,
the
> >>fasta description line in the output file may not be exactly as it
was
> >>in the input fasta file - if this really matters, you may need to
get
> >>back to us. Also, if the input fasta file is huge (many thousands of
> >>sequences) it may be wise to create an index of the fasta file in
order
> >>to speed up retrieval.
> >>
> >>You may find this page helpful:
> >>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>Anyway, hope this helps to get you started.
> >>Nath
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >>
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================


From thiago.venancio at gmail.com  Tue Oct  2 17:41:06 2007
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Tue, 2 Oct 2007 18:41:06 -0300
Subject: [Bioperl-l] frac_* methods
Message-ID: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>

Hi all,

This topic was discussed before, but I would like to put it on the list
again, maybe someone has an update.

The methods frac_identical, frac_conserved, frac_aligned_query and
frac_aligned_hit can also be used in the hit context, after HSP tilling. In
my point of view, it is better to use it just in HSPs individually, because
there are some rare/strange kinds of alignments. However, we frequently need
to get one measure of the whole alignment.

Any of the BioPerl masters has an update on this topic ? What is the best
current usage ?

Best.

Thiago

-- 
"Innovation distinguishes between a leader and a follower."
    Steve Jobs

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================

From outaleb at web.de  Tue Oct  2 17:47:07 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 23:47:07 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
Message-ID: <4702BC5B.7040407@web.de>

thx for this, but i want just create new fasta file with my accNumbers 
which i search in the FASTA file(localdbase).
so --> just search this Numbers in the FASTA file, if yes then copy the 
Header and Sequence to other new fasta file .
i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
i get crazy guys.
common some expert in this area??
 


Smithies, Russell wrote:

>I know this is the Bioperl list but how about just doing it with grep?
>
>	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
>
>
>
>  
>
>>-----Original Message-----
>>From: bioperl-l-bounces at lists.open-bio.org
>>    
>>
>[mailto:bioperl-l-bounces at lists.open-
>  
>
>>bio.org] On Behalf Of outaleb Issame
>>Sent: Wednesday, 3 October 2007 3:51 a.m.
>>To: outaleb Issame
>>Cc: bioperl-l at lists.open-bio.org
>>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
>>
>>hi again,
>>i think i can resolve this problem with the method : id_parser();
>>how can i do that?
>>any suggestion .or experience??
>>ehx again
>>
>>
>>
>>outaleb Issame wrote:
>>
>>    
>>
>>>thx for the help, but i got a empty output file,
>>>i think its problem with matching the acc number, my fasta file look
>>>      
>>>
>like:
>  
>
>>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>      
>>>
>>protein
>>    
>>
>>>DDHHHU...
>>>      
>>>
>>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>DDHHHU..
>>>      
>>>
>>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>MMMMM..*
>>>
>>>and my i Accnum File look like:
>>>*IPI00177321
>>>IPI00453473
>>>
>>>*i hopt it helps to understand.*
>>>*.
>>>
>>>
>>>Nathan S. Haigh wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>outaleb Issame wrote:
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>hi,
>>>>>with this file i mean, i picked out this Accession Number from
>>>>>IPI-Human Dbase,they come from a fasta file,
>>>>>so they re under eachother like a i a table in separate file now.
>>>>>what i want is how how can i check it in the fasta File (so in the
>>>>>IPI-Human FAsta File), i they re really there;
>>>>>if yes please copy the entire entry of this Number (>....the
>>>>>          
>>>>>
>sequence
>  
>
>>>>>also)in new fasta file.so that i get at the end a new
>>>>>FASTA file with jus this IPI Accession Number.
>>>>>thx and hope was clearly.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Ok, first of all, I'd read the contents of your Accession numbers
>>>>        
>>>>
>into a
>  
>
>>>>hash, something like the following (this could be written in a
>>>>        
>>>>
>shorter
>  
>
>>>>form, but since you're a newbie I'll leave it in a longer form so
>>>>        
>>>>
>you
>  
>
>>>>can follow easier).
>>>>
>>>>-- start script --
>>>>use strict;
>>>>use Bio::SeqIO;
>>>>
>>>># change the following three lines to point to the relevant paths
>>>># of your list of accessions file, your fasta file and your output
>>>># fasta file
>>>>my $acc_file = "/path/to/your/file";
>>>>my $fasta_file_in = "/path/to/your/fasta/file";
>>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>>
>>>># Use a hash to keep a record of accessions we want to find
>>>>my %hash_of_req_acc;
>>>>
>>>># read all the required accessions from the file into the hash as
>>>>        
>>>>
>keys
>  
>
>>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>>>while (<ACC_FILE>) {
>>>>my $line = $_;
>>>>chomp $line;
>>>>$hash_of_req_acc{$_} = 1;
>>>>}
>>>>close ACC_FILE;
>>>>
>>>>my $seqio_object_in = Bio::SeqIO->new(
>>>>-file => $fasta_file_in,
>>>>-format => 'fasta'
>>>>);
>>>>my $seqio_object_out = Bio::SeqIO->new(
>>>>-file => $fasta_file_out,
>>>>-format => 'fasta'
>>>>);
>>>>
>>>># loop through all the sequences in the fasta file
>>>>while (my $seq_object = $seqio_object_in->next_seq) {
>>>># get the sequence accession for easy matching
>>>>my $seq_acc = $seq_object->accession_number;
>>>>
>>>># write the sequence object to the output fasta file if we have a
>>>>matching accession
>>>>$seqio_object_out->write_seq($seq_object) if exists
>>>>$hash_of_req_acc{$seq_acc};
>>>>}
>>>>-- end script --
>>>>
>>>>I haven't tested this, but it should at least get you started. Also,
>>>>        
>>>>
>the
>  
>
>>>>fasta description line in the output file may not be exactly as it
>>>>        
>>>>
>was
>  
>
>>>>in the input fasta file - if this really matters, you may need to
>>>>        
>>>>
>get
>  
>
>>>>back to us. Also, if the input fasta file is huge (many thousands of
>>>>sequences) it may be wise to create an index of the fasta file in
>>>>        
>>>>
>order
>  
>
>>>>to speed up retrieval.
>>>>
>>>>You may find this page helpful:
>>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>>
>>>>Anyway, hope this helps to get you started.
>>>>Nath
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>
>=======================================================================
>Attention: The information contained in this message and/or attachments
>from AgResearch Limited is intended only for the persons or entities
>to which it is addressed and may contain confidential and/or privileged
>material. Any review, retransmission, dissemination or other use of, or
>taking of any action in reliance upon, this information by persons or
>entities other than the intended recipients is prohibited by AgResearch
>Limited. If you have received this message in error, please notify the
>sender immediately.
>=======================================================================
>
>  
>


From jason at bioperl.org  Tue Oct  2 18:22:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 15:22:59 -0700
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>

I think my answer before was something to the tune of:

Use an alignment algorithm that finds a single best alignment like  
FASTA or Smith-Waterman (SW) if what you want is a single number that  
represents the alignment.  BLAST is great for fast searching but  
FASTA or SW/SSEARCH are going to be better at creating an alignment.   
Consider the -postsw option in WUBLAST as well as it will realign the  
HSPs with SW.

I personally never use the frac alignment summary stats for the Hit  
object for this reason unless I know I am going to have a single HSP.

-jason

On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago
>
> -- 
> "Innovation distinguishes between a leader and a follower."
>     Steve Jobs
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From cjfields at uiuc.edu  Tue Oct  2 18:32:30 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 17:32:30 -0500
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <B9E32251-2A8E-4079-B256-9665D9987B02@uiuc.edu>

I think their use is based on what you are trying to accomplish.  For  
instance I am currently running a lot of small BLASTN queries  
(limiting by normalized bit score), so I tend to look at the HSP data  
more.  However, in other circumstances I might want the overall  
frac_identical for all HSPs ($hit->frac_identical).  YMMV.

chris

On Oct 2, 2007, at 4:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago



From razi.khaja at gmail.com  Tue Oct  2 19:46:12 2007
From: razi.khaja at gmail.com (Razi Khaja)
Date: Tue, 2 Oct 2007 19:46:12 -0400
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4702BC5B.7040407@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de> <470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
	<4702BC5B.7040407@web.de>
Message-ID: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>

Here is the easiest non-bioperl solution using executables provided
with ncbi's blast:

(1) format your multifasta file into a blast database

> /usr/local/ncbi/blast-2.2.16/bin/formatdb -i yourmultifastafile -t yourblastdb

(2) extract sequences from the newly created blast database with a
file containing a list of accession numbers (one on each line)

> /usr/local/ncib/blast-2.2.16/bin/fastacmd -d yourblastdb -i inputfilewithaccessionnumbers -o outputfile

Your outputfile should be a multifasta file of your list of accession numbers

blast executables are available from
http://www.ncbi.nlm.nih.gov/blast/download.shtml

Hope that helps.
Razi Khaja

On 10/2/07, outaleb Issame <outaleb at web.de> wrote:
> thx for this, but i want just create new fasta file with my accNumbers
> which i search in the FASTA file(localdbase).
> so --> just search this Numbers in the FASTA file, if yes then copy the
> Header and Sequence to other new fasta file .
> i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
> i get crazy guys.
> common some expert in this area??
>
>
>
> Smithies, Russell wrote:
>
> >I know this is the Bioperl list but how about just doing it with grep?
> >
> >       grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
> >
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: bioperl-l-bounces at lists.open-bio.org
> >>
> >>
> >[mailto:bioperl-l-bounces at lists.open-
> >
> >
> >>bio.org] On Behalf Of outaleb Issame
> >>Sent: Wednesday, 3 October 2007 3:51 a.m.
> >>To: outaleb Issame
> >>Cc: bioperl-l at lists.open-bio.org
> >>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> >>
> >>hi again,
> >>i think i can resolve this problem with the method : id_parser();
> >>how can i do that?
> >>any suggestion .or experience??
> >>ehx again
> >>
> >>
> >>
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>>thx for the help, but i got a empty output file,
> >>>i think its problem with matching the acc number, my fasta file look
> >>>
> >>>
> >like:
> >
> >
> >>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>
> >>>
> >>protein
> >>
> >>
> >>>DDHHHU...
> >>>
> >>>
> >>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>DDHHHU..
> >>>
> >>>
> >>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>MMMMM..*
> >>>
> >>>and my i Accnum File look like:
> >>>*IPI00177321
> >>>IPI00453473
> >>>
> >>>*i hopt it helps to understand.*
> >>>*.
> >>>
> >>>
> >>>Nathan S. Haigh wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>outaleb Issame wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>hi,
> >>>>>with this file i mean, i picked out this Accession Number from
> >>>>>IPI-Human Dbase,they come from a fasta file,
> >>>>>so they re under eachother like a i a table in separate file now.
> >>>>>what i want is how how can i check it in the fasta File (so in the
> >>>>>IPI-Human FAsta File), i they re really there;
> >>>>>if yes please copy the entire entry of this Number (>....the
> >>>>>
> >>>>>
> >sequence
> >
> >
> >>>>>also)in new fasta file.so that i get at the end a new
> >>>>>FASTA file with jus this IPI Accession Number.
> >>>>>thx and hope was clearly.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>Ok, first of all, I'd read the contents of your Accession numbers
> >>>>
> >>>>
> >into a
> >
> >
> >>>>hash, something like the following (this could be written in a
> >>>>
> >>>>
> >shorter
> >
> >
> >>>>form, but since you're a newbie I'll leave it in a longer form so
> >>>>
> >>>>
> >you
> >
> >
> >>>>can follow easier).
> >>>>
> >>>>-- start script --
> >>>>use strict;
> >>>>use Bio::SeqIO;
> >>>>
> >>>># change the following three lines to point to the relevant paths
> >>>># of your list of accessions file, your fasta file and your output
> >>>># fasta file
> >>>>my $acc_file = "/path/to/your/file";
> >>>>my $fasta_file_in = "/path/to/your/fasta/file";
> >>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>>>
> >>>># Use a hash to keep a record of accessions we want to find
> >>>>my %hash_of_req_acc;
> >>>>
> >>>># read all the required accessions from the file into the hash as
> >>>>
> >>>>
> >keys
> >
> >
> >>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>>>while (<ACC_FILE>) {
> >>>>my $line = $_;
> >>>>chomp $line;
> >>>>$hash_of_req_acc{$_} = 1;
> >>>>}
> >>>>close ACC_FILE;
> >>>>
> >>>>my $seqio_object_in = Bio::SeqIO->new(
> >>>>-file => $fasta_file_in,
> >>>>-format => 'fasta'
> >>>>);
> >>>>my $seqio_object_out = Bio::SeqIO->new(
> >>>>-file => $fasta_file_out,
> >>>>-format => 'fasta'
> >>>>);
> >>>>
> >>>># loop through all the sequences in the fasta file
> >>>>while (my $seq_object = $seqio_object_in->next_seq) {
> >>>># get the sequence accession for easy matching
> >>>>my $seq_acc = $seq_object->accession_number;
> >>>>
> >>>># write the sequence object to the output fasta file if we have a
> >>>>matching accession
> >>>>$seqio_object_out->write_seq($seq_object) if exists
> >>>>$hash_of_req_acc{$seq_acc};
> >>>>}
> >>>>-- end script --
> >>>>
> >>>>I haven't tested this, but it should at least get you started. Also,
> >>>>
> >>>>
> >the
> >
> >
> >>>>fasta description line in the output file may not be exactly as it
> >>>>
> >>>>
> >was
> >
> >
> >>>>in the input fasta file - if this really matters, you may need to
> >>>>
> >>>>
> >get
> >
> >
> >>>>back to us. Also, if the input fasta file is huge (many thousands of
> >>>>sequences) it may be wise to create an index of the fasta file in
> >>>>
> >>>>
> >order
> >
> >
> >>>>to speed up retrieval.
> >>>>
> >>>>You may find this page helpful:
> >>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>>>
> >>>>Anyway, hope this helps to get you started.
> >>>>Nath
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l at lists.open-bio.org
> >>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>_______________________________________________
> >>>Bioperl-l mailing list
> >>>Bioperl-l at lists.open-bio.org
> >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >=======================================================================
> >Attention: The information contained in this message and/or attachments
> >from AgResearch Limited is intended only for the persons or entities
> >to which it is addressed and may contain confidential and/or privileged
> >material. Any review, retransmission, dissemination or other use of, or
> >taking of any action in reliance upon, this information by persons or
> >entities other than the intended recipients is prohibited by AgResearch
> >Limited. If you have received this message in error, please notify the
> >sender immediately.
> >=======================================================================
> >
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From jason at bioperl.org  Tue Oct  2 20:50:37 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 17:50:37 -0700
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
Message-ID: <CF48176B-CE5B-40EC-81DE-8C3114502ADE@bioperl.org>

http://bioperl.open-bio.org/wiki/ 
FAQ#How_do_I_use_Bio::Index::Fasta_and_index_on_different_ids.3F

On Oct 2, 2007, at 7:51 AM, outaleb Issame wrote:

> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
>
>
>
> outaleb Issame wrote:
>
>> thx for the help, but i got a empty output file,
>> i think its problem with matching the acc number, my fasta file  
>> look like:
>>
>> *>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to  
>> NOD3 protein
>> DDHHHU...
>>> IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> DDHHHU..
>>> IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> MMMMM..*
>>
>> and my i Accnum File look like:
>> *IPI00177321
>> IPI00453473
>>
>> *i hopt it helps to understand.*
>> *.
>>
>>
>> Nathan S. Haigh wrote:
>>
>>
>>
>>> outaleb Issame wrote:
>>>
>>>
>>>
>>>
>>>> hi,
>>>> with this file i mean, i picked out this Accession Number from
>>>> IPI-Human Dbase,they come from a fasta file,
>>>> so they re under eachother like a i a table in separate file now.
>>>> what i want is how how can i check it in the fasta File (so in the
>>>> IPI-Human FAsta File), i they re really there;
>>>> if yes please copy the entire entry of this Number (>....the  
>>>> sequence
>>>> also)in new fasta file.so that i get at the end a new
>>>> FASTA file with jus this IPI Accession Number.
>>>> thx and hope was clearly.
>>>>
>>>>
>>>>
>>>>
>>> Ok, first of all, I'd read the contents of your Accession numbers  
>>> into a
>>> hash, something like the following (this could be written in a  
>>> shorter
>>> form, but since you're a newbie I'll leave it in a longer form so  
>>> you
>>> can follow easier).
>>>
>>> -- start script --
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> # change the following three lines to point to the relevant paths
>>> # of your list of accessions file, your fasta file and your output
>>> # fasta file
>>> my $acc_file = "/path/to/your/file";
>>> my $fasta_file_in = "/path/to/your/fasta/file";
>>> my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>
>>> # Use a hash to keep a record of accessions we want to find
>>> my %hash_of_req_acc;
>>>
>>> # read all the required accessions from the file into the hash as  
>>> keys
>>> open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>> while (<ACC_FILE>) {
>>> my $line = $_;
>>> chomp $line;
>>> $hash_of_req_acc{$_} = 1;
>>> }
>>> close ACC_FILE;
>>>
>>> my $seqio_object_in = Bio::SeqIO->new(
>>> -file => $fasta_file_in,
>>> -format => 'fasta'
>>> );
>>> my $seqio_object_out = Bio::SeqIO->new(
>>> -file => $fasta_file_out,
>>> -format => 'fasta'
>>> );
>>>
>>> # loop through all the sequences in the fasta file
>>> while (my $seq_object = $seqio_object_in->next_seq) {
>>> # get the sequence accession for easy matching
>>> my $seq_acc = $seq_object->accession_number;
>>>
>>> # write the sequence object to the output fasta file if we have a
>>> matching accession
>>> $seqio_object_out->write_seq($seq_object) if exists
>>> $hash_of_req_acc{$seq_acc};
>>> }
>>> -- end script --
>>>
>>> I haven't tested this, but it should at least get you started.  
>>> Also, the
>>> fasta description line in the output file may not be exactly as  
>>> it was
>>> in the input fasta file - if this really matters, you may need to  
>>> get
>>> back to us. Also, if the input fasta file is huge (many thousands of
>>> sequences) it may be wise to create an index of the fasta file in  
>>> order
>>> to speed up retrieval.
>>>
>>> You may find this page helpful:
>>> http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>
>>> Anyway, hope this helps to get you started.
>>> Nath
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From Russell.Smithies at agresearch.co.nz  Tue Oct  2 21:05:25 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 14:05:25 +1300
Subject: [Bioperl-l] coloring of HSPs in blast panel
In-Reply-To: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk><47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de><D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz><4702BC5B.7040407@web.de>
	<62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDC73@imail.agresearch.co.nz>

Hi all,
I'm using a modified version of Lincoln's tutorial
(http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output)
and I'm colouring the HSPs by setting the -bgcolor by score with a sub
to give a similar image to that from NCBI but for some reason, my
colours are coming out wrong (see attached example)
They seem to be off by one but I can't see why.

Any ideas?

I can't be certain but I think it's only started doing this since our
BLAST upgrade to 2.2.17 a few weeks ago.

Here's the colouring code:
------------------------------------------------------------------------
-------
my $track = $panel->add_track(
                              -glyph       => 'segments',
                              -label       => 1,
                              -connector   => 'dashed',
                              -bgcolor     => sub {
                                my $feature = shift;
                                my $score = $feature->score;
			return 'red'       if $score >= 200;
                                    return 'fuchsia' if $score >= 80;
                                    return 'lime'      if $score >= 50;
			return 'blue'      if $score >= 40;
                                    return 'black';
                               },
                              -font2color  => 'gray',
                              -sort_order  => 'high_score',
                              -description => sub {
                                my $feature = shift;
                                return unless
$feature->has_tag('description');
                                my ($description) =
$feature->each_tag_value('description');
                                my $score = $feature->score;
                                "$description, score=$score";
                               },
                             );
------------------------------------------------------------------------
---------


Thanx,

Russell Smithies




=======================================================================
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From aaron.j.mackey at gsk.com  Tue Oct  2 21:40:14 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Tue, 2 Oct 2007 21:40:14 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
Message-ID: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>

Let me second Jason's comment that while BLAST is a great search program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with the 
FASTA package) is now vector-parallelized on most i386 architectures, it 
is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run 
BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 10:50:47 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 10:50:47 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
References: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
	<OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>

I agree that BLAST is not a very good alignment algorithm but believe
there are plenty of reasons to run BLAST, especially when placing a
contig /BAC/PAC to a genome. In those cases, fully implementation of SW
requires an unpractical matrix of n X m.   

Currently we are developing an algorithm which will run global alignment
after BLAST. Hopefully a Perl wrapper will become available next year.


Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Tuesday, October 02, 2007 9:40 PM
To: Jason Stajich
Cc: bioperl-l list; Thiago Venancio
Subject: Re: [Bioperl-l] frac_* methods

Let me second Jason's comment that while BLAST is a great search
program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
the 
FASTA package) is now vector-parallelized on most i386 architectures, it

is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run

BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l


From aaron.j.mackey at gsk.com  Wed Oct  3 11:53:12 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Wed, 3 Oct 2007 11:53:12 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
Message-ID: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are expected 
to occur naturally (i.e. are not an artifact of the experiment that in an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very 
good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical significance)

Please don't get me wrong, I think BLAST is an invaluable tool that fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures, it
> 
> is only about 10 times slower than BLAST for complete database searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> > Consider the -postsw option in WUBLAST as well as it will realign the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the 
> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From vebaev at gmail.com  Wed Oct  3 12:44:35 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 19:44:35 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
Message-ID: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>

Hi,
What methods should I use to draw a CG plot of a sequence (with
bio::graphics)?

Thanks

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 13:37:51 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 13:37:51 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
References: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
	<OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C36@NIHCESMLBX8.nih.gov>

I agree what you said. 

One of the reasons that we introduce 'BLAST-guided-global alignment
(NW)' is that a significant amount of clones are either of low quality,
partially sequenced, erroneously assembled, or come from non reference
strain.   

Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Wednesday, October 03, 2007 11:53 AM
To: Cui, Wenwu (NIH/NLM/NCBI) [C]
Cc: bioperl-l list; Jason Stajich; Thiago Venancio
Subject: RE: [Bioperl-l] frac_* methods

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance
for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling
algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are
expected 
to occur naturally (i.e. are not an artifact of the experiment that in
an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very

good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical
significance)

Please don't get me wrong, I think BLAST is an invaluable tool that
fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of
SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global
alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with
so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures,
it
> 
> is only about 10 times slower than BLAST for complete database
searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even
run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number
that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment.

> > Consider the -postsw option in WUBLAST as well as it will realign
the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single
HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the

> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs
individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From cjfields at uiuc.edu  Wed Oct  3 14:19:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 13:19:43 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
Message-ID: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>

You should look at Bio::Graphics::Glyph::dna.  From the POD:

---------------------------

This glyph draws DNA sequences.  At high magnifications, this glyph
will draw the actual base pairs of the sequence (both strands).  At
low magnifications, the glyph will plot the GC content.  By default,
the GC calculation will use non-overlapping bins, but this can be
changed by specifying the gc_window option, in which case, a
sliding window calculation will be used.

For this glyph to work, the feature must return a DNA sequence string
in response to the dna() method. For example, you can use a
Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
like this:
     my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
     my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end  
=> 800 );
     $feature->attach_seq($dna);
     $panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used.

---------------------------

chris

On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:

> Hi,
> What methods should I use to draw a CG plot of a sequence (with
> bio::graphics)?
>
> Thanks
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From vebaev at gmail.com  Wed Oct  3 14:31:49 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 21:31:49 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
Message-ID: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>

Thanks,
I will use Bio::Graphics::Glyph::dna for the classical CG%
(this type is for C+G % or CpG)?


and if I want to draw a similar plot but for example for a % of dinucleotide
(NpN) occurrances in a sliding windiw, what should I use?


Thanks!




2007/10/3, Chris Fields <cjfields at uiuc.edu>:
>
> You should look at Bio::Graphics::Glyph::dna.  From the POD:
>
> ---------------------------
>
> This glyph draws DNA sequences.  At high magnifications, this glyph
> will draw the actual base pairs of the sequence (both strands).  At
> low magnifications, the glyph will plot the GC content.  By default,
> the GC calculation will use non-overlapping bins, but this can be
> changed by specifying the gc_window option, in which case, a
> sliding window calculation will be used.
>
> For this glyph to work, the feature must return a DNA sequence string
> in response to the dna() method. For example, you can use a
> Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
> like this:
>      my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
>      my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end
> => 800 );
>      $feature->attach_seq($dna);
>      $panel->add_track( $feature, -glyph => 'dna' );
>
> A Bio::Graphics::Feature object may also be used.
>
> ---------------------------
>
> chris
>
> On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:
>
> > Hi,
> > What methods should I use to draw a CG plot of a sequence (with
> > bio::graphics)?
> >
> > Thanks
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

From dave at davemessina.com  Wed Oct  3 14:22:23 2007
From: dave at davemessina.com (Dave Messina)
Date: Wed, 3 Oct 2007 20:22:23 +0200
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <37574C6D-98BA-47A5-875E-9255377133B8@sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the  
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Panel.html

I think the example code will help you to do what you want.


Dave


From cjfields at uiuc.edu  Wed Oct  3 15:10:46 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 14:10:46 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
	<a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
Message-ID: <7B62B534-2A8C-4EAE-B956-F0FADB726195@uiuc.edu>

On Oct 3, 2007, at 1:31 PM, Vesselin Baev wrote:

> Thanks,
> I will use Bio::Graphics::Glyph::dna for the classical CG%
> (this type is for C+G % or CpG)?
>
>
> and if I want to draw a similar plot but for example for a % of  
> dinucleotide
> (NpN) occurrances in a sliding windiw, what should I use?
>
>
> Thanks!

It would be GC content, not CpG.  Not sure what you would use for  
dinucleotide content; you could look at the Bio::Graphics::Glyph::dna  
code and either subclass it for your needs (probably the best option)  
or add an extra parameter and 'rewire' the appropriate methods to do  
what you want.

chris

From dmessina at sbc.su.se  Wed Oct  3 14:55:10 2007
From: dmessina at sbc.su.se (dmessina at sbc.su.se)
Date: Wed, 3 Oct 2007 20:55:10 +0200 (CEST)
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <61118.217.213.158.117.1191437710.squirrel@mail.sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html

I think the example code will help you to do what you want.


Dave



From lzhtom at hotmail.com  Wed Oct  3 18:30:43 2007
From: lzhtom at hotmail.com (zhihuali)
Date: Wed, 3 Oct 2007 22:30:43 +0000
Subject: [Bioperl-l] Loading Blast Report in a minimal way
Message-ID: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>


Hi netters,

I'm using SearchIO to parse my blast reports. They are extremely huge, and not surprisingly, it's extremely slow and sometimes the system crashed due to memmory problem. As I can handle small reports quickly, it seems like a problem related to the way SearchIO works: it slurps the whole report into the memory and builds millions of objects.

I've checked old posts and some people used FastHitEventBuilder to build hit objects without any hsp objects. And some people suggested using tabular output of blast. But in my case I need to go to each of the hsps of each hit, parse the alignment, and gather the information needed if that hsp fits certain criteria, and then move on to the next hsp/or jump over to the next hit/ or exit the processing, according to the information I have already got. An ideal way would be to read one hsp at a time from the report to the memory.  Is there some way to modify SearchIO (or build another Search Event) to do this?

Thanks a lot!


Zhihua Li
_________________________________________________________________
?? Live Search ??????????????
http://www.live.com/?searchOnly=true

From budd at embl-heidelberg.de  Thu Oct  4 09:43:57 2007
From: budd at embl-heidelberg.de (Aidan Budd)
Date: Thu, 4 Oct 2007 15:43:57 +0200 (CEST)
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
Message-ID: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>

Hi bioperlers,

I've been trying to add info to a feature in a RichSeq object so that when 
the Seq is written in swissprot format I can put information in the final
field of the feature

FT   DOMAIN      208    392       Helicase ATP-binding.

i.e. where it says "Helicase ATP-binding."

I can control what goes in the primary field, and set the location, but 
haven't been able to work out how to add info to go in this final field.

Thanks,

Aidan

-- 
----------------------------------------------------------------------
Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
Meyerhofstr. 1, 69117 Heidelberg, Germany

URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html


From cjfields at uiuc.edu  Thu Oct  4 10:32:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 09:32:43 -0500
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
In-Reply-To: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
References: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
Message-ID: <84A6CB47-6890-476B-A375-6FCF37655330@uiuc.edu>

Try adding it as a tag value with the name 'description','note', or  
'product' (the first two are probably the best to use for most  
purposes).  There is a quick explanation here:

http://www.bioperl.org/wiki/HOWTO:Feature- 
Annotation#Building_Your_Own_Sequences

You can also do something like:

$sf->add_tag_value('description', 'Helicase ATP-binding');

See Bio::SeqFeature::Generic POD for more.

chris

On Oct 4, 2007, at 8:43 AM, Aidan Budd wrote:

> Hi bioperlers,
>
> I've been trying to add info to a feature in a RichSeq object so  
> that when
> the Seq is written in swissprot format I can put information in the  
> final
> field of the feature
>
> FT   DOMAIN      208    392       Helicase ATP-binding.
>
> i.e. where it says "Helicase ATP-binding."
>
> I can control what goes in the primary field, and set the location,  
> but
> haven't been able to work out how to add info to go in this final  
> field.
>
> Thanks,
>
> Aidan
>
> -- 
> ----------------------------------------------------------------------
> Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
> Meyerhofstr. 1, 69117 Heidelberg, Germany
>
> URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From cain.cshl at gmail.com  Thu Oct  4 11:08:52 2007
From: cain.cshl at gmail.com (Scott Cain)
Date: Thu, 04 Oct 2007 11:08:52 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
Message-ID: <1191510532.2787.16.camel@localhost.localdomain>

Hi Chris,

I think adding the type=MYISAM is the right thing to do; please go ahead
and commit it.

Scott



On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
> Just thought I would forward this on to the GBrowse list as well in  
> case anyone has run into the same problem.  The issue pops up when  
> using bioperl from CVS and appears to be related to a fix Lincoln  
> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using  
> FULLTEXT, which only works for MyISAM currently.
> 
> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE  
> queries does work when InnoDB is set to the default.  Should I go  
> ahead and commit?
> 
> chris
> 
> Begin forwarded message:
> 
> > I'm getting the following error on my local MySQL (v 5.0.41) with
> > bp_seqfeature_load:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: The used table type doesn't support FULLTEXT indexes
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /Library/
> > Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
> > STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
> > Bio/DB/SeqFeature/Store.pm:382
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
> > 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
> > STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
> > SeqFeature/Store.pm:345
> > STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
> > -------------------------------------------
> >
> > The default setting for storage is InnoDB; switching to MyISAM fixes
> > the issue.  Should we specify TYPE = MyISAM with the various CREATE
> > TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
> > safe side?
> >
> > chris
> 
> 
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
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> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory


From cjfields at uiuc.edu  Thu Oct  4 11:14:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 10:14:37 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <1191510532.2787.16.camel@localhost.localdomain>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
	<1191510532.2787.16.camel@localhost.localdomain>
Message-ID: <9DEFB5C1-6F79-465B-8FB4-68305C53E427@uiuc.edu>

Done.  If we run into issues and need to roll back let me know.

chris

On Oct 4, 2007, at 10:08 AM, Scott Cain wrote:

> Hi Chris,
>
> I think adding the type=MYISAM is the right thing to do; please go  
> ahead
> and commit it.
>
> Scott
>
>
>
> On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
>> Just thought I would forward this on to the GBrowse list as well in
>> case anyone has run into the same problem.  The issue pops up when
>> using bioperl from CVS and appears to be related to a fix Lincoln
>> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using
>> FULLTEXT, which only works for MyISAM currently.
>>
>> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE
>> queries does work when InnoDB is set to the default.  Should I go
>> ahead and commit?
>>
>> chris
>>
>> Begin forwarded message:
>>
>>> I'm getting the following error on my local MySQL (v 5.0.41) with
>>> bp_seqfeature_load:
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: The used table type doesn't support FULLTEXT indexes
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database / 
>>> Library/
>>> Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
>>> STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
>>> Bio/DB/SeqFeature/Store.pm:382
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
>>> 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
>>> STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
>>> SeqFeature/Store.pm:345
>>> STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
>>> -------------------------------------------
>>>
>>> The default setting for storage is InnoDB; switching to MyISAM fixes
>>> the issue.  Should we specify TYPE = MyISAM with the various CREATE
>>> TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
>>> safe side?
>>>
>>> chris
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.net email is sponsored by: Microsoft
>> Defy all challenges. Microsoft(R) Visual Studio 2005.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a  
> browser.
> Download your FREE copy of Splunk now >> http://get.splunk.com/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From cjfields at uiuc.edu  Thu Oct  4 15:30:48 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 14:30:48 -0500
Subject: [Bioperl-l] blastxml oddity
Message-ID: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>

Just noticed an oddity from BLASTXML output from the NCBI server; I'm  
cc'ing this to NCBI so maybe they can explain.  BTW, the following  
doesn't occur via URLAPI.

When running a standard BLAST query using the NCBI web page, if  
requesting XML output after the run I get the entire query seq masked  
out and no midline.  This occurs with all default settings except  
output type (set to XML).  Can anyone replicate this?

Here's a sample:

<Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
               <Hsp_bit-score>320.472</Hsp_bit-score>
               <Hsp_score>820</Hsp_score>
               <Hsp_evalue>2.17708e-86</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>181</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
               <Hsp_hit-to>181</Hsp_hit-to>
               <Hsp_query-frame>0</Hsp_query-frame>
               <Hsp_hit-frame>0</Hsp_hit-frame>
               <Hsp_identity>0</Hsp_identity>
               <Hsp_positive>0</Hsp_positive>
               <Hsp_gaps>0</Hsp_gaps>
               <Hsp_align-len>181</Hsp_align-len>
                
<Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
                
<Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPV 
TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAV 
LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
                
<Hsp_midline>                                                            
                                                                         
                                                    </Hsp_midline>
             </Hsp>
           </Hit_hsps>



<notblast>chris</notblast>

From cjfields at uiuc.edu  Thu Oct  4 16:36:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 15:36:25 -0500
Subject: [Bioperl-l] blastxml oddity
In-Reply-To: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
References: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
Message-ID: <86D7D694-1ACF-4D91-9FEC-0FEA21C1B689@uiuc.edu>

NCBI's BLAST team is working on this; it occurs only if you use an GI/ 
accession instead of a full sequence, and only for XML.

chris

On Oct 4, 2007, at 2:30 PM, Chris Fields wrote:

> Just noticed an oddity from BLASTXML output from the NCBI server; I'm
> cc'ing this to NCBI so maybe they can explain.  BTW, the following
> doesn't occur via URLAPI.
>
> When running a standard BLAST query using the NCBI web page, if
> requesting XML output after the run I get the entire query seq masked
> out and no midline.  This occurs with all default settings except
> output type (set to XML).  Can anyone replicate this?
>
> Here's a sample:
>
> <Hit_hsps>
>              <Hsp>
>                <Hsp_num>1</Hsp_num>
>                <Hsp_bit-score>320.472</Hsp_bit-score>
>                <Hsp_score>820</Hsp_score>
>                <Hsp_evalue>2.17708e-86</Hsp_evalue>
>                <Hsp_query-from>1</Hsp_query-from>
>                <Hsp_query-to>181</Hsp_query-to>
>                <Hsp_hit-from>1</Hsp_hit-from>
>                <Hsp_hit-to>181</Hsp_hit-to>
>                <Hsp_query-frame>0</Hsp_query-frame>
>                <Hsp_hit-frame>0</Hsp_hit-frame>
>                <Hsp_identity>0</Hsp_identity>
>                <Hsp_positive>0</Hsp_positive>
>                <Hsp_gaps>0</Hsp_gaps>
>                <Hsp_align-len>181</Hsp_align-len>
>
> <Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
>
> <Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGN 
> PV
> TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQL 
> AV
> LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
>
> <Hsp_midline>
>
>                                                     </Hsp_midline>
>              </Hsp>
>            </Hit_hsps>
>
>
>
> <notblast>chris</notblast>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From e-just at northwestern.edu  Fri Oct  5 15:35:25 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 14:35:25 -0500
Subject: [Bioperl-l] bp_search2gff.pl
Message-ID: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>

Hello,

I have been playing with the bp_search2gff.pl script (on HEAD of
bioperl-live).    There are a couple of issues I was wondering about.

One is the ID that gets generated for a match feature when the --match
option is set.   The ID is  set to the ID of the query sequence.  This
can be problematic if you are representing the query sequence and the
blast hit in the same gff file.  When using the resultant gff file for
loading into Chado, it also creates a problem if you have more than
one hit for a given query sequence, for example if you ran two
different analyses that each had a hit for a given query.  Would it be
possible to have an option to create a unique ID for match features.
One suggestion could be to create an ID based on the ID of the query +
the id of the hit + the source

As long as two different analyses were loaded as different sources,
this would ensure unique IDs for the match features.


Also, is there a reason for writing the Target string as

Target=Sequence:SOME_ID

as opposed to

Target=SOME_ID


The latter seems a little more in line with the gff3 spec and plays a
little nicer with the GMOD tools.

Thanks for looking into this.

Eric

From cjfields at uiuc.edu  Fri Oct  5 15:51:20 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 5 Oct 2007 14:51:20 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
Message-ID: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>

We might want to file this as a bug so we can track it.

The core devs have been mulling over the state of GFF/GFF3 in  
BioPerl; proper handling of any SearchIO data is certainly included  
in that.  I believe some road forward is to be planned soon (after  
Genome Informatics).

chris

On Oct 5, 2007, at 2:35 PM, Eric Just wrote:

> Hello,
>
> I have been playing with the bp_search2gff.pl script (on HEAD of
> bioperl-live).    There are a couple of issues I was wondering about.
>
> One is the ID that gets generated for a match feature when the --match
> option is set.   The ID is  set to the ID of the query sequence.  This
> can be problematic if you are representing the query sequence and the
> blast hit in the same gff file.  When using the resultant gff file for
> loading into Chado, it also creates a problem if you have more than
> one hit for a given query sequence, for example if you ran two
> different analyses that each had a hit for a given query.  Would it be
> possible to have an option to create a unique ID for match features.
> One suggestion could be to create an ID based on the ID of the query +
> the id of the hit + the source
>
> As long as two different analyses were loaded as different sources,
> this would ensure unique IDs for the match features.
>
>
> Also, is there a reason for writing the Target string as
>
> Target=Sequence:SOME_ID
>
> as opposed to
>
> Target=SOME_ID
>
>
> The latter seems a little more in line with the gff3 spec and plays a
> little nicer with the GMOD tools.
>
> Thanks for looking into this.
>
> Eric
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From e-just at northwestern.edu  Fri Oct  5 16:06:48 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 15:06:48 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
	<54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
Message-ID: <fa1fe35c0710051306v1636d6er6f02133f4ecef91c@mail.gmail.com>

Thanks Chris, I'll enter it as a bug.  I'd also be glad to help on the
solution if there is an executive decision made at some point.



On 10/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
> We might want to file this as a bug so we can track it.
>
> The core devs have been mulling over the state of GFF/GFF3 in
> BioPerl; proper handling of any SearchIO data is certainly included
> in that.  I believe some road forward is to be planned soon (after
> Genome Informatics).
>
> chris
>
> On Oct 5, 2007, at 2:35 PM, Eric Just wrote:
>
> > Hello,
> >
> > I have been playing with the bp_search2gff.pl script (on HEAD of
> > bioperl-live).    There are a couple of issues I was wondering about.
> >
> > One is the ID that gets generated for a match feature when the --match
> > option is set.   The ID is  set to the ID of the query sequence.  This
> > can be problematic if you are representing the query sequence and the
> > blast hit in the same gff file.  When using the resultant gff file for
> > loading into Chado, it also creates a problem if you have more than
> > one hit for a given query sequence, for example if you ran two
> > different analyses that each had a hit for a given query.  Would it be
> > possible to have an option to create a unique ID for match features.
> > One suggestion could be to create an ID based on the ID of the query +
> > the id of the hit + the source
> >
> > As long as two different analyses were loaded as different sources,
> > this would ensure unique IDs for the match features.
> >
> >
> > Also, is there a reason for writing the Target string as
> >
> > Target=Sequence:SOME_ID
> >
> > as opposed to
> >
> > Target=SOME_ID
> >
> >
> > The latter seems a little more in line with the gff3 spec and plays a
> > little nicer with the GMOD tools.
> >
> > Thanks for looking into this.
> >
> > Eric
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>

From bix at sendu.me.uk  Sun Oct  7 08:40:44 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sun, 07 Oct 2007 13:40:44 +0100
Subject: [Bioperl-l] Bio::FeatureIO::gff bug?
In-Reply-To: <5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
References: <46F784EB.9050507@sendu.me.uk>	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>	<46F7B9A1.9080206@sendu.me.uk>	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>	<46F8DC34.6020908@sendu.me.uk>	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
Message-ID: <4708D3CC.60909@sendu.me.uk>

Hilmar Lapp wrote:
> On Sep 28, 2007, at 5:34 PM, Chris Fields wrote:
> 
>> The section writing the gff header info in _initialize() checks the  
>> file specifically for '>' prior to output; I think Sendu planned on  
>> changing that to use mode() instead.
> 
> What if we pass in a file handle?

mode() is supposed to work in that instance as well: it sees if the file 
handle is writable.

From er at xs4all.nl  Sun Oct  7 10:13:45 2007
From: er at xs4all.nl (Erik)
Date: Sun, 7 Oct 2007 16:13:45 +0200 (CEST)
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <4708D3CC.60909@sendu.me.uk>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
Message-ID: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>


http://bioperl.org/
http://www.bioperl.org/wiki/Main_Page

seems to be having problems - I only receive an empty
screen...

regards,
Erik





From cjfields at uiuc.edu  Sun Oct  7 17:16:02 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 7 Oct 2007 16:16:02 -0500
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
	<12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
Message-ID: <EBD33439-22B4-44FC-A60C-D3EC653EC363@uiuc.edu>

Should be back up.  Jason was running some wiki updates.

chris

On Oct 7, 2007, at 9:13 AM, Erik wrote:

>
> http://bioperl.org/
> http://www.bioperl.org/wiki/Main_Page
>
> seems to be having problems - I only receive an empty
> screen...
>
> regards,
> Erik



From alan at tll.org.sg  Mon Oct  8 01:02:45 2007
From: alan at tll.org.sg (alan)
Date: Mon, 8 Oct 2007 13:02:45 +0800
Subject: [Bioperl-l] exonerate
In-Reply-To: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
	<73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
Message-ID: <F5563806-FCAE-46C6-8EE3-3C55FCDD906C@tll.org.sg>

Hi Chris,

On 02 Oct 2007, at 11:03 PM, Chris Fields wrote:

> One option is to try running $run->cleanup() after you finish  
> parsing, which gets rid of the tempfiles on each run.
>

I tried this option in the past but it did not change anything.

I found a temporary solution: I am using tcsh and the ulimit for open  
files (descriptors) was set to 256. I changed this limit to 2000 and  
I got my code to run to completion. This imply that I am  
circumventing the real problem of open files. I will continue to look  
at the file closing step in bioperl but the ulimit or limit option  
allows me to get a quick work around for now.

for bash shell (ulimit -n [number])

for tcsh shell (limit descriptors [number])

alan




> chris
>
> On Sep 30, 2007, at 8:53 PM, alan wrote:
>
>> Hi,
>>
>>
>>>> I am calling exonerate.pm within my script while attempting to
>>>> align cDNA  to multiple genomic fragments. After processing about
>>>> 120+ genomic fragments my code crashes with the following error:
>>>>
>>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>>> aborting...
>>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>>
>>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>>> routine yet I get the error message about "too many open files".
>>>> Any suggestions on how I should be closing these files?
>>>>
>>>>
>>>> Extract from my code that runs exonerate is listed below.
>>>>
>>>> foreach my $f(@files) {
>>>>   next unless (-f  "$dir/$f");
>>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>>   my $query_obj = $q_in->next_seq();
>>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>>> format=>"Fasta");
>>>>   my $target_obj = $target_in->next_seq();
>>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>>
>>>>   [code for parsing the data.......]
>>>>
>>>>   $exonerate_io->close; #tried this line out of desperation but it
>>>> did not help :-)
>>>> }
>>>>
>>>> thanks
>>>> alan
>
>


From bix at sendu.me.uk  Mon Oct  8 05:54:15 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Mon, 08 Oct 2007 10:54:15 +0100
Subject: [Bioperl-l] Loading Blast Report in a minimal way
In-Reply-To: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
References: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
Message-ID: <4709FE47.3040103@sendu.me.uk>

zhihuali wrote:
> Hi netters,
> 
> I'm using SearchIO to parse my blast reports. They are extremely 
> huge, and not surprisingly, it's extremely slow and sometimes the 
> system crashed due to memmory problem. As I can handle small reports 
> quickly, it seems like a problem related to the way SearchIO works: 
> it slurps the whole report into the memory and builds millions of 
> objects.
> 
> I've checked old posts and some people used FastHitEventBuilder to 
> build hit objects without any hsp objects. And some people suggested 
> using tabular output of blast. But in my case I need to go to each of
>  the hsps of each hit, parse the alignment, and gather the
> information needed if that hsp fits certain criteria, and then move
> on to the next hsp/or jump over to the next hit/ or exit the
> processing, according to the information I have already got. An ideal
> way would be to read one hsp at a time from the report to the memory.
> Is there some way to modify SearchIO (or build another Search Event)
> to do this?

Use Bio::SearchIO::blast_pull

(ie.
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                             -file =>
't/data/new_blastn.txt');
)

It doesn't yet support all kinds of Blast report, however. Let me know
how you get on.

Cheers,
Sendu.

From bix at sendu.me.uk  Wed Oct 10 10:09:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 15:09:24 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
Message-ID: <470CDD14.4000005@sendu.me.uk>

Once I store a feature like so:

$db = Bio::DB::SeqFeature::Store->new( # mysql );
$db->new_feature(-primary_tag  => 'X',
                  -seq_id       => 'Y',
                  #...
		 -source       => 'Z');

How do I search for it again? I could have sworn that in the past the 
source somehow became one of the feature's attributes so that I could do:

@feats = $db->features(-attributes => {source => 'Z'});

(Or does/did some other feature-related module store source as an 
attribute, and in the past I stored those features in my db?)

The obvious isn't implemented:

@feats = $db->features(-source => 'Z');

Looking at the code I see I can do type and source at the same time:

@feats = $db->features(-type => 'X:Z');

which works, but how do I just search for all Z, regardless of type?

From lstein at cshl.edu  Wed Oct 10 10:20:33 2007
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 10 Oct 2007 10:20:33 -0400
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <470CDD14.4000005@sendu.me.uk>
References: <470CDD14.4000005@sendu.me.uk>
Message-ID: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>

Hi Sendu,

This may be a glaring omission on my part. Try searching for:

 @feats = $db->get_features_by_type(":$source");

Remove the colon in front of $source.

This might not work, but give it a try.

Lincoln

On 10/10/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> Once I store a feature like so:
>
> $db = Bio::DB::SeqFeature::Store->new( # mysql );
> $db->new_feature(-primary_tag  => 'X',
>                   -seq_id       => 'Y',
>                   #...
>                  -source       => 'Z');
>
> How do I search for it again? I could have sworn that in the past the
> source somehow became one of the feature's attributes so that I could do:
>
> @feats = $db->features(-attributes => {source => 'Z'});
>
> (Or does/did some other feature-related module store source as an
> attribute, and in the past I stored those features in my db?)
>
> The obvious isn't implemented:
>
> @feats = $db->features(-source => 'Z');
>
> Looking at the code I see I can do type and source at the same time:
>
> @feats = $db->features(-type => 'X:Z');
>
> which works, but how do I just search for all Z, regardless of type?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu

From bix at sendu.me.uk  Wed Oct 10 11:10:45 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 16:10:45 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
References: <470CDD14.4000005@sendu.me.uk>
	<6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
Message-ID: <470CEB75.7050804@sendu.me.uk>

Lincoln Stein wrote:
> Hi Sendu,
> 
> This may be a glaring omission on my part. Try searching for:
> 
>  @feats = $db->get_features_by_type(":$source");
> 
> Remove the colon in front of $source.

It doesn't, unfortunately, colon or not. get_features_by_type is 
implemented using _features(-type => ), just like features(). In any 
case, I'm searching for multiple things at the same time so need to use 
the features() method.


The following patch seems to do the job in my hands, allowing:

@feats = $db->features(-source => 'Z');
to work as expected.

Also, we now have:
@feats = $db->features(-type => 'X', -source => 'Z');
as a nicer (ie. matching the syntax the user used to create the feature 
in the first place) alternative to:
@feats = $db->features(-type => 'X:Y');

Of course, this patch is specific to the mysql implementation. You may 
want to check it over to see if it is sane, see if there is a cleaner 
way to do it, or see if there's a more general way to apply it to all 
implementations.


RCS file: 
/home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.33
diff -r1.33 mysql.pm
724c724,725
<       $iterator
---
 >       $iterator,
 >       $sources
731a733
 >             ['SOURCE','SOURCES']
760c762,785
<
---
 >
 >   if (defined($sources)) {
 >     my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources);
 >     if (defined($types)) {
 >         my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types);
 >         my @final_types;
 >         foreach my $type (@types) {
 >             # *** not sure what to do if user supplies both -source
 >             #     and -type where the type includes a source!
 >             if ($type =~ /:/) {
 >                 push(@final_types, $type);
 >             }
 >             else {
 >                 foreach my $source (@sources) {
 >                     push(@final_types, $type.':'.$source);
 >                 }
 >             }
 >         }
 >         $types = \@final_types;
 >     }
 >     else {
 >         $types = [map { ':'.$_ } @sources];
 >     }
 >   }
939,940c964,971
<       push @matches,"tl.tag=?";
<       push @args,"$primary_tag:$source_tag";
---
 >       if (length($primary_tag)) {
 >         push @matches,"tl.tag=?";
 >         push @args,"$primary_tag:$source_tag";
 >       }
 >       else {
 >         push @matches,"tl.tag LIKE ?";
 >         push @args,"%:$source_tag";
 >       }

From bix at sendu.me.uk  Thu Oct 11 06:40:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 11 Oct 2007 11:40:24 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
Message-ID: <470DFD98.4030603@sendu.me.uk>

Following Chris's changes to SF::Annotated et al., lots of existing user 
code breaks. Also, at least some Bioperl code breaks, notably 
Bio::DB::SeqFeature::Store, which in mysql mode calls 
_get_location_and_bin() which calls $feature->seq_id which ends up 
storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
the database, instead of an actual sequence id (which completely breaks 
searching by seq_id).

I propose its API be changed to be more consistent with 
Bio::SeqFeatureI, eg. instead of:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : a Bio::Annotation::SimpleValue object representing the
            seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

we have:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : string representing the seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

This would apply to seq_id(), name(), type(), source(), phase() and 
frame(). Internally the implementation could store the string value in a 
SimpleValue object.


However, I'm obviously missing something, because I have no idea what 
the justification for returning SimpleValue objects was in the first 
place (what other module needs them?), nor even what the point of 
SimpleValue objects is in the first place.

From ULNJUJERYDIX at spammotel.com  Thu Oct 11 07:32:33 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Thu, 11 Oct 2007 19:32:33 +0800
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>

wow thanks for the replies!
I have gotten the answer from the blast help

Subsequence range can be specified by the ?L parameter. Please refer
to this web document for more information:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node60.html



Other end-user oriented standalone blast documents are at:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/


but will try this method as well to see which works better.

cheers!
kevin

There is a script that comes with the bioperl core distribution,

> bp_split_seq.pl, which does this.  Here's the CVS location:
>
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
> scripts/seq/?cvsroot=bioperl
>
> chris
>


From cjfields at uiuc.edu  Thu Oct 11 09:49:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 08:49:59 -0500
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
	<5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
Message-ID: <F866A1FE-EBC7-4722-A3E6-2F4A10FD0373@uiuc.edu>

Yep, started using this myself for mapping old predicted CDS onto new  
assemblies using BLASTX.  Works very well, particularly since it  
retains the seq position on hits, where using bp_slit_seq would  
require mapping to the correct coordinates.

chris

On Oct 11, 2007, at 6:32 AM, Kevin Lam wrote:

> wow thanks for the replies!
> I have gotten the answer from the blast help
>
> Subsequence range can be specified by the ?L parameter. Please refer
> to this web document for more information:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ 
> blastall_node60.html
>
>
>
> Other end-user oriented standalone blast documents are at:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
>
>
> but will try this method as well to see which works better.
>
> cheers!
> kevin
>
> There is a script that comes with the bioperl core distribution,
>
>> bp_split_seq.pl, which does this.  Here's the CVS location:
>>
>> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
>> scripts/seq/?cvsroot=bioperl
>>
>> chris
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Thu Oct 11 10:19:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 09:19:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>


On Oct 11, 2007, at 5:40 AM, Sendu Bala wrote:

> Following Chris's changes to SF::Annotated et al., lots of existing  
> user
> code breaks. Also, at least some Bioperl code breaks, notably
> Bio::DB::SeqFeature::Store, which in mysql mode calls
> _get_location_and_bin() which calls $feature->seq_id which ends up
> storing something like 'Bio::Annotation::SimpleValue=HASH 
> (0x1f435d0)' in
> the database, instead of an actual sequence id (which completely  
> breaks
> searching by seq_id).
>
> I propose its API be changed to be more consistent with
> Bio::SeqFeatureI, eg. instead of:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> we have:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> This would apply to seq_id(), name(), type(), source(), phase() and
> frame(). Internally the implementation could store the string value  
> in a
> SimpleValue object.

Agreed.  It would be easy to change over but we need to also make  
sure FeatureIO fixes are in place.  In reality all FeatureIO methods  
should be changed over to recognize any SeqFeatureI or (if we retain  
it) the stricter TypedSeqFeatureI.  Using only Bio::SF::Annotated  
limits other more lightweight implementations.  I simply haven't had  
time to work on it yet due to $job; if you want to make the necessary  
changes you are more than welcome; the few tests I found I moved into  
SeqFeatAnnotated.t, which likely expects the wrong behavior.

> However, I'm obviously missing something, because I have no idea what
> the justification for returning SimpleValue objects was in the first
> place (what other module needs them?), nor even what the point of
> SimpleValue objects is in the first place.

I believe it was to ensure any data stored or retrieved was strongly  
typed (i.e. scalars in SimpleValue, dbxrefs in DBLink, comments in  
Comment, etc).  Since B::SF::Generic is also AnnotatableI, it can  
store a mix of scalars in methods as well as Bio::Annotation data;  
this class attempts to lump them all together as Bio::Annotation in a  
Collection in a strongly typed, uniform way.  Hilmar's  
Bio::SF::AnnotationAdaptor frankly does a better job of describing  
the reasoning behind this and is more flexible; I use that now for  
typing via feature(), though I just realized it should be changed to  
be a singleton instance per class (oops!).

B::SF::A violated the SeqFeatureI interface from the get-go by  
returning objects.  To trick it's way around the issue it used  
overloading so that calling it in some contexts (print, comparison)  
returned a string or value; removing the overloads unmasked that  
behavior.  To me an object returned (regardless of overloading) is  
still an object and not a scalar, and still violates the interface  
methods where scalars are expected.  I can't fault the authors  
involved completely since the idea was to radically change the way  
SFs/Annotation worked together, but the implementation was never  
completed so I rolled it back and limited typing to B::SF::A until  
something else can be worked out.

Personally I think it's too 'heavy' and other options should be  
explored, such as abstracting out the type checking into a separate  
utility class which FeatureIO can use on any SeqFeatureI (TypeMapper  
does something like this for the primary_tag()).

chris

From jaudall at gmail.com  Thu Oct 11 20:51:50 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 18:51:50 -0600
Subject: [Bioperl-l] Hsp_hit-from
Message-ID: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>

Bioperl -

I'm parsing an XML blast output using SearchIO and the usual fields seem to
work fine.

print $result->query_name . "\t" . $hit->name . "\n";

However, I'm curious as to the 5' position distribution of my hits.  So I'd
like to access this data field <Hsp_query-from> in the xml output file.  I
searched both the mailing lists and the Search docs including
*Bio::Search::Hit::HitI,
*but I can't seem to find an example of someone accessing this data field.
Perhaps, I missed it, but do any of you have any suggestions as to how I
might get at the <Hsp_query-from> for each hit?  Thanks.

Josh

From cjfields at uiuc.edu  Thu Oct 11 22:14:21 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 21:14:21 -0500
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
Message-ID: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>


On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:

> Bioperl -
>
> I'm parsing an XML blast output using SearchIO and the usual fields  
> seem to
> work fine.
>
> print $result->query_name . "\t" . $hit->name . "\n";
>
> However, I'm curious as to the 5' position distribution of my  
> hits.  So I'd
> like to access this data field <Hsp_query-from> in the xml output  
> file.  I
> searched both the mailing lists and the Search docs including
> *Bio::Search::Hit::HitI,
> *but I can't seem to find an example of someone accessing this data  
> field.
> Perhaps, I missed it, but do any of you have any suggestions as to  
> how I
> might get at the <Hsp_query-from> for each hit?  Thanks.
>
> Josh

That tag (as well as related tags) are mapped to start(), end(), and  
strand() in the HSP objects.  To access the relevant data pass  
'query' or 'hit' to the method, so for the query use: $hsp->start 
('query') or $hsp->end('query').

Note: in BioPerl all location starts are less than the end (strand  
determines the orientation for DNA).

chris

From hlapp at gmx.net  Thu Oct 11 23:25:22 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 11 Oct 2007 23:25:22 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>


On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:

> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.

type() and source() should be ontology-typed in a TypedSeqFeatureI  
(and therefore be instances of Bio::Annotation::OntologyTerm, not  
Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't  
understand what the benefit of typing seq_id() any stronger than a  
string would be.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From jaudall at gmail.com  Thu Oct 11 23:34:18 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 20:34:18 -0700
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
	<162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
Message-ID: <52cea20c0710112034k60f14241k8884a07d26939e86@mail.gmail.com>

Thanks!  For some reason I was stuck on the idea that it would be different
with an xml file.  I'm glad it's not ...

On 10/11/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:
>
> > Bioperl -
> >
> > I'm parsing an XML blast output using SearchIO and the usual fields
> > seem to
> > work fine.
> >
> > print $result->query_name . "\t" . $hit->name . "\n";
> >
> > However, I'm curious as to the 5' position distribution of my
> > hits.  So I'd
> > like to access this data field <Hsp_query-from> in the xml output
> > file.  I
> > searched both the mailing lists and the Search docs including
> > *Bio::Search::Hit::HitI,
> > *but I can't seem to find an example of someone accessing this data
> > field.
> > Perhaps, I missed it, but do any of you have any suggestions as to
> > how I
> > might get at the <Hsp_query-from> for each hit?  Thanks.
> >
> > Josh
>
> That tag (as well as related tags) are mapped to start(), end(), and
> strand() in the HSP objects.  To access the relevant data pass
> 'query' or 'hit' to the method, so for the query use: $hsp->start
> ('query') or $hsp->end('query').
>
> Note: in BioPerl all location starts are less than the end (strand
> determines the orientation for DNA).
>
> chris
>

From pellet at cervi-lyon.inserm.fr  Fri Oct 12 04:48:06 2007
From: pellet at cervi-lyon.inserm.fr (Johann PELLET)
Date: Fri, 12 Oct 2007 10:48:06 +0200
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
Message-ID: <470F34C6.9050800@cervi-lyon.inserm.fr>

Hi,
I have two questions:
First, I have problems for example with this genbank entry: NC_008210. 
Indeed, for one CDS, the location is : 
join(161990..162784,complement(88222..88806),complement(86666..87448))

When I parse a genbank file with this entry.

my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
                               -file => $input_file);

while( my $seq = $seq_in->next_seq() ) {
    my @features = $seq->get_SeqFeatures();
    for ( my $i =0; $i < scalar @features; $i++ ){
        my $feat = @features[$i];
         if ( $feat->primary_tag eq 'CDS' ){


             my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
             my $seq_CDS=$seq_CDS_obj->seq;


I have this error:
Can't call method "isa" without a package or object reference at ....

Secondly, When location is like: 
join(complement(AY421753.1:1..6),complement(3813..5699)) I know that we 
must use spliced_seq with the argument db, but it's not working.
      my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
How can we valid a Bio::DB::RandomAccessI?

Thanks

-- 
Johann Pellet
phone (work): +33(0)4 37282352
E-mail:    pellet at cervi-lyon.inserm.fr
Centre d'Etudes et de Recherche en Virologie et Immunologie
INSERM U503
21, Avenue Tony Garnier
69365 Lyon cedex 07 France 


From bix at sendu.me.uk  Fri Oct 12 09:04:25 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 14:04:25 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
Message-ID: <470F70D9.6030108@sendu.me.uk>

Chris Fields wrote:
> B::SF::A violated the SeqFeatureI interface from the get-go by returning 
> objects.

On that note, the other major change I'd propose is to make B::SF::A 
inherit from B::SeqFeatureI. I really need this for RangeI methods.

Or, heck, since it's such a mess, do we just want to drop Annotated 
entirely and recommend using AnnotationAdaptor with Generic? What does 
Annotated bring to the table?

(Since its one of the modules added in 1.5 I think it's fair to drop it 
from the 1.6 release: stuff that doesn't work can and should be moved 
out of the path of stable branches.)

From hlapp at gmx.net  Fri Oct 12 10:46:19 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 10:46:19 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>


On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

My recollection may be wrong since it's been quite a while, but I  
believe one of the main motivations was to reflect the ontology- 
typing of feature type and other annotation that GFF3 requires.

The motivation of AnnotationAdaptor was primarily to provide a view  
onto a SeqFeatureI that makes tag/value annotation transparently  
appear as B:AnnotatableI and B:AnnotationCollectionI compliant, mixed  
in with the annotation collection that B:S:Generic may hold already.

Although sometimes confused, these are not the same motivations.  
AnnotationAdaptor provides a view - you use it when that's the view  
you need on a SeqFeatureI object you have in hand. For example,  
bioperl-db uses it so it doesn't have to bother about how to de/ 
serialize tag/value pairs, when it knows how to de/serialize  
annotation collections already from sequence objects.  
AnnotationAdaptor doesn't care whether the primary_tag, or any other  
tag, is from an ontology.

>
> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
>> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

I agree with that unless someone steps up and makes it work.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From cjfields at uiuc.edu  Fri Oct 12 10:49:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 09:49:25 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>


On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> B::SF::A violated the SeqFeatureI interface from the get-go by  
>> returning
>> objects.
>
> On that note, the other major change I'd propose is to make B::SF::A
> inherit from B::SeqFeatureI. I really need this for RangeI methods.

It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,  
which itself is-a SeqFeatureI.  We might want to run the tests on  
that but a quick inheritance tree check on my ends seems to confirm  
that.  If the Range methods don't work there may be an issue within  
B::SF::A (which wouldn't surprise me).

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

I agree about getting rid of B::SF::A, but if we do we will need a  
reasonable replacement for SFs in FeatureIO, as it relies directly on  
B::SF::A.  As for AnnotationAdaptor, it runs a simple type check on  
the data within a SF but I don't think it checks the primary_tag  
against the current SO or other ontologies for GFF3.

My inclination is to hold back FeatureIO from 1.6 and retool it to  
use any SeqFeatureI, then find a way to optionally type a  
SeqFeatureI.  This is so we don't have to completely retool every  
Bio::Tools* class.  For instance:

# a SF::Generic with a few type-related methods added to SeqFeatureI
$sf->type(); # undef, not checked
$sf->ontology_term; # undef, not checked

# call proper methods to type check
# or use a utility class dedicated to this function

$sf->validate_sf_type(); # or...
$util->validate_sf_type($sf);

$sf->type(); # returns string
$sf->ontology_term; # returns Bio::Ontology::TermI

My feeling is that FeatureIO needs the ability to validate SFs and  
maybe have it turned on by default, but it should be optional.  The  
TermI would be a Bio::Annotation::OntologyTerm if we insist on using  
AnnotationAdaptor for richly typed SFs, which may not be necessary  
(Hilmar?).  As not all SeqFeatureI are also AnnotatableI that should  
probably be optional anyway.

> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

Agreed.  If anyone wants to use experimental stuff they can always  
use bioperl-live.

chris

From cjfields at uiuc.edu  Fri Oct 12 11:02:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 10:02:03 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
Message-ID: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>


On Oct 12, 2007, at 9:46 AM, Hilmar Lapp wrote:

>
> On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:
>
>> Or, heck, since it's such a mess, do we just want to drop Annotated
>> entirely and recommend using AnnotationAdaptor with Generic? What  
>> does
>> Annotated bring to the table?
>
> My recollection may be wrong since it's been quite a while, but I  
> believe one of the main motivations was to reflect the ontology- 
> typing of feature type and other annotation that GFF3 requires.
>
> The motivation of AnnotationAdaptor was primarily to provide a view  
> onto a SeqFeatureI that makes tag/value annotation transparently  
> appear as B:AnnotatableI and B:AnnotationCollectionI compliant,  
> mixed in with the annotation collection that B:S:Generic may hold  
> already.
>
> Although sometimes confused, these are not the same motivations.  
> AnnotationAdaptor provides a view - you use it when that's the view  
> you need on a SeqFeatureI object you have in hand. For example,  
> bioperl-db uses it so it doesn't have to bother about how to de/ 
> serialize tag/value pairs, when it knows how to de/serialize  
> annotation collections already from sequence objects.  
> AnnotationAdaptor doesn't care whether the primary_tag, or any  
> other tag, is from an ontology.

Ah, forgot it returns a Collection.  It doesn't modify the SF I assume?

>> (Since its one of the modules added in 1.5 I think it's fair to  
>> drop it
>>> from the 1.6 release: stuff that doesn't work can and should be  
>>> moved
>> out of the path of stable branches.)
>
> I agree with that unless someone steps up and makes it work.
>
> 	-hilmar

Making it work may be more trouble than it's worth.  Sincerest  
apologies to the authors of the module but we should probably  
deprecate it in favor of something more flexible when we can.  It's  
obvious anything reliant on it would also have to be dropped.

The GMOD meeting is a few weeks away, where I assume some things will  
be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth  
saving; maybe retooling it would be in our best interests, but it  
needs a decent roadmap to move forward.

chris

From bix at sendu.me.uk  Fri Oct 12 11:06:30 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 16:06:30 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
Message-ID: <470F8D76.8080101@sendu.me.uk>

Chris Fields wrote:
> 
> On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:
> 
>> Chris Fields wrote:
>>> B::SF::A violated the SeqFeatureI interface from the get-go by
>>> returning objects.
>> 
>> On that note, the other major change I'd propose is to make
>> B::SF::A inherit from B::SeqFeatureI. I really need this for RangeI
>> methods.
> 
> It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,
> which itself is-a SeqFeatureI.  We might want to run the tests on
> that but a quick inheritance tree check on my ends seems to confirm
> that.  If the Range methods don't work there may be an issue within
> B::SF::A (which wouldn't surprise me).

Sorry, I was looking at the docs on the website and for whatever reason
its failing to display all the inherited modules. If RangeI methods
don't work I'll post back, but for now assume they do (I'm not in a
position to test right now).


> My inclination is [snip]

I still don't really understand what the deal is with all these modules,
so I'll leave it your hands to make further recommendations and take action.

 From my limited understanding what you said seems reasonable, except for
excluding FeatureIO completely. At least, I'd really like to see it in
1.6; it would be a shame to miss it just because of Annotated. Worst
case, isn't Generic 'good enough' as a replacement?


> The GMOD meeting is a few weeks away, where I assume some things will
> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
> saving; maybe retooling it would be in our best interests, but it
> needs a decent roadmap to move forward.

Agreed. I guess we'll wait for the results of that meeting? Is anyone 
going planning to discuss this issue?

From cjfields at uiuc.edu  Fri Oct 12 12:15:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 11:15:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F8D76.8080101@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
	<470F8D76.8080101@sendu.me.uk>
Message-ID: <EAD0DE5B-3E55-453B-A57B-C478F2BB9AE4@uiuc.edu>


On Oct 12, 2007, at 10:06 AM, Sendu Bala wrote:
...

>
> I still don't really understand what the deal is with all these  
> modules,
> so I'll leave it your hands to make further recommendations and  
> take action.
>
> From my limited understanding what you said seems reasonable,  
> except for
> excluding FeatureIO completely. At least, I'd really like to see it in
> 1.6; it would be a shame to miss it just because of Annotated. Worst
> case, isn't Generic 'good enough' as a replacement?

It probably could work, but type checking, ontology_term(), and SF  
data validation wouldn't be implemented immediately as it would  
require additional code.  I'll try looking into it this weekend to  
see what needs to be done and work from there.

>> The GMOD meeting is a few weeks away, where I assume some things will
>> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
>> saving; maybe retooling it would be in our best interests, but it
>> needs a decent roadmap to move forward.
>
> Agreed. I guess we'll wait for the results of that meeting? Is  
> anyone going planning to discuss this issue?

Jason is going to be there and intends to bring it up as it affects  
GBrowse/GMOD/Chado.

chris


From jason at bioperl.org  Fri Oct 12 12:18:15 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 12 Oct 2007 09:18:15 -0700
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
In-Reply-To: <470F34C6.9050800@cervi-lyon.inserm.fr>
References: <470F34C6.9050800@cervi-lyon.inserm.fr>
Message-ID: <90E849A1-C5AB-40B3-9AB1-2DC79EBF5C4C@bioperl.org>

1.

Always 'use strict;' in your code - you'll see the bug more clearly  
that you should use $feat not $cds in the if stmt.


2.
You should pass in an actual Bio::DB::GenBank object to the -db  
argument.

my $db = Bio::DB::GenBank->new;
my $cds = $seq->spliced_seq(-db => $db);

-jason
On Oct 12, 2007, at 1:48 AM, Johann PELLET wrote:

> Hi,
> I have two questions:
> First, I have problems for example with this genbank entry: NC_008210.
> Indeed, for one CDS, the location is :
> join(161990..162784,complement(88222..88806),complement(86666..87448))
>
> When I parse a genbank file with this entry.
>
> my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
>                                -file => $input_file);
>
> while( my $seq = $seq_in->next_seq() ) {
>     my @features = $seq->get_SeqFeatures();
>     for ( my $i =0; $i < scalar @features; $i++ ){
>         my $feat = @features[$i];
>          if ( $feat->primary_tag eq 'CDS' ){
>
>
>              my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
>              my $seq_CDS=$seq_CDS_obj->seq;
>


>
> I have this error:
> Can't call method "isa" without a package or object reference at ....
>
> Secondly, When location is like:
> join(complement(AY421753.1:1..6),complement(3813..5699)) I know  
> that we
> must use spliced_seq with the argument db, but it's not working.
>       my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
> How can we valid a Bio::DB::RandomAccessI?
>
> Thanks
>
> -- 
> Johann Pellet
> phone (work): +33(0)4 37282352
> E-mail:    pellet at cervi-lyon.inserm.fr
> Centre d'Etudes et de Recherche en Virologie et Immunologie
> INSERM U503
> 21, Avenue Tony Garnier
> 69365 Lyon cedex 07 France
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From hlapp at gmx.net  Fri Oct 12 13:22:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 13:22:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
	<D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
Message-ID: <9762F1F9-68C8-42E2-8488-6656C76D36B8@gmx.net>


On Oct 12, 2007, at 11:02 AM, Chris Fields wrote:

>> Although sometimes confused, these are not the same motivations.  
>> AnnotationAdaptor provides a view - you use it when that's the  
>> view you need on a SeqFeatureI object you have in hand. For  
>> example, bioperl-db uses it so it doesn't have to bother about how  
>> to de/serialize tag/value pairs, when it knows how to de/serialize  
>> annotation collections already from sequence objects.  
>> AnnotationAdaptor doesn't care whether the primary_tag, or any  
>> other tag, is from an ontology.
>
> Ah, forgot it returns a Collection.  It doesn't modify the SF I  
> assume?

No, not if you only use getters. It does support adding annotation  
too, though.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From smwilson at hpc.unm.edu  Fri Oct 12 13:45:41 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Fri, 12 Oct 2007 11:45:41 -0600
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
	against latest Homo_sapiens.ags file
Message-ID: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>

Hi,

I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
memory.  I get a simple "Out of memory" output even with the  
following code:

#!/usr/bin/perl
use strict;
use Bio::ASN1::EntrezGene;
   my $parser = Bio::ASN1::EntrezGene->new('file' =>  
"Homo_sapiens.xml");
   while(my $result = $parser->next_seq)
   {
   }



Thanks.
Susan




From arareko at campus.iztacala.unam.mx  Fri Oct 12 14:10:44 2007
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 12 Oct 2007 14:10:44 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FB8A4.2050601@campus.iztacala.unam.mx>

Hi Susan,

Bio::ASN1::EntrezGene is not part of the BioPerl distribution, even 
though it shares the same namespace and is used by BP. Maybe you'd want 
to contact Mingyi Liu who is the author of the module. for more info 
take a look here:

http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene/

Regards,
Mauricio.

Susan Wilson wrote:
> Hi,
> 
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
> 
> 
> 
> Thanks.
> Susan
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM


From Kevin.M.Brown at asu.edu  Fri Oct 12 14:19:48 2007
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 12 Oct 2007 11:19:48 -0700
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>

> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> machine with 256GB of memory.  I get a simple "Out of memory" 
> output even with the following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }

I think most systems have a per process memory limit (either hardcoded
in the OS or configured depending on the OS) and IIRC most of the IO
handlers for BioPerl load entire file contents into memory to process
them.  Some of the IO parsers have been changed recently (a new one
added for blast) so that it only pulls into memory as much as it needs
to process the next result rather than the whole file in one shebang.


From stefan.kirov at bms.com  Fri Oct 12 14:34:49 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:34:49 -0400
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <470FBE49.7010703@bms.com>

Kevin Brown wrote:
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
>> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
>> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
>> machine with 256GB of memory.  I get a simple "Out of memory" 
>> output even with the following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>     
>
> I think most systems have a per process memory limit (either hardcoded
> in the OS or configured depending on the OS) and IIRC most of the IO
> handlers for BioPerl load entire file contents into memory to process
> them.  Some of the IO parsers have been changed recently (a new one
> added for blast) so that it only pulls into memory as much as it needs
> to process the next result rather than the whole file in one shebang.
>   
The file is approx. 6GB, so on a 256GB machine this is not going to
create any problem. I think this might be deep not well controlled
recursion problem.
Stefan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   


From mingyi.liu at gpc-biotech.com  Fri Oct 12 15:06:25 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 15:06:25 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <470FC5B1.3090606@gpc-biotech.com>

BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi

From j_martin at lbl.gov  Fri Oct 12 14:58:41 2007
From: j_martin at lbl.gov (Joel Martin)
Date: Fri, 12 Oct 2007 11:58:41 -0700
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FBE49.7010703@bms.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
	<470FBE49.7010703@bms.com>
Message-ID: <20071012185841.GE13838@eniac.jgi-psf.org>

Hello,
    Just a suggestion, is /usr/bin/perl a 64 bit perl?
Even on our sun machines with 72+ GB memory, for some reason they're
distributed with a 32 bit perl which can handle large files but would
probably have out of memory errrors if trying to read one into memory.

% file /usr/bin/perl 
/usr/bin/perl:  ELF 32-bit MSB executable SPARC Version 1, dynamically
linked, stripped

Joel

On Fri, Oct 12, 2007 at 02:34:49PM -0400, Stefan Kirov wrote:
> Kevin Brown wrote:
> >> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> >> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> >> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> >> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> >> machine with 256GB of memory.  I get a simple "Out of memory" 
> >> output even with the following code:
> >>
> >> #!/usr/bin/perl
> >> use strict;
> >> use Bio::ASN1::EntrezGene;
> >>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> >> "Homo_sapiens.xml");
> >>    while(my $result = $parser->next_seq)
> >>    {
> >>    }
> >>     
> >
> > I think most systems have a per process memory limit (either hardcoded
> > in the OS or configured depending on the OS) and IIRC most of the IO
> > handlers for BioPerl load entire file contents into memory to process
> > them.  Some of the IO parsers have been changed recently (a new one
> > added for blast) so that it only pulls into memory as much as it needs
> > to process the next result rather than the whole file in one shebang.
> >   
> The file is approx. 6GB, so on a 256GB machine this is not going to
> create any problem. I think this might be deep not well controlled
> recursion problem.
> Stefan
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >   
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

From stefan.kirov at bms.com  Fri Oct 12 14:20:38 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:20:38 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FBAF6.1050509@bms.com>

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   
Susan,
Are you running the latest version of Bio::ASN1::EntrezGene? You may
have a better chance of getting a fast (and useful) answer if you
contact Mingyi Liu (see on CPAN) directly- the module is not part of
Bioperl. Just to mention- I have also seen similar problems and there
seems to be particular problematic records. I think NCBI made some
changes/additions to their format (might have to do something with the
number/structure of contigs). I will have to run my pipeline soon again
and if I run into the same problem I will probably create bug report for
Mingyi. I hope you do it before me- it is boring and long process.
Stefan


From mingyi.liu at gpc-biotech.com  Fri Oct 12 14:50:08 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 14:50:08 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FC1E0.4070708@gpc-biotech.com>

Hi, Susan,

Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, it's better to directly contact me.  I actually deleted a few messages of this discussion before one caught my eye. Nowadays I'm working in some other areas and not tracking bioperl mailing list closely, a direct email to me would usually work out better.

As for the problem you mentioned, there could be two reasons: 1. It 
seems that you converted the file to XML file instead of ASN file. My 
parser is designed for ASN file, so please use gene2xml to convert the 
downloaded file to ASN file instead of XML file.  It is likely the wrong 
syntax of the file caused my parser to attempt to read the entire file 
as a string (because it couldn't find the start/end).  However, there's 
another minor possibility (which you might have taken care of already): 
2. Perl 5.8 added 64 bit support, but I don't know if you have perl 5.8 
64 bit installed on your system to support the 256 GB system memory you 
have?  If not, your >5 GB file is over the 4 GB 32 bit Perl limit.

Let me know if my suggestions work out for you.

Best,

Mingyi

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   


From gyang at plantbio.uga.edu  Fri Oct 12 16:52:06 2007
From: gyang at plantbio.uga.edu (Guojun Yang)
Date: Fri, 12 Oct 2007 16:52:06 -0400
Subject: [Bioperl-l] hide XML display on web
In-Reply-To: 41A08079-6EEC-4B62-8104-C41E70C03083@uiuc.edu
Message-ID: <20071012205206.9105fd09@dogwood.plantbio.uga.edu>

Hi, All,  
I have a cgi script that uses remoteblast (xml output). Every time, before and after the blast is finished, a lot of information is displayed on the client's screen, it's a nuisance but I am wondering if anyone knows how to rid of these. See below for examples:  
   
Thanks  
Guojun Yang  
_______________________example_____________________  
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>NCBI Blast:</title>
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
<!--[if lte IE 6]>
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
<![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="js/results.js"></script>
</head>

<body id="type-a" class="noToggleCheck" >
<div id="wrap">
   <div id="header">
  <div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span class="desc"> Basic Local Alignment Search Tool</span>
  </div>
  <div id="search">
  <div><script language="JavaScript" type="text/javascript"><!--
    var myncbi_xo = 0;
    var myncbi_x = MyNCBI_find();
    var myncbi_cu = unescape('http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3F');
    function MyNCBI_find()
    {
        var cs = document.cookie.split('; ');
        for(var i = 0; i < cs.length; i++) {
            // a name/value pair (a crumb) is separated by an equal sign
            var c = cs[i].split('=');
            if(c[0] == 'WebCubbyUser') { return c[1]; }
        }
        return '';
    }
.........

From hlapp at gmx.net  Sat Oct 13 17:49:49 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 13 Oct 2007 17:49:49 -0400
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <F2EFD76D-AA02-4FF7-8CAA-86AAC58E2D2E@gmx.net>


On Oct 12, 2007, at 2:19 PM, Kevin Brown wrote:

> IIRC most of the IO handlers for BioPerl load entire file contents  
> into memory to process them

As was determined already this most likely isn't the issue here, but  
I'm still confused by your statement. Most BioPerl Bio::SeqIO,  
Bio::ClusterIO, and Bio::OntologyIO parsers read an input file line  
by line, or at least by chunk.

Did you possibly mean something else?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From mingyi.liu at gpc-biotech.com  Sat Oct 13 23:28:09 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Sat, 13 Oct 2007 23:28:09 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <47118CC9.8090807@gpc-biotech.com>

Hi, Susan,

Let us know how my suggestions worked for you.  I replied to both you 
and the bioperl mailing list last Friday in the hope that my answer 
could be helpful for the list discussion, but it seems that the mailing 
list server had serious problems and dropped both of my emails.  I'm 
therefore replying again and combined the content of my 2 emails 
together below. Hopefully the email gets sent out to the mailing list.  
If not, would one of you please forward it out?  Thanks.

Mingyi Liu wrote:
> Hi, Susan,
>
> Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, 
> it's better to directly contact me.  I actually deleted a few messages 
> of this discussion before one caught my eye. Nowadays I'm working in 
> some other areas and not tracking bioperl mailing list closely, a 
> direct email to me would usually work out better.
>
> As for the problem you mentioned, there could be two reasons: 1. It 
> seems that you converted the file to XML file instead of ASN file. My 
> parser is designed for ASN file, so please use gene2xml to convert the 
> downloaded file to ASN file instead of XML file.  It is likely the 
> wrong syntax of the file caused my parser to attempt to read the 
> entire file as a string (because it couldn't find the start/end).  
> However, there's another minor possibility (which you might have taken 
> care of already): 2. Perl 5.8 added 64 bit support, but I don't know 
> if you have perl 5.8 64 bit installed on your system to support the 
> 256 GB system memory you have?  If not, your >5 GB file is over the 4 
> GB 32 bit Perl limit.
>
> Let me know if my suggestions work out for you.
>
> Best,
>
> Mingyi
>
BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped 
binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus 
SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi

> Susan Wilson wrote:
>> Hi,
>>
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
>> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
>> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB 
>> of  memory.  I get a simple "Out of memory" output even with the  
>> following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>
>>
>>
>> Thanks.
>> Susan
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>   
>
>


From smwilson at hpc.unm.edu  Mon Oct 15 11:08:55 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 15 Oct 2007 09:08:55 -0600
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC5B1.3090606@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
	<470FC5B1.3090606@gpc-biotech.com>
Message-ID: <72C50125-E169-448C-8F25-AB13A8AD308D@hpc.unm.edu>

Mingyi,

Thank you very much for your advice.  The text ASN file 1/4 the size  
of the (evil, evil) XML file and parsing it ran just fine.  We are  
still pursuing a 64-bit perl on our 256GB server and I will let you  
know how it works.

Thanks.
Susan



On Oct 12, 2007, at 1:06 PM, Mingyi Liu wrote:

> BTW, here's the syntax in one of my messages last year about how to  
> convert the compressed binary ASN format NCBI provides to the text  
> ASN format my module (or Stefan's SeqIO::entrezgene) expects (the - 
> x switch does the trick, overwriting the default option to produce  
> XML output):
>
> my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i  
> Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the  
> gzipped binary file directly downloaded from NCBI
>
> Same syntax should be used when you're using SeqIO (thus  
> SeqIO::entrezgene).
>
> BTW, text ASN is both smaller and faster to parse than XML format.
>
> Best,
>
> Mingyi


From wgallin at ualberta.ca  Mon Oct 15 18:25:14 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 15 Oct 2007 16:25:14 -0600
Subject: [Bioperl-l] Capturing Joined Sequence from two records
Message-ID: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>

I have encountered a case of a protein sequence record for which the  
coding sequence is a join with ranges from two nucleotide sequence  
records:

gi # is 7648673

Relevant annotation is:

   CDS             1..630
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"


Is there any way using Bio::Seq objects to seamlessly get the CDS  
nucleic acid sequence, or do I need to just treat it as an oddity and  
cobble together something manually?

Warren Gallin

From esnyder at vbi.vt.edu  Mon Oct 15 16:38:06 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 16:38:06 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713CFAE.7020007@vbi.vt.edu>

Hello Again,

I think I've discovered the problem.  Apparently I've got an old version 
of BioPerl which expected an array of arguments rather than a named 
list.  When I cut-and-pasted the new code for translate() into my 
distribution, the problem went away.

So, the next question is: how can I be sure that I have the most 
up-to-date distribution available (or at least the one that matches the 
BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within 
the last year but I don't know where it actually came from.

Thanks,
eesnyder

-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"



From jason at bioperl.org  Mon Oct 15 18:54:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 15 Oct 2007 15:54:38 -0700
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
Message-ID: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>

pass in a db handle to spliced_seq. There was a question about this  
on the list a few days ago.
http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html

  - does anyone want to add this solution in more example to FAQ?

-jason

On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:

> I have encountered a case of a protein sequence record for which the
> coding sequence is a join with ranges from two nucleotide sequence
> records:
>
> gi # is 7648673
>
> Relevant annotation is:
>
>    CDS             1..630
>                       /gene="KCND2"
>                       /coded_by="join
> (AF166007.1:430..1544,AF166008.1:345..507,
>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>                        
> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>
>
> Is there any way using Bio::Seq objects to seamlessly get the CDS
> nucleic acid sequence, or do I need to just treat it as an oddity and
> cobble together something manually?
>
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org

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From torsten.seemann at infotech.monash.edu.au  Mon Oct 15 20:49:16 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Tue, 16 Oct 2007 10:49:16 +1000
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <a79f6a4b0710151749o240a5e72j697a1cff6bf39baf@mail.gmail.com>

>  pass in a db handle to spliced_seq. There was a question about this on the
> list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?

Done.

http://www.bioperl.org/wiki/FAQ#How_do_I_get_the_complete_spliced_sequence_when_the_coordinates_refer_to_Genbank_identifiers.3F

If anyone spots any errors or wants to improve it, please do so.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010

From cjfields at uiuc.edu  Mon Oct 15 21:02:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:02:25 -0500
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
In-Reply-To: <4713CFAE.7020007@vbi.vt.edu>
References: <4713CFAE.7020007@vbi.vt.edu>
Message-ID: <67EBC789-C27F-4918-941C-46E62ACFE934@uiuc.edu>

http://www.bioperl.org/wiki/ 
FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F

If you installed BioPerl via CPAN you more than likely have 1.4.  The  
most recent dev release is 1.5.2.

chris

On Oct 15, 2007, at 3:38 PM, Eric E. Snyder wrote:

> Hello Again,
>
> I think I've discovered the problem.  Apparently I've got an old  
> version
> of BioPerl which expected an array of arguments rather than a named
> list.  When I cut-and-pasted the new code for translate() into my
> distribution, the problem went away.
>
> So, the next question is: how can I be sure that I have the most
> up-to-date distribution available (or at least the one that matches  
> the
> BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within
> the last year but I don't know where it actually came from.
>
> Thanks,
> eesnyder
>
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0447
> USA
>
> Office:    (540) 231-5428
> Mobile:    (540) 230-5225
> Fax:    (540) 231-2606
> Email:    eesnyder at vbi.vt.edu
> JDAM:    N 37 12'01.6", W 80 24'26.9"
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From cjfields at uiuc.edu  Mon Oct 15 21:39:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:39:37 -0500
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>

Would spliced_seq() work with a protein sequence this way?  The  
location string is in a tag 'coded_by', which would require a little  
more work to get the sequence.

chris

On Oct 15, 2007, at 5:54 PM, Jason Stajich wrote:

> pass in a db handle to spliced_seq. There was a question about this  
> on the list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?
>
> -jason
>
> On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:
>
>> I have encountered a case of a protein sequence record for which the
>> coding sequence is a join with ranges from two nucleotide sequence
>> records:
>>
>> gi # is 7648673
>>
>> Relevant annotation is:
>>
>>    CDS             1..630
>>                       /gene="KCND2"
>>                       /coded_by="join
>> (AF166007.1:430..1544,AF166008.1:345..507,
>>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>>                        
>> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>>
>>
>> Is there any way using Bio::Seq objects to seamlessly get the CDS
>> nucleic acid sequence, or do I need to just treat it as an oddity and
>> cobble together something manually?
>>
>> Warren Gallin
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From Russell.Smithies at agresearch.co.nz  Mon Oct 15 23:51:40 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 16 Oct 2007 16:51:40 +1300
Subject: [Bioperl-l] Parsing EMBL records
In-Reply-To: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca><EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
	<50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05EFC097@imail.agresearch.co.nz>

I've got some output from "newcpgreport" that looks like embl format but
I'm having trouble parsing it.
One of the reasons might be because of this warning but I'm not sure.
	-------------------- WARNING ---------------------
	MSG: Got a sequence with no letters in it cannot guess alphabet
[]
	---------------------------------------------------

I need to get it into gff or tabbed format and don't want to have to
resort to Perl regexes to do it.
Has anyone got some example code for parsing embl or swiss output I
could borrow?

The "newcpgreport " output looks like this:
-----------------------------------------------------
ID   BTA28  46084206 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       181953..182223
FT                    /size=271
FT                    /Sum C+G=162
FT                    /Percent CG=59.78
FT                    /ObsExp=0.75
FT   CpG island       222609..223040
FT                    /size=432
FT                    /Sum C+G=290
FT                    /Percent CG=67.13
FT                    /ObsExp=0.97
FT   CpG island       288537..288741
FT                    /size=205
FT                    /Sum C+G=112
FT                    /Percent CG=54.63
FT                    /ObsExp=0.85 
------------------------------------------------------


Any help greatly appreciated  :-)

Russell Smithies

=======================================================================
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From esnyder at vbi.vt.edu  Mon Oct 15 14:50:54 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 14:50:54 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713B68E.2040804@vbi.vt.edu>

Hello,

I am having trouble with translate() when supplying parameters such as 
-frame, -codontable_id, etc.  I am working straight out of the tutorial 
with a very simple program-- which has me stumped!

use Bio::SeqIO;
foreach my $file ( @ARGV ){
     my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
                                     -format =>  "fasta" );
     my $seq_obj = $seqio_obj->next_seq;

     print "loaded one sequence:\n\tdisplay_id\t" .
	   $seq_obj->display_id() . "\n" .
     	   "\tdescription\t" . $seq_obj->description() . "\n";

     foreach my $frame ( 0 .. 2){
         $prot_obj = $seq_obj->translate( '-frame' => $frame );
         print "translation = " . $prot_obj->seq . "\n";
     }
}

Everything works as expected until calling translate.  The output I get 
is the translation of my FASTA sequence (in frame zero, repeated three 
times) in which every "stop" is replaced with "-frame" (!!).  However, 
with no parameters, translate works as advertised.

This is getting me down because by using the full complement of 
translate options, including specifying frame, genetic code, alternative 
start codons, etc., BioPerl will save me a huge amount of time... but 
only if I can figure out how to use it properly!

Any assistance would be greatly appreciated!!!

Sincerely,
eesnyder


-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"


From bosborne11 at verizon.net  Tue Oct 16 08:57:46 2007
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 16 Oct 2007 08:57:46 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
 parameters
In-Reply-To: <4713B68E.2040804@vbi.vt.edu>
Message-ID: <C33A2D8A.FF00%bosborne11@verizon.net>

Eric,

I took your code, unmodified, and ran it using a file in the distribution.
The output looks OK, different frames are used and I don't see "-frame" in
the output sequence (see below). This is using the latest bioperl-live -
what version Bioperl are you using?

Brian O.


269 ~/bioperl-live>./test.pl t/data/HUMBETGLOA.fa
loaded one sequence:
        display_id      HUMBETGLOA
        description     Human haplotype C4 beta-globin gene, complete cds.
translation = 
TSYLTPLITPLIVTLWVVSDFLFICIFDCIKRSLVFYLLFPKT**VTNAQSTLICIYSIFRHNLLACMSKLRKTTT
NECIYMYMYVCTYTHIYIYIFFLFLPEGFNPNKEKICLELR*SFHPFCPVSILHILETQEEIHLHIPKLNYGRQNS
STFSASTSYLCNKKIGKTIFNMLTKL*FQILRKYTCKGGCF**QFVLMVWGQEIYLRGRAEGLKSNS*ASARRAKD
RYGCHHLDLTLWSHTLGLANLLPGAGRAGARAGHKSQGRAIYCLHLLLTQLCSLATSNRHHGASDS*GEVCRYCPV
GQGERG*SWW*GPGQVGIKVTRQV*GDQ*KLGMWRQRRLLGF**ALTLSAYWSIFPPLGCWWSTLGPRGSLSPLGI
CPLLMLLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWILRTSG*VYGTLDVFFPLLFYG*VH
VIGRG*VTGYSLEWETDE*LHQCGSLRIVLVSFICCS*QLFSFV*FLLSFFFFSAIFTIILNALTLCITKGNISEI
H*VT*KKTLHSLPSTLLFGIYVCLFAYS*SPYFIFFYF*LIHNHYTYLWVKV*CFNMCTHIDQIRVILHL*F*KML
SSFNILFCLSYF*YFP*SLSFRAIMIQCIMPLCTILKNNSDNFWVKAIAISLHINISAYKL*LM*EVSYC**QLQS
SYHSAFILWLG*GWIILSPS*ALLLIMFIPLIFLPQLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHK
YH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHCNDVFKLFLNILLKRECGRSVHLKHKEMKS
*FKPWENTLYLKLHERR*GCKQLMHIGNSPDAYALFIPQKRIQVEA*FGG*SFAMLYFTLLIVLAVLMNVFSLPIC
LSCISQP*LHSVLLLRDTTFPLKCSFHVLRRDGFSSPGHSALVVSVVL*RST*RRKNRGHGLTVL*ALLPCLPHSQ
*PGICSASLPELS
translation = 
PPI*HH*LPH**SHFGL*VTFYLFVFLTALRGL*FFTSCFPKPNK*LMHRAH*FVFILFLDIIY*HA*AN*EKQQQ
MNAYICICMCVHIHIYIYIYFFFSYQKVLIQIRRRYA*N*GRVFIHSVL*VFCIFWRRRKRSIYISQS*IMVDKTL
PLLVHQLLICVIRKLGKRSSICLPSCDSKYYVNTLAKEDVFSSNLY*WYGAKRYILEGGLRV*SPTPKPVPEEPRT
GTAVIT*TSPCGATP*GWPIYSQEQGGQEPGLGIKVRAEPSIAYICF*HNCVH*QPQTDTMVHLTPEEKSAVTALW
GKVNVDEVGGEALGRLVSRLQDRFKETNRNWACGDREDSWVSDRH*LSLPIGLFSHP*AAGGLPLDPEVL*VLWGS
VHS*CCYGQP*GEGSWQESARCL**WPGSPGQPQGHLCHTE*AAL*QAARGS*ELQGESMGPLMFSFPFFSMVKFM
S*EGDK*QGTV*NGKQTNDCISVEVSGSF*FLLFAVHNNCFLLFNSCFLFFSSPQFLLLYLMP*HCV*QKEISLRY
IK*LKKKLYTVCLVHYYLEYMCAYLHIHNLPTLFSFIFN*YIIIIHIYGLKCNVLICVHILTKSG*FCICNFKKCF
LLLIYFFVYLISNTFPNLFLSGQ**YNVSCLFAPF*RITVIISGLRQ*QYLCI*IFLHINCN*CKRFHIANSSYNP
ATILLLFYGWDKAGLF*VQARPFC*SCSYLLSSSHSSWATCWSVCWPITLAKNSPHQCRLPIRKWWLVWLMPWPTS
ITKLAFLLSNFY*RFLCSLSPTTKLGDIMKGLEHLDSA**KTFIFIAMMYLNYF*IFY*KGNVGGQCI*NIKK*RA
SSNLGKIHYILNSMKEGEAANS*CTLATALMHMPYSSLRKGFK*RLDLEVKVLLCCILHYLLF*LSS*MSFHYPFA
YPASLSLDSTQFSCLEIPPFP*SVPSMFYGEMVSPRLATQP*LSLLSYRGLLEEGKTGVMV*LSCEPFFPASPTHS
DPESAVLVSRNY
translation = 
LLFDTTDYPIDSHTLGCK*LFIYLYF*LH*EVSSFLPLVSQNLISN*CTEHIDLYLFYF*T*FISMHEQIKKNNNK
*MHIYVYVCVYIYTYIYIYIFSFLTRRF*SK*GEDMLRTEVEFSSILSCKYFAYSGDAGRDPSTYPKAELW*TKLF
HF*CINFLFV**ENWENDLQYAYQAVIPNIT*IHLQRRMFLVAICTDGMGPRDIS*REG*GFEVQLLSQCQKSQGQ
VRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQSHLLLTFASDTTVFTSNLKQTPWCI*LLRRSLPLLPCG
AR*TWMKLVVRPWAGWYQGYKTGLRRPIETGHVETEKTLGFLIGTDSLCLLVYFPTLRLLVVYPWTQRFFESFGDL
STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRVSLWDP*CFLSPSFLWLSSC
HRKGISNRVQFRMGNRRMIASVWKSQDRFSFFYLLFITIVFFCLILAFFFFLLRNFYYYT*CLNIVYNKRKYL*DT
LSNLKKNFTQSA*YITIWNICVLICIFIISLLYFLLFLIDT*SLYIFMG*SVMF*YVYTY*PNQGNFAFVILKNAF
FF*YTFLFILFLILSLISFFQGNNDTMYHASLHHSKE*Q**FLG*GNSNISAYKYFCI*IVTDVRGFILLIAATIQ
LPFCFYFMVGIRLDYSESKLGPFANHVHTSYLPPTAPGQRAGLCAGPSLWQRIHPTSAGCLSESGGWCG*CPGPQV
SLSSLSCCPISIKGSFVP*VQLLNWGIL*RALSIWILPNKKHLFSLQ*CI*IISEYFTKKGMWEVSAFKT*RNEEL
VQTLGKYTIS*TP*KKVRLQTANAHWQQP*CICLIHPSEKDSSRGLIWRLKFCYAVFYITYCFSCPHECLFTTHLL
ILHLSALTPLSSLA*RYHLSPEVFLPCFTARWFLLAWPLSLSCLCCLIEVYLKKEKQGSWFDCPVSPSSLPPPLTV
TRNLQC*SPGTI



On 10/15/07 2:50 PM, "Eric E. Snyder" <esnyder at vbi.vt.edu> wrote:

> Hello,
> 
> I am having trouble with translate() when supplying parameters such as
> -frame, -codontable_id, etc.  I am working straight out of the tutorial
> with a very simple program-- which has me stumped!
> 
> use Bio::SeqIO;
> foreach my $file ( @ARGV ){
>      my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
>                                      -format =>  "fasta" );
>      my $seq_obj = $seqio_obj->next_seq;
> 
>      print "loaded one sequence:\n\tdisplay_id\t" .
>   $seq_obj->display_id() . "\n" .
>   "\tdescription\t" . $seq_obj->description() . "\n";
> 
>      foreach my $frame ( 0 .. 2){
>          $prot_obj = $seq_obj->translate( '-frame' => $frame );
>          print "translation = " . $prot_obj->seq . "\n";
>      }
> }
> 
> Everything works as expected until calling translate.  The output I get
> is the translation of my FASTA sequence (in frame zero, repeated three
> times) in which every "stop" is replaced with "-frame" (!!).  However,
> with no parameters, translate works as advertised.
> 
> This is getting me down because by using the full complement of
> translate options, including specifying frame, genetic code, alternative
> start codons, etc., BioPerl will save me a huge amount of time... but
> only if I can figure out how to use it properly!
> 
> Any assistance would be greatly appreciated!!!
> 
> Sincerely,
> eesnyder
> 



From sheris at berkeley.edu  Tue Oct 16 19:15:43 2007
From: sheris at berkeley.edu (Sheri Simmons)
Date: Tue, 16 Oct 2007 16:15:43 -0700
Subject: [Bioperl-l] what are the key features of genbank file recognized by
	SeqIO?
Message-ID: <200710161615.43420.sheris@berkeley.edu>

I'm hoping someone can help me with figuring out how to generate genbank files 
from scratch that can be interpreted with SeqIO. The problem is that genbank 
files generated via the artemis program are not recognized by SeqIO, so I am 
attempting to generate SeqIO-compatible genbank files so they can be 
converted to other formats later. 
I produced a file which looks by eye exactly like standard genbank files, but 
which is not recognized by SeqIO. Could anyone tell me or refer me to a 
source that explains the exact format that SeqIO::genbank requires? 
FYI here's a snippet of the file generated by my program:

########
LOCUS   Contig2406              66712 bp        dna     linear  UNK
FEATURES             Location/Qualifiers
     CDS                 83..1222
                            /gene="org_2406_0001"
     CDS                1259..1576
                           /gene="org_2406_0002"
     CDS                complement(1830..3284)
                           /gene="org_2406_0003c"
(more CDS)
BASE COUNT      14091 a         19796 c         18841 g         13747 t
ORIGIN
        1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
      61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
(more sequence)
###########

Thanks,
Sheri

-- 
Sheri Simmons
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
http://webfiles.berkeley.edu/~sheris

From barry.moore at genetics.utah.edu  Tue Oct 16 19:47:56 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 16 Oct 2007 17:47:56 -0600
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>

Hi Sheri,

You would need to look at the source code for Bio::SeqIO::genbank.pm  
specifically the next_seq method.  If you let us know what kind of  
errors you're getting, or what data is missing in your seq object  
perhaps we could help you narrow it down.  You could also send one of  
your GenBank style files that isn't working and someone might be  
willing to take a stab at running it.

Barry

On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:

> I'm hoping someone can help me with figuring out how to generate  
> genbank files
> from scratch that can be interpreted with SeqIO. The problem is  
> that genbank
> files generated via the artemis program are not recognized by  
> SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank  
> files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me  
> to a
> source that explains the exact format that SeqIO::genbank requires?
> FYI here's a snippet of the file generated by my program:
>
> ########
> LOCUS   Contig2406              66712 bp        dna     linear  UNK
> FEATURES             Location/Qualifiers
>      CDS                 83..1222
>                             /gene="org_2406_0001"
>      CDS                1259..1576
>                            /gene="org_2406_0002"
>      CDS                complement(1830..3284)
>                            /gene="org_2406_0003c"
> (more CDS)
> BASE COUNT      14091 a         19796 c         18841 g          
> 13747 t
> ORIGIN
>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta  
> acatacacaa
>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg  
> ccgatatcaa
> (more sequence)
> ###########
>
> Thanks,
> Sheri
>
> --
> Sheri Simmons
> Department of Earth and Planetary Sciences
> University of California, Berkeley
> Berkeley, CA 94720-4767
> http://webfiles.berkeley.edu/~sheris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From jason at bioperl.org  Tue Oct 16 19:58:46 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Oct 2007 16:58:46 -0700
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
References: <200710161615.43420.sheris@berkeley.edu>
	<020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
Message-ID: <74393EF9-C4B9-4F3B-8150-E22BECE81587@bioperl.org>

I am sure we should also let the Artemis developers know what is  
going on so they can help fix the bug on their end as well.

Have you also tried dumping EMBL from Artemis, a format I assume they  
are more likely to use, and seeing if that parses fine in BioPerl?

-jason
On Oct 16, 2007, at 4:47 PM, Barry Moore wrote:

> Hi Sheri,
>
> You would need to look at the source code for Bio::SeqIO::genbank.pm
> specifically the next_seq method.  If you let us know what kind of
> errors you're getting, or what data is missing in your seq object
> perhaps we could help you narrow it down.  You could also send one of
> your GenBank style files that isn't working and someone might be
> willing to take a stab at running it.
>
> Barry
>
> On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:
>
>> I'm hoping someone can help me with figuring out how to generate
>> genbank files
>> from scratch that can be interpreted with SeqIO. The problem is
>> that genbank
>> files generated via the artemis program are not recognized by
>> SeqIO, so I am
>> attempting to generate SeqIO-compatible genbank files so they can be
>> converted to other formats later.
>> I produced a file which looks by eye exactly like standard genbank
>> files, but
>> which is not recognized by SeqIO. Could anyone tell me or refer me
>> to a
>> source that explains the exact format that SeqIO::genbank requires?
>> FYI here's a snippet of the file generated by my program:
>>
>> ########
>> LOCUS   Contig2406              66712 bp        dna     linear  UNK
>> FEATURES             Location/Qualifiers
>>      CDS                 83..1222
>>                             /gene="org_2406_0001"
>>      CDS                1259..1576
>>                            /gene="org_2406_0002"
>>      CDS                complement(1830..3284)
>>                            /gene="org_2406_0003c"
>> (more CDS)
>> BASE COUNT      14091 a         19796 c         18841 g
>> 13747 t
>> ORIGIN
>>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta
>> acatacacaa
>>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg
>> ccgatatcaa
>> (more sequence)
>> ###########
>>
>> Thanks,
>> Sheri
>>
>> --
>> Sheri Simmons
>> Department of Earth and Planetary Sciences
>> University of California, Berkeley
>> Berkeley, CA 94720-4767
>> http://webfiles.berkeley.edu/~sheris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From torsten.seemann at infotech.monash.edu.au  Tue Oct 16 21:31:03 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Wed, 17 Oct 2007 11:31:03 +1000
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <a79f6a4b0710161831x30efa062oacc64844706e8a96@mail.gmail.com>

On 17/10/2007, Sheri Simmons <sheris at berkeley.edu> wrote:
> I'm hoping someone can help me with figuring out how to generate genbank files
> from scratch that can be interpreted with SeqIO. The problem is that genbank
> files generated via the artemis program are not recognized by SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me to a
> source that explains the exact format that SeqIO::genbank requires?

Here is NCBI's documentation on the feature table format.
http://www.ncbi.nlm.nih.gov/collab/FT/

Regarding Artemis: if you load an EMBL file, then save as EMBL, it
seems to keep the header. If you save it as Genbank though, it
discards the header and only outputs the feature table and sequence.
Also, Artemis for many of its Save options only saves the feature
table. Both of these last two can't be read by BioPerl. At one stage I
had some code to whack in a fake header and empty sequence at the end
to get it to load.

Now, regarding your example output. I'm never sure if the first line
is LOCUS or ID, I guess one is deprecated. You also don't have a Date
at the end of the first line, but maybe it is optional. You are also
missing the "//" on the final line. Finally, Genbank is strict on
correct spacing etc, but I'm sure the Bioperl parser is written
relatively defensively here, so that might not be the problem.

Hope this helps,

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010

From wgallin at ualberta.ca  Wed Oct 17 21:42:54 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Wed, 17 Oct 2007 19:42:54 -0600
Subject: [Bioperl-l] Still trouble with remote joined records
Message-ID: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>

I must be missing something, but I can not get the procedure outlined  
in FAQ 5.5 to do what I think it should (maybe my expectations are  
incorrect.

I think I have an up-to-date release:

GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print  
$Bio::Root::Version::VERSION,"\n"'
1.005002102


If I run the following script (not that gi7648673 is a protein record):
___________________________________________________________
#! /usr/bin/perl

#071017 - Small script to test the method for getting the ORF sequence
#using dbh passing into the sequence method.


use strict;
use warnings;
use LWP::Simple;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::Seq;

#Create handles to GenBank and GenPept

my $gbh = Bio::DB::GenBank -> new;
my $gph = Bio::DB::GenPept -> new;

#This is the gi number of the entry being tested

my $test_gi = 7648673;

#Get the protein sequence file from GENBANK

my $test_na_record = $gph -> get_Seq_by_gi ($test_gi);

#Go through the features - when the CDS feature is found splice  
together the sequence and translate.


   for my $feat ( $test_na_record->get_SeqFeatures ) {
     if ( $feat->primary_tag eq 'CDS' ) {
        my $cds = $feat->spliced_seq(-db => $gbh, -nosort => 1);
        print $cds->translate->seq, "\n";
     }
   }


exit;
_______________________________________________________________________
I get an error that a protein sequence can not be translated.  I  
thought that by feeding the handle to GenBank into the spliced_seq  
method that it would retrieve the necessary nucleic acid sequence  
records and splice together the specified ranges.

So I tried using the corresponding nucleic acid record, gi7648671,  
which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).

That yielded the correct amino acid sequence for the first half the  
protein, encoded by the sequence in the record itself, but it did not  
retrieve the other nucleic acid record that is specified to contain  
the 3' end of the sequence.

So, as far as I can see, passing the DB handle isn't causing the  
spliced_seq method to go elsewhere for the nucleic acid sequence data.

I thought that was the purpose.

Can anyone enlighten me, or is this a bug?

Warren Gallin


From cjfields at uiuc.edu  Wed Oct 17 22:49:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 21:49:37 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
Message-ID: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>

On Oct 17, 2007, at 8:42 PM, Warren Gallin wrote:

> I must be missing something, but I can not get the procedure outlined
> in FAQ 5.5 to do what I think it should (maybe my expectations are
> incorrect.
>
> I think I have an up-to-date release:
>
> GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print
> $Bio::Root::Version::VERSION,"\n"'
> 1.005002102
> ...
> I get an error that a protein sequence can not be translated.  I
> thought that by feeding the handle to GenBank into the spliced_seq
> method that it would retrieve the necessary nucleic acid sequence
> records and splice together the specified ranges.

No, the error is expected:

MSG: Can't translate an amino acid sequence.

The record in question is a protein record, so you are retrieving a  
protein sequence, which can't be translated (the exception is valid,  
in other words).  Note that the 'CDS' feature in this case has a  
specified location of 1..630 (indicated by arrow):

      CDS             1..630   <---------
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"

The tag name 'coded_by' has the data you want; however it is stored  
as a string only.

> So I tried using the corresponding nucleic acid record, gi7648671,
> which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).
>
> That yielded the correct amino acid sequence for the first half the
> protein, encoded by the sequence in the record itself, but it did not
> retrieve the other nucleic acid record that is specified to contain
> the 3' end of the sequence.
> ...
> So, as far as I can see, passing the DB handle isn't causing the
> spliced_seq method to go elsewhere for the nucleic acid sequence data.
>
> I thought that was the purpose.
>
> Can anyone enlighten me, or is this a bug?
>
> Warren Gallin

This appears to be a bug.  The remote sequence is designated in the  
feature:

      CDS             join 
(430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
                      AF166008.1:9952..10044,AF166008.1:13222..13469,
                      AF166008.1:15123..15300)
                      /gene="KCND2"
                      /codon_start=1
                      /product="voltage-gated potassium channel Kv4.2"
                      /protein_id="AAF65618.1"
                      /db_xref="GI:7648673"

but the location is truncated when passed through SeqIO to genbank  
output, which explains the spliced_seq() problem:

      CDS             430..1544
                      /db_xref="GI:7648673"
                      /codon_start=1
                      /protein_id="AAF65618.1"
                      /gene="KCND2"

I'll try looking into this; if I can't get to it immediately I'll  
file a bug report.  Thanks!

chris

From cjfields at uiuc.edu  Wed Oct 17 23:45:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 22:45:55 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
	<8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
Message-ID: <872F9A22-AC32-4381-B7FE-4554943C8D75@uiuc.edu>


On Oct 17, 2007, at 9:49 PM, Chris Fields wrote:

> ...
>> So, as far as I can see, passing the DB handle isn't causing the
>> spliced_seq method to go elsewhere for the nucleic acid sequence  
>> data.
>>
>> I thought that was the purpose.
>>
>> Can anyone enlighten me, or is this a bug?
>>
>> Warren Gallin
>
> This appears to be a bug.  The remote sequence is designated in the
> feature:
>
>       CDS             join
> (430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
>                       AF166008.1:9952..10044,AF166008.1:13222..13469,
>                       AF166008.1:15123..15300)
>                       /gene="KCND2"
>                       /codon_start=1
>                       /product="voltage-gated potassium channel Kv4.2"
>                       /protein_id="AAF65618.1"
>                       /db_xref="GI:7648673"
>
> but the location is truncated when passed through SeqIO to genbank
> output, which explains the spliced_seq() problem:
>
>       CDS             430..1544
>                       /db_xref="GI:7648673"
>                       /codon_start=1
>                       /protein_id="AAF65618.1"
>                       /gene="KCND2"
>
> I'll try looking into this; if I can't get to it immediately I'll
> file a bug report.  Thanks!
>
> chris

Looked into it and there isn't a problem with BioPerl, but there  
appears to be an error on NCBI's end with some full GenBank seqs and  
remote locations.  The default return type for records using  
Bio::DB::GenBank is 'gbwithparts' (which retrieves full records for  
everything), but this particular record version has a truncated  
location.  You can see the truncated version here via eutils:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
db=nucleotide&retmode=text&id=7648671&rettype=gbwithparts

You can get around this in your script by changing the requested  
format to 'gb', which has the correct location string and returns the  
full protein seq:

my $gbh = Bio::DB::GenBank->new(-format => 'gb');

chris

From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From cjfields at uiuc.edu  Fri Oct 19 00:47:12 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 18 Oct 2007 23:47:12 -0500
Subject: [Bioperl-l] Bioperl DB RefSeq
In-Reply-To: <534058.73546.qm@web38804.mail.mud.yahoo.com>
References: <534058.73546.qm@web38804.mail.mud.yahoo.com>
Message-ID: <744D3248-EA8E-4832-847D-4434DFF258E6@uiuc.edu>

Use an eval {} block, described here:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Error_Handling

my $seq;
eval {
   $seq =  $seq = $seq_refseq->get_Seq_by_id("$acc");
};

print "ID does not exist!\n" if $@;

chris

On Oct 18, 2007, at 10:11 PM, Steven Mei wrote:

> Hi,
>
> I have a list of refseq accession  numbers and  wish  to get  their  
> sequences. I used Bio::DB:: RefSeq module
>
> However, if the $acc is bad (such as deleted accession), an  
> exception  would  printed out  and the script stops execution.
>
>
> ---------------EXCEPTION-------------------
> MSG: id does not exist
> ...
> ----------------------------------------------------
>
> my $seq = $seq_refseq->get_Seq_by_id("$acc");
>
>
> What I wish to happen is the script would handle the next accession  
> (bypass the bad accession) and continue until all the accessions  
> have been processed.
>
> Anyone have idea how to handle this issue? Thanks
>
> -- Mike


From j.s.soares at gmail.com  Fri Oct 19 08:45:25 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 05:45:25 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of the gene. This is the thing where the script goes weird. It doesn't
reset the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need to know how
many repetitions of the pattern there are in each gene, as above, it does
not reset the counting of repetitions and istead gives me the repitions in
the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;

#print "What is the pattern you're looking for?";
#chomp (my $pat = <>);# Taking the pattern input from the user and cuting
the new line character in the end

#print "How many letters in the pattern?";
#chomp (my $patlen = <>);# Taking the length of the pattern input from the
user and cuting the new line character in the end

print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";# Taking the file to analyse
input from the user and cuting the new line character in the end

print "Where do you want to store the rough file?";
chomp (my $rough = <>);# Taking the rough file input from the user and
cuting the new line character in the end

print "Where do you want to store the final file?";
chomp (my $final = <>);# Taking the clean file input from the user and
cuting the new line character in the end

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0,
0);#Initialization of the variables common to the whole script:
#$count_of_pat3 is used to count how many times the pattern appears in a DNA
sequence.
#$position states the location in number of bases from the start of the
sequence to the first base of the pattern. 
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');#A
BioPerl module was used here (Bio::Tools::SeqPattern in order to give the
program a better direction telling it what exactly the pattern is about. If
it's DNA, RNA or Protein. In this case it's DNA.

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {#Using
BioPerl module Bio::SeqIO to open the file that contains the sequences to be
analysed
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
#Using Perl's simple default function open to create the rough file and make
it writable

        while (my $seq_obj = $in->next_seq) {
#This while loop uses BioPerl objects: $seq_obj and next_seq. It basically
states that for each sequence in the Sequences file it will run the lines
that follow and after that it will pick up the next sequence

        	#my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE
=>'Dna');#A BioPerl module was used here (Bio::Tools::SeqPattern in order to
give the program a better direction telling it what exactly the pattern is
about. If it's DNA, RNA or Protein. In this case it's DNA.

                my $id1 = $seq_obj->display_id();
#We use the $seq_obj->display_id() object here to be able to chop the fasta
header from each sequence and store it as the variable $id1

                     
				foreach ($seq_obj->seq =~ m/$pat/g){#for each sequence that contains the
pattern we are looking for, we start the count of the times the pattern
repeats itself
								++$count_of_pat;
							
							print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",#The Fasta Header,
the number of pattern repitions and the position where each repition was
found in each sequence is printed on the rough file
							$position + $-[0] + 1, "\n"; #This resets the position for the next
repetition
							$position = $position + length($seq_obj) - $patlen + 1;
							#print $-;
							#print "$count_of_pat\n";
							#print "$position\n";
							#print $seq_obj->seq, "\n";
							}#The positon is set to start from 1 rather than the default Perl
start position 0.
				
							
					}
					
					
        close MOTIFCOUNT;#With the file completelly scanned, the rough file
is closed

        open (SYM, "+< $rough") or die "The file doesn't exist";#The rough
file is open again and if it hasn't been created it prints out that it
doesn't exist

        open (TAB, ">> $final") or die "The gene list wasn't
transformed";#Another file is created and made writable, the final file.
This is done as can be seen in the following lines in order to substitute
any space by a tab and to print, as a header in the file, the motif we were
looking for.

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;#The regexp that substitutes each space
for a tab 
        		print TAB "$line";
        	}
        }
        close (SYM);#Closing both files the rough and the final
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;


Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
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From j.s.soares at gmail.com  Fri Oct 19 09:10:18 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 06:10:18 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of each gene. This is where the script goes weird. It doesn't reset
the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need the
information on how many repetitions of the pattern there are in each gene,
as above, it does not reset the counting of repetitions and instead gives me
the repitions in the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Perl;
use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;




print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";
print "Where do you want to store the rough file?";
chomp (my $rough = <>);
print "Where do you want to store the final file?";
chomp (my $final = <>);

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";


        while (my $seq_obj = $in->next_seq) {

                #my $id1 = $seq_obj->display_id();
				my $seq_length = length($seq_obj);
				#print "$seq_length\n";
				foreach ($seq_obj->seq =~ m/$pat/g){
								++$count_of_pat;
								
								my $id1 = $seq_obj->display_id();
								print $seq_obj->seq, "\n";							
								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
								$position + $-[0] + 1, "\n";
								$position = $position + length($seq_obj) - $patlen + 1;
								#print "$id1\n";
								#print "$count_of_pat\n";
								#print "$position\n";
								
								}
					
					#print "$seq_length\n";
					print $seq_obj->seq, "\n";
					}
					
					
        close MOTIFCOUNT;

        open (SYM, "+< $rough") or die "The file doesn't exist";

        open (TAB, ">> $final") or die "The gene list wasn't transformed";

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;
        		print TAB "$line";
        	}
        }
        close (SYM);
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;



Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From chemmeri at cgb.indiana.edu  Fri Oct 19 09:40:22 2007
From: chemmeri at cgb.indiana.edu (Chris Hemmerich)
Date: Fri, 19 Oct 2007 09:40:22 -0400 (EDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <13293737.post@talk.nabble.com>
References: <13293737.post@talk.nabble.com>
Message-ID: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>



Djoja,

Perhaps this is a problem with scope. Since you declare $position outside 
of

         while (my $seq_obj = $in->next_seq) {

it will not be reset for each sequence.  The line

 		$position = $position + length($seq_obj) - $patlen + 1;

will continue to increase $position for each sequence processed. From a 
quick look, I don't think you need $position at all in this script and can 
just print $-[0]+1.

Hope this helps,

  Chris


On Fri, 19 Oct 2007, Djodja wrote:

>
> Hi all,
>
> This is my first post. I am very puzzeled about a script that i wrote last
> year, that was working fine, and all of sudden, with no change to the code
> it just stopped doing what it was supposed to do. Basically I'm searching
> for patterns on a whole genome database.
>
> The pattern that I'm searching for at the moment is AACAAAG.
>
> My script finds the pattern, no problem on regexps or anything. It also
> searches the whole genome divided in fasta headers for each gene. The
> problem is that I need to know the position of the pattern, relative to the
> start of each gene. This is where the script goes weird. It doesn't reset
> the counter to the start of each gene. It instead continues to count
> patterns as if the genes aren't separated at all. Also I need the
> information on how many repetitions of the pattern there are in each gene,
> as above, it does not reset the counting of repetitions and instead gives me
> the repitions in the whole genome.
>
> here is the code:
>
> #!/usr/lib/perl -w
>
> use Bio::Perl;
> use Bio::Seq ();
> use Bio::SeqIO ();
> use Bio::Tools::SeqPattern ();
> use strict;
> use warnings;
>
>
>
>
> print 'Where is the file that you want to analise?';
> chomp (my $Fasfile = <>) or die "No such file";
> print "Where do you want to store the rough file?";
> chomp (my $rough = <>);
> print "Where do you want to store the final file?";
> chomp (my $final = <>);
>
> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>
> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>
>
>        while (my $seq_obj = $in->next_seq) {
>
>                #my $id1 = $seq_obj->display_id();
> 				my $seq_length = length($seq_obj);
> 				#print "$seq_length\n";
> 				foreach ($seq_obj->seq =~ m/$pat/g){
> 								++$count_of_pat;
>
> 								my $id1 = $seq_obj->display_id();
> 								print $seq_obj->seq, "\n";
> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
> 								$position + $-[0] + 1, "\n";
> 								$position = $position + length($seq_obj) - $patlen + 1;
> 								#print "$id1\n";
> 								#print "$count_of_pat\n";
> 								#print "$position\n";
>
> 								}
>
> 					#print "$seq_length\n";
> 					print $seq_obj->seq, "\n";
> 					}
>
>
>        close MOTIFCOUNT;
>
>        open (SYM, "+< $rough") or die "The file doesn't exist";
>
>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>
> 	print TAB "Motif: $pat\n";
>        while (my $line = <SYM>){
>
>        	foreach ($line){
>                	$line =~ s/\|/\t/g;
>        		print TAB "$line";
>        	}
>        }
>        close (SYM);
>        close(TAB);
>
>        print "The gene list was created and transformed successfully.\n\a"
> }
> exit;
>
>
>
> Can anyone help me out? This is kind of in the way of my PhD progression.
>
> All the best,
>
> Djodja
> -- 
> View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

From smei_26 at yahoo.com  Fri Oct 19 13:51:48 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Fri, 19 Oct 2007 10:51:48 -0700 (PDT)
Subject: [Bioperl-l] Please help: GenBank ID map
Message-ID: <560962.35266.qm@web38802.mail.mud.yahoo.com>

Hi, 

I have list of GenBank ID inlcuding ids for EST, gemonics sequence and UniGene. I wish to map these ids to RefSeq Ids using BioPerl. Anyone know how to do this? Thanks

example of the GenBank Id list: 

NM_000137
BC004558
BF939919
AL031588
AI673812
NM_006024
AK024914
AK026008
NM_014823
AA523958
NM_001677
AW291083
AL049246
AF116615
AI672084


-- Mike

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 


From j.s.soares at gmail.com  Sat Oct 20 03:11:17 2007
From: j.s.soares at gmail.com (Djodja)
Date: Sat, 20 Oct 2007 00:11:17 -0700 (PDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
References: <13293737.post@talk.nabble.com>
	<Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
Message-ID: <13307407.post@talk.nabble.com>


I will have to give you the credit here as well!

THank you so much Chris.

I have declared both $position and $count_of_pat inside the while loop.

Will rearrange the script and I'm going to make it a subroutine as I have
many other patterns to search for.

Thank you thank you thankyou.

Also, I am in England in Exeter. If you want I could look on ways to get you
here for a nice talk for you to expose your work.

Let me know.

Djodja

Chris Hemmerich wrote:
> 
> 
> 
> Djoja,
> 
> Perhaps this is a problem with scope. Since you declare $position outside 
> of
> 
>          while (my $seq_obj = $in->next_seq) {
> 
> it will not be reset for each sequence.  The line
> 
>  		$position = $position + length($seq_obj) - $patlen + 1;
> 
> will continue to increase $position for each sequence processed. From a 
> quick look, I don't think you need $position at all in this script and can 
> just print $-[0]+1.
> 
> Hope this helps,
> 
>   Chris
> 
> 
> On Fri, 19 Oct 2007, Djodja wrote:
> 
>>
>> Hi all,
>>
>> This is my first post. I am very puzzeled about a script that i wrote
>> last
>> year, that was working fine, and all of sudden, with no change to the
>> code
>> it just stopped doing what it was supposed to do. Basically I'm searching
>> for patterns on a whole genome database.
>>
>> The pattern that I'm searching for at the moment is AACAAAG.
>>
>> My script finds the pattern, no problem on regexps or anything. It also
>> searches the whole genome divided in fasta headers for each gene. The
>> problem is that I need to know the position of the pattern, relative to
>> the
>> start of each gene. This is where the script goes weird. It doesn't reset
>> the counter to the start of each gene. It instead continues to count
>> patterns as if the genes aren't separated at all. Also I need the
>> information on how many repetitions of the pattern there are in each
>> gene,
>> as above, it does not reset the counting of repetitions and instead gives
>> me
>> the repitions in the whole genome.
>>
>> here is the code:
>>
>> #!/usr/lib/perl -w
>>
>> use Bio::Perl;
>> use Bio::Seq ();
>> use Bio::SeqIO ();
>> use Bio::Tools::SeqPattern ();
>> use strict;
>> use warnings;
>>
>>
>>
>>
>> print 'Where is the file that you want to analise?';
>> chomp (my $Fasfile = <>) or die "No such file";
>> print "Where do you want to store the rough file?";
>> chomp (my $rough = <>);
>> print "Where do you want to store the final file?";
>> chomp (my $final = <>);
>>
>> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
>> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>>
>> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>>
>>
>>        while (my $seq_obj = $in->next_seq) {
>>
>>                #my $id1 = $seq_obj->display_id();
>> 				my $seq_length = length($seq_obj);
>> 				#print "$seq_length\n";
>> 				foreach ($seq_obj->seq =~ m/$pat/g){
>> 								++$count_of_pat;
>>
>> 								my $id1 = $seq_obj->display_id();
>> 								print $seq_obj->seq, "\n";
>> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
>> 								$position + $-[0] + 1, "\n";
>> 								$position = $position + length($seq_obj) - $patlen + 1;
>> 								#print "$id1\n";
>> 								#print "$count_of_pat\n";
>> 								#print "$position\n";
>>
>> 								}
>>
>> 					#print "$seq_length\n";
>> 					print $seq_obj->seq, "\n";
>> 					}
>>
>>
>>        close MOTIFCOUNT;
>>
>>        open (SYM, "+< $rough") or die "The file doesn't exist";
>>
>>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>>
>> 	print TAB "Motif: $pat\n";
>>        while (my $line = <SYM>){
>>
>>        	foreach ($line){
>>                	$line =~ s/\|/\t/g;
>>        		print TAB "$line";
>>        	}
>>        }
>>        close (SYM);
>>        close(TAB);
>>
>>        print "The gene list was created and transformed
>> successfully.\n\a"
>> }
>> exit;
>>
>>
>>
>> Can anyone help me out? This is kind of in the way of my PhD progression.
>>
>> All the best,
>>
>> Djodja
>> -- 
>> View this message in context:
>> http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13307407
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From avilella at gmail.com  Mon Oct 22 04:53:45 2007
From: avilella at gmail.com (Albert Vilella)
Date: Mon, 22 Oct 2007 09:53:45 +0100
Subject: [Bioperl-l] java runnables
Message-ID: <358f4d650710220153o4a941088qd5a109d546a1e140@mail.gmail.com>

Hi all,

A question related to java runnables in bioperl-run:

I would like to have a Pecan (http://www.bioperl.org/wiki/PECAN) runnable in
bioperl-run,
and there are a couple of java runnables already written, eponine and vista.

I was wondering if the current state of the java runnables satifies
everybody or if people
can think of a more clean or generic way of calling java from bioperl-run.

Comments?

Cheers,

    Albert.

From wgallin at ualberta.ca  Mon Oct 22 13:53:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 11:53:24 -0600
Subject: [Bioperl-l] Problem with EUtilities
Message-ID: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>

I've encountered a problem with retrieving a set of records using  
efetch.

Code snippet:

     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'efetch',
         -db      => 'protein',
         -rettype => 'genbank',
         -id      => \@ginumber_search
     );
     $file = 'temp_hold.gb';

     $gpeptfactory->get_Response( -file => $file );



If the array of gi numbers that I submit is large (482 elements does  
not give the problem but 1517 does) I am getting an error at the  
get_response step:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:144
-----------------------------------------------------------


Am I correct in thinking that the individual array elements are being  
submitted as part of the URI, and therefore a large array is  
exceeding the acceptable size limit for a URI?

If so, is there a workaround?  Breaking the large request into a set  
of smaller requests?
Or is there a way of submitting a file of gi numbers using  
EUtilities, rather than an array?

Warren Gallin

From cjfields at uiuc.edu  Mon Oct 22 14:16:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 13:16:19 -0500
Subject: [Bioperl-l] Problem with EUtilities
In-Reply-To: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
References: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
Message-ID: <DB401D8A-0DC9-46EB-89A9-58093B8FB171@uiuc.edu>


On Oct 22, 2007, at 12:53 PM, Warren Gallin wrote:

> I've encountered a problem with retrieving a set of records using
> efetch.
>
> Code snippet:
>
>      my $gpeptfactory = Bio::DB::EUtilities->new(
>          -eutil   => 'efetch',
>          -db      => 'protein',
>          -rettype => 'genbank',
>          -id      => \@ginumber_search
>      );
>      $file = 'temp_hold.gb';
>
>      $gpeptfactory->get_Response( -file => $file );
>
>
>
> If the array of gi numbers that I submit is large (482 elements does
> not give the problem but 1517 does) I am getting an error at the
> get_response step:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:144
> -----------------------------------------------------------
>
>
> Am I correct in thinking that the individual array elements are being
> submitted as part of the URI, and therefore a large array is
> exceeding the acceptable size limit for a URI?

Yes.

> If so, is there a workaround?  Breaking the large request into a set
> of smaller requests?
> Or is there a way of submitting a file of gi numbers using
> EUtilities, rather than an array?
>
> Warren Gallin

You can use epost and post your IDs first, then retrieve them.   
Alternatively, you can fetch them in small batches.  The following  
two code bits should help:

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_post_a_specific_list_of_UIDs_to_NCBI. 
27s_history_server.3F

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_usi 
ng_a_query.3F

chris

From er at xs4all.nl  Mon Oct 22 12:05:29 2007
From: er at xs4all.nl (Erikjan)
Date: Mon, 22 Oct 2007 18:05:29 +0200 (CEST)
Subject: [Bioperl-l] postgres datatype: VARCHAR to TEXT - patch
Message-ID: <22811.156.83.0.216.1193069129.squirrel@webmail.xs4all.nl>

Hello,

Using load_seqdatabase.pl to load uniprot_sprot.dat into
postgres (8.2.5), biosql gave me:

ERROR:  value too long for type character varying(40)

(all fresh from cvs)

Changing 'VARCHAR(N)' to 'TEXT' fixed those errors.

Generally, VARCHAR[(N)], (=character varying) are probably
better replaced with 'TEXT' as VARCHAR(N) is implemented
as TEXT with a check on length.



Attached is a patch for the table definitions in
biosqldb-pg.sql; I haven't changed the other scripts, as I
don't know if you will agree with this improvement.

(The other table-creating scripts are probably also better
off with a change from VARCHAR (=character varying) to the
text datatype.)

(loading uniprot_sprot.dat took 20 hours to load, but now
without errors, so I won't complain :)


Thanks,

Erik



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From hangsyin at gmail.com  Mon Oct 22 18:30:10 2007
From: hangsyin at gmail.com (Hang)
Date: Mon, 22 Oct 2007 22:30:10 +0000 (UTC)
Subject: [Bioperl-l] Extract features from GFF
Message-ID: <loom.20071022T221835-291@post.gmane.org>

Hello,

I have a list of about 100,000 short genomic regions with paired start and end
coordinations on reference fly genome (R5.3). I also have GFF files from the
same genome release. I wonder how I can extract all overlapping features from
these regions.

For example:

region A is on chromosome 2L between 123,456 bp to 123,489 bp. What code should
I use to extract feature, like gene, CDS etc., that overlaps with this region?

Thank you in advance!

-- Hang


From wgallin at ualberta.ca  Mon Oct 22 20:28:55 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 18:28:55 -0600
Subject: [Bioperl-l] More on EUtilities problem
Message-ID: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>

I seem to be missing something here.

I took the code from the HOWTO as a template and wrote the following  
code snippet (@gisearch_number is an array of gi numbers, prints out  
as expected and can be used to successfully download the relevant  
records using Batch Entrez):
______________________________________________________________

#Create new EUTILS  history object for submitting a large array of gi  
numbers
     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'epost',
         -db      => 'protein',
         -id      => \@ginumber_search,
         -keep_histories => 1
     );

     my $count = @ginumber_search;


     my $history;
     if ($history = $gpeptfactory -> next_History){
    		print "Posted successfully\n";                            
#Prints as expected for successful history
     	print "WebEnv    : ", $history -> get_webenv,"\n";
     	print "Query_key : ",$history->get_query_key,"\n";
     }
     $file = 'temp_hold.gb';

     $gpeptfactory->set_parameters (-eutil => 'efetch',
     							   -rettype => 'genbank',
     							   -history => $history,
     							
	);
	my ($retmax, $retstart) = (300,0);
	my $retry = 0;
RETRIEVE_SEQS: while ($retstart < $count) {
	
     $gpeptfactory->set_parameters(
     						-retmax => $retmax,
                             -retstart => $retstart,
                             );
     eval{
         $gpeptfactory->get_Response(-file => $file);
         print "Output file is $file.\n";
     };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++ && goto RETRIEVE_SEQS;
     }
     else{
     	
     	my $retend = $retstart + $ retmax;
     	print "Loaded entries $retstart through $retend on retry # 
$retry.\n";

     	$retstart += $retmax;
     	$retry = 0;
     }
}

         $retr_seq = Bio::SeqIO->new(
             -file   => $file,
             -format => 'genbank'
         );

________________________________________________
At this point the program fails because there is no file written.

It appears that the get_Response method is not doing its thing.

Also, on each iteration of the loop enclosing the eval the first pass  
fails with the following error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:177
-----------------------------------------------------------
  and then the second pass evaluates as correct - but the output file  
is never opened or written to.

I've tried to pass $file,  "$file" , ">>$file"  and a literal string  
of a file name, with and without the >>, but to no avail.

So I think that I must be missing something basic here, but I am  
unable to see what.

Any advice would be most welcome.

Warren Gallin



From cjfields at uiuc.edu  Mon Oct 22 20:43:31 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 19:43:31 -0500
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>


On Oct 22, 2007, at 5:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang

Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
depend on the GFF version of the data you have.

chris

From cjfields at uiuc.edu  Mon Oct 22 23:50:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 22:50:19 -0500
Subject: [Bioperl-l] More on EUtilities problem
In-Reply-To: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
References: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
Message-ID: <52D724FE-A586-489A-81BE-F9AAA6963435@uiuc.edu>


On Oct 22, 2007, at 7:28 PM, Warren Gallin wrote:

> I seem to be missing something here.
>
> I took the code from the HOWTO as a template and wrote the following
> code snippet (@gisearch_number is an array of gi numbers, prints out
> as expected and can be used to successfully download the relevant
> records using Batch Entrez):
> ...

One problem (but not the main one):

>      $file = 'temp_hold.gb';

You don't indicate the file needs appending (such as when rewriting  
to the same file in the loop below); you should change it to:

$file = '>>temp_hold.gb';

The below section is the main issue:

>      $gpeptfactory->set_parameters (-eutil => 'efetch',
>      							   -rettype => 'genbank',
>      							   -history => $history,
>      							
> 	);

In general, unless you're absolutely sure you want to carry over  
parameters from the previous eutil search (such as when you are  
looping through and changing the retmax/retstart parameters below),  
use reset_parameters():

$gpeptfactory->reset_parameters(
        -eutil => 'efetch',
        -db  => 'protein',
        -rettype => 'genbank',
        -history => $history
);

What's I believe is happening is the id parameter setting from your  
first eutil search is carried over and is reposted in the URL (thus  
getting the error).  reset_parameters() resets all parameters to  
undef unless new parameter args are passed in, in which case those  
are set to the new values, so nothing carries over.

 From that point on everything works fine (though again you'll want  
to specify that you are appending to a file instead of overwriting it  
within the loop).

chris

> 	my ($retmax, $retstart) = (300,0);
> 	my $retry = 0;
> RETRIEVE_SEQS: while ($retstart < $count) {
> 	
>      $gpeptfactory->set_parameters(
>      						-retmax => $retmax,
>                              -retstart => $retstart,
>                              );
>      eval{
>          $gpeptfactory->get_Response(-file => $file);
>          print "Output file is $file.\n";
>      };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++ && goto RETRIEVE_SEQS;
>      }
>      else{
>      	
>      	my $retend = $retstart + $ retmax;
>      	print "Loaded entries $retstart through $retend on retry #
> $retry.\n";
>
>      	$retstart += $retmax;
>      	$retry = 0;
>      }
> }
>
>          $retr_seq = Bio::SeqIO->new(
>              -file   => $file,
>              -format => 'genbank'
>          );
>
> ________________________________________________
> At this point the program fails because there is no file written.
>
> It appears that the get_Response method is not doing its thing.
>
> Also, on each iteration of the loop enclosing the eval the first pass
> fails with the following error message:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:177
> -----------------------------------------------------------
>   and then the second pass evaluates as correct - but the output file
> is never opened or written to.
>
> I've tried to pass $file,  "$file" , ">>$file"  and a literal string
> of a file name, with and without the >>, but to no avail.
>
> So I think that I must be missing something basic here, but I am
> unable to see what.
>
> Any advice would be most welcome.
>
> Warren Gallin
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From barry.moore at genetics.utah.edu  Tue Oct 23 00:09:05 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:09:05 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <7691F0B8-9771-477F-A982-21360F769D4A@genetics.utah.edu>

Hang-

Something like this would work, although for simply querying the  
coordinates on GFF like that you could iterate over the file with  
your own while loop, split the columns and do the same thing with  
about as many lines.  You'll need to do each chromosome as a separate  
GFF file or add some code to the loop to check the chromosome  
($feature->seq_id I think).

     use Bio::Tools::GFF;

     my $coord_start = 12345;
     my $coord_end  = 67890;

     # specify input via -fh or -file
     my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version =>  
2);
     my $feature;
     # loop over the input stream
     while($feature = $gffio->next_feature()) {
	 if ($coord_start <= $feature->start && $coord_end >= $feature->end) {
	 	print $feature->gff_string;
	}
     }
     $gffio->close();

Barry

On Oct 22, 2007, at 4:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From barry.moore at genetics.utah.edu  Tue Oct 23 00:37:07 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:37:07 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <C837CA5E-4E55-4B23-8451-27E74426BB52@genetics.utah.edu>

Oh yeah, much better option if you've got a database running.  Look  
at the docs for the modules Chris suggested.  Something like:

my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                  -dsn     =>  
'dbi:mysql:test',
                                                  -write   => 1 );
# load an entire GFF3 file, using the GFF3 loader...
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    =>  
$db,
							   -verbose  => 1,
							   -fast     => 1);

$loader->load('./my_genome.gff3');

@features = $db->get_features_by_location(-seq_id=>'Chr1',- 
start=>4000,-end=>600000);

Barry

On Oct 22, 2007, at 6:43 PM, Chris Fields wrote:

>
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
>
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files
>> from the
>> same genome release. I wonder how I can extract all overlapping
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
>
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will
> depend on the GFF version of the data you have.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From sdavis2 at mail.nih.gov  Tue Oct 23 07:00:12 2007
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 23 Oct 2007 07:00:12 -0400
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <471DD43C.8060203@mail.nih.gov>

Chris Fields wrote:
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
> 
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired  
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files  
>> from the
>> same genome release. I wonder how I can extract all overlapping  
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with  
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
> 
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
> depend on the GFF version of the data you have.
> 
> chris

Not a bioperl solution, but still a very cool application, see:

http://main.g2.bx.psu.edu/

It is web-based and allows for set operations (intersection, union,
etc.) on genomic coordinates.  If you have two sets of regions of
interest, you can then ask (very quickly) for all regions that overlap,
contain, are distinct, etc.

Sean

From forrest_zhang at 163.com  Tue Oct 23 23:27:00 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Wed, 24 Oct 2007 11:27:00 +0800
Subject: [Bioperl-l]
	=?gb2312?B?tPC4tDogW0Jpb3BlcmwtbF0gbG9hZF9zZXFkYXRhYmFzZS5wbCBlcnJvcg==?=
In-Reply-To: <FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
Message-ID: <000101c815ed$bdafb2e0$390f18a0$@com>

Dear Chris:
	What's the result of test? In my computer, the test haven't been
passed.

Forrest Zhang

-----????????-----
??????: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] ???? Chris Fields
????????: 2007??9??29?? 6:03
??????: Forrest Zhang
????: bioperl-l at bioperl.org BioPerl
????: Re: [Bioperl-l] load_seqdatabase.pl error

Okay, fixed the recursion (extra copy of a BasePersistentAdaptor  
module I was working which tripped it, so nothing in CVS).

Forrest, I get all tests passing.  I used a database without taxonomy  
loaded with bioperl-db and bioperl from cvs and it worked w/o  
problems.  I'll try working with your sequence when I have time this  
weekend.

chris

On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:

> I'm actually getting some odd recursion issues again; not sure what's
> causing it, but a reinstall of both bioperl and bioperl-db fixed it
> last time.  It may be related to the rollback, just not sure yet.
>
> I'll try tracking it down if it persists (bad pun).
>
> t/04swiss....ok 3/52
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
> t/04swiss....ok
> All tests successful.
> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
> CPU)
>
> The specific error under verbose running is:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:680
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:658
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:252
> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> PrimarySeqAdaptor.pm:229
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/src/
> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:213
> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
> STACK toplevel t/04swiss.t:37
> ---------------------------------------------------
>
>
> chris
>
> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>
>> Chris let me know if you get stumped. I'm surprised that the special
>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>> assign ranks to them? I thought I filter them out. Needs to be looked
>> into too.), but at any rate I don't understand why they aren't being
>> accepted.
>>
>> Also, maybe we need a more verbose output here - Forrest, can you run
>> this with adding a --printerror argument. (I'm embarrassed to find
>> that this doesn't seem to be documented. Sigh.)
>>
>> 	-hilmar
>>
>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>
>>> If this is occurring using bioperl from CVS then I'll try taking a
>>> look at it.
>>>
>>> chris
>>>
>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>
>>>> Hilmar,
>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I
>>>> was
>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>> | rosids
>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>> Euphyllophyta |
>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>> ---------------------------------------------------
>>>> Could not store Q40784:
>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>> by unique
>>>> key
>>>> STACK: Error::throw
>>>> STACK: Bio::Root::Root::throw
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:206
>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:244
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:169
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:251
>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:271
>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>> -----------------------------------------------------------
>>>> Sigh~~~~~~
>>>>
>>>> Forrest Zhang
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>> Lapp
>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>> To: Forrest
>>>> Cc: bioperl-l at bioperl.org
>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>
>>>> Forrest,
>>>>
>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>> the
>>>> code will try to use it to look up species and their lineage,  
>>>> rather
>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>> sequence record.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>
>>>>> Hi, all
>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>> swissport data.
>>>>> But the programe show some error as below:
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>> mysql
>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>> Could not store Q6DAH5:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>> subsp.
>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>> Pectobacterium |
>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>> Proteobacteria | Bacteria')
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>> STACK: Bio::Species::classification
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:552
>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:1305
>>>>> STACK:  
>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:973
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:852
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:182
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: load_seqdatabase.pl:620
>>>>> -----------------------------------------------------------
>>>>>
>>>>>  at load_seqdatabase.pl line 633
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>
>>>>> How can I solve it, please help me, Thank you.
>>>>>
>>>>> Thanks
>>>>> Forrest zhang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



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From cjfields at uiuc.edu  Wed Oct 24 00:21:00 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 23 Oct 2007 23:21:00 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000101c815ed$bdafb2e0$390f18a0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
Message-ID: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From martin.burkert at uni-bielefeld.de  Wed Oct 24 08:25:13 2007
From: martin.burkert at uni-bielefeld.de (Martin Burkert)
Date: Wed, 24 Oct 2007 14:25:13 +0200
Subject: [Bioperl-l] Problems parsing Glimmer output
Message-ID: <471F39A9.6050909@uni-bielefeld.de>

Hello,

i can't figure out why my Glimmer files can not be parsed from
Bio::Tools::Glimmer.

---- pbglimmer.pl ----
use strict;
use Bio::Tools::Glimmer;

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
my $predictionCount = 0;

while(my $gene = $parser->next_prediction()) {
	$predictionCount++;
	print $predictionCount.	':' .$gene->display_name().
				', '.$gene->start().
				', '.$gene->stop()."\n";
}
print "Total predictions: ".$predictionCount;

---- pb4.predict ----
>pb4
orf00001     1022     1138  +2     0.90
orf00002     1655     1131  -3     2.77
orf00003     1638     2390  +3     3.59
orf00004     3176     3472  +2     0.30
orf00006     4395     5561  +3     2.96
orf00008     5576     8719  +2     2.98
orf00012     8725    10152  +1     2.96
orf00013    10906    11019  +1     0.21
orf00014    12188    12292  +2     2.41
orf00017    12518    14077  +2     2.97
orf00019    15356    15246  -3     2.21
orf00020    17864    17748  -3     0.23
orf00021    18153    18037  -1     0.32
orf00023    19253    19462  +2     0.48
orf00025    21018    20902  -1     0.23
orf00027    21658    24708  +1     2.92
orf00030    26115    24898  -1     2.96
orf00031    26414    26112  -3     3.21
orf00032    28015    28473  +1     3.54
orf00033    28044    27223  -1     2.85
orf00037    30137    30033  -3     2.80
orf00041    30183    33152  +3     2.98
orf00045    34860    33637  -1     2.96
orf00047    35142    34909  -1     2.54
orf00050    36606    36737  +3     1.44
orf00052    37616    37789  +2     2.23
orf00054    37786    40344  +1     2.98
orf00056    40624    40505  -2     0.79
orf00057    42508    43890  +1     2.96
orf00059    44183    44680  +2     1.49
orf00060    44705    44908  +2     0.05
orf00063    44920    46632  +1     2.97
orf00068    47296    47865  +1     0.39
orf00071    47953    49134  +1     2.90
orf00072    49208    49318  +2     1.15
orf00074    51139    51270  +1     1.16
orf00083    58362    53767  -1     2.99
orf00088    60846    58783  -1     2.98
orf00090    63298    61394  -2     2.97
orf00093    65553    63295  -1     2.98
orf00095    65959    65588  -2     1.13
orf00096    66185    65964  -3     2.98
orf00098    66610    66933  +1     0.11
orf00099    67371    67658  +3     0.27
orf00102    71019    68134  -1     2.98
orf00103    71825    72628  +2     2.71
orf00105    75062    73740  -3     2.96
orf00106    75817    76221  +1     0.73
orf00109    78206    76734  -3     2.92
orf00113      198    79299  -3     4.22


The program always outputs "Total predictions: 0".

I also tried to force the parsing format to be just 'Glimmer'
(prokaryotic) and not 'GlimmerHmm'  with:

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', -format =>
'Glimmer');

The pb4.predict was generated by glimmer3.02. I also tried to parse an
output from glimmer2.X, but without success.

Printing $parser with Data::Dumper outputs:

$VAR1 = bless( {
                 '_file' => 'pb4.predict',
                 '_preds_parsed' => 0,
                 '_analysis_date' => undef,
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_analysis_sbjct' => undef,
                 '_analysis_progVersion' => undef,
                 '_flush_on_write' => 1,
                 '_analysis_prog' => undef,
                 '_filehandle' => \*Symbol::GEN0,
                 '_analysis_query' => undef,
                 '_root_verbose' => 0,
                 '_preds' => []
               }, 'Bio::Tools::Glimmer' );

My installation:

Perl v5.8.8 built for MSWin32-x86-multi-thread
Bioperl 1.4

Thank you.

-- 
Viele Gr??e,

MARTIN BURKERT
mailto:martin.burkert at uni-bielefeld.de

From cjfields at uiuc.edu  Wed Oct 24 09:38:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 08:38:03 -0500
Subject: [Bioperl-l] Problems parsing Glimmer output
In-Reply-To: <471F39A9.6050909@uni-bielefeld.de>
References: <471F39A9.6050909@uni-bielefeld.de>
Message-ID: <37465B90-4A03-4A53-B4EF-BCC8296BAE2C@uiuc.edu>

Update to bioperl-live (from CVS).  The Glimmer parser was recently  
revised by Mark Johnson for Glimmer3 output.  I added a few fixes  
myself to correct start/end issues.

chris

On Oct 24, 2007, at 7:25 AM, Martin Burkert wrote:

> Hello,
>
> i can't figure out why my Glimmer files can not be parsed from
> Bio::Tools::Glimmer.
>
> ---- pbglimmer.pl ----
> use strict;
> use Bio::Tools::Glimmer;
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
> my $predictionCount = 0;
>
> while(my $gene = $parser->next_prediction()) {
> 	$predictionCount++;
> 	print $predictionCount.	':' .$gene->display_name().
> 				', '.$gene->start().
> 				', '.$gene->stop()."\n";
> }
> print "Total predictions: ".$predictionCount;
>
> ---- pb4.predict ----
>> pb4
> orf00001     1022     1138  +2     0.90
> orf00002     1655     1131  -3     2.77
> orf00003     1638     2390  +3     3.59
> orf00004     3176     3472  +2     0.30
> orf00006     4395     5561  +3     2.96
> orf00008     5576     8719  +2     2.98
> orf00012     8725    10152  +1     2.96
> orf00013    10906    11019  +1     0.21
> orf00014    12188    12292  +2     2.41
> orf00017    12518    14077  +2     2.97
> orf00019    15356    15246  -3     2.21
> orf00020    17864    17748  -3     0.23
> orf00021    18153    18037  -1     0.32
> orf00023    19253    19462  +2     0.48
> orf00025    21018    20902  -1     0.23
> orf00027    21658    24708  +1     2.92
> orf00030    26115    24898  -1     2.96
> orf00031    26414    26112  -3     3.21
> orf00032    28015    28473  +1     3.54
> orf00033    28044    27223  -1     2.85
> orf00037    30137    30033  -3     2.80
> orf00041    30183    33152  +3     2.98
> orf00045    34860    33637  -1     2.96
> orf00047    35142    34909  -1     2.54
> orf00050    36606    36737  +3     1.44
> orf00052    37616    37789  +2     2.23
> orf00054    37786    40344  +1     2.98
> orf00056    40624    40505  -2     0.79
> orf00057    42508    43890  +1     2.96
> orf00059    44183    44680  +2     1.49
> orf00060    44705    44908  +2     0.05
> orf00063    44920    46632  +1     2.97
> orf00068    47296    47865  +1     0.39
> orf00071    47953    49134  +1     2.90
> orf00072    49208    49318  +2     1.15
> orf00074    51139    51270  +1     1.16
> orf00083    58362    53767  -1     2.99
> orf00088    60846    58783  -1     2.98
> orf00090    63298    61394  -2     2.97
> orf00093    65553    63295  -1     2.98
> orf00095    65959    65588  -2     1.13
> orf00096    66185    65964  -3     2.98
> orf00098    66610    66933  +1     0.11
> orf00099    67371    67658  +3     0.27
> orf00102    71019    68134  -1     2.98
> orf00103    71825    72628  +2     2.71
> orf00105    75062    73740  -3     2.96
> orf00106    75817    76221  +1     0.73
> orf00109    78206    76734  -3     2.92
> orf00113      198    79299  -3     4.22
>
>
> The program always outputs "Total predictions: 0".
>
> I also tried to force the parsing format to be just 'Glimmer'
> (prokaryotic) and not 'GlimmerHmm'  with:
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', - 
> format =>
> 'Glimmer');
>
> The pb4.predict was generated by glimmer3.02. I also tried to parse an
> output from glimmer2.X, but without success.
>
> Printing $parser with Data::Dumper outputs:
>
> $VAR1 = bless( {
>                  '_file' => 'pb4.predict',
>                  '_preds_parsed' => 0,
>                  '_analysis_date' => undef,
>                  '_root_cleanup_methods' => [
>                                               sub { "DUMMY" }
>                                             ],
>                  '_analysis_sbjct' => undef,
>                  '_analysis_progVersion' => undef,
>                  '_flush_on_write' => 1,
>                  '_analysis_prog' => undef,
>                  '_filehandle' => \*Symbol::GEN0,
>                  '_analysis_query' => undef,
>                  '_root_verbose' => 0,
>                  '_preds' => []
>                }, 'Bio::Tools::Glimmer' );
>
> My installation:
>
> Perl v5.8.8 built for MSWin32-x86-multi-thread
> Bioperl 1.4
>
> Thank you.
>
> -- 
> Viele Gr??e,
>
> MARTIN BURKERT
> mailto:martin.burkert at uni-bielefeld.de
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From forrest_zhang at 163.com  Wed Oct 24 12:00:24 2007
From: forrest_zhang at 163.com (Forrest)
Date: Thu, 25 Oct 2007 00:00:24 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
Message-ID: <000001c81657$0067fd40$0137f7c0$@com>

Dear Chris,
	I was using different swissprot data all of the have some error about the taxon.
Maybe I should re-install bioperl and biosql. Could you give me the install protocol 
what you used.


Forrest Zhang

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Wednesday, October 24, 2007 12:21 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign








From cjfields at uiuc.edu  Wed Oct 24 12:47:45 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 11:47:45 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000001c81657$0067fd40$0137f7c0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
	<000001c81657$0067fd40$0137f7c0$@com>
Message-ID: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From joseph.fass at gmail.com  Wed Oct 24 14:56:55 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 11:56:55 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
Message-ID: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>

Has anyone else encountered a problem parsing wu-blast output with
Bio::SearchIO ?

The ->next_hit method first returns the "unfiltered+1" sequence; that is,
the plus strand representation of the query sequence that is listed (before
the minus strand) before the summary of hits and e-values.

Then, the next time the next_hit method is called, it returns the second hit
on the list.

The only caveat to my "bug" report here is that I was searching a database
that included the query sequence, so the first hit was identical to the
query (and maybe somehow retained the "unfiltered+1" tag?) ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From joseph.fass at gmail.com  Wed Oct 24 15:39:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 12:39:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
Message-ID: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>

I'm relatively new to both objects and bioperl, and I'm having trouble
finding documentation on what values an attribute can have.  For example, in
Bio::Assembly::Contig the example script invokes the 'new' method with an
example filename and assigns the -format attribute (I think that's the
correct terminology) a value of 'phrap' ...

now, I'm wanting to process contig output from the cap3 program, so I'll try
assigning 'cap3' to the -format attribute (haven't tried yet so I don't know
if it will work), but where do I look for a complete list of what possible
values I can use?  I can't find it via either the Pdoc or CPAN documentation
links from the bioperl wiki pages.  Any help would be appreciated ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From David.Messina at sbc.su.se  Wed Oct 24 16:35:48 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:35:48 +0200
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
Message-ID: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>

Hi Joseph,

Could you post the blast report that's giving you trouble? And also could
you tell us what version of WU-BLAST you're running and what version of
BioPerl you're using?

I'd like to try and reproduce your problem.

Thanks,
Dave

From David.Messina at sbc.su.se  Wed Oct 24 16:59:12 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:59:12 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
Message-ID: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>

I couldn't find the formats for Bio::Assembly::Contig in any of the
documentation either.

In situations like these, I poke around in the code for methods that deal
with whatever I'm looking for. In this case, I went to the pdoc for
Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
_guess_format method:

sub _guess_format {

   my $class = shift;
   my $arg   = shift;


return unless defined($arg);
   return 'ace'
 if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap'
 if ($arg =~ /\.phrap\.out$/i);

}

So it looks like 'ace' and 'phrap' are the two assembly formats that are
supported.

The other place where the question of formats often comes up is with
sequence formats. Those are better documented, in the SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats


Dave

From florent.angly at gmail.com  Wed Oct 24 17:25:25 2007
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 24 Oct 2007 14:25:25 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
Message-ID: <471FB845.2080201@gmail.com>

Dave,
Have a look in Bio::Assembly::Contig::IO, that's where all the supported 
assembly input/output formats are located. It's convenient to use the 
BioPerl Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query 
<http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query>
'ace' and 'phrap' are the supported formats. The 'tigr' assembler format 
has been added in the CVS version recently too.
Florent


Dave Messina wrote:
> I couldn't find the formats for Bio::Assembly::Contig in any of the
> documentation either.
>
> In situations like these, I poke around in the code for methods that deal
> with whatever I'm looking for. In this case, I went to the pdoc for
> Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> _guess_format method:
>
> sub _guess_format {
>
>    my $class = shift;
>    my $arg   = shift;
>
>
> return unless defined($arg);
>    return 'ace'
>  if ($arg =~ /\.ace\.\d+$/i);
>    return 'phrap'
>  if ($arg =~ /\.phrap\.out$/i);
>
> }
>
> So it looks like 'ace' and 'phrap' are the two assembly formats that are
> supported.
>
> The other place where the question of formats often comes up is with
> sequence formats. Those are better documented, in the SeqIO HOWTO:
>
> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
>
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   


From joseph.fass at gmail.com  Wed Oct 24 17:43:08 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:43:08 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
Message-ID: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From joseph.fass at gmail.com  Wed Oct 24 17:45:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:45:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <471FB845.2080201@gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
Message-ID: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>

thanks, both of you!

On 10/24/07, Florent Angly <florent.angly at gmail.com> wrote:
>
> Dave,
> Have a look in Bio::Assembly::Contig::IO, that's where all the supported
> assembly input/output formats are located. It's convenient to use the
> BioPerl Deobfuscator:
>
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> <
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> >
> 'ace' and 'phrap' are the supported formats. The 'tigr' assembler format
> has been added in the CVS version recently too.
> Florent
>
>
> Dave Messina wrote:
> > I couldn't find the formats for Bio::Assembly::Contig in any of the
> > documentation either.
> >
> > In situations like these, I poke around in the code for methods that
> deal
> > with whatever I'm looking for. In this case, I went to the pdoc for
> > Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> > Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> > _guess_format method:
> >
> > sub _guess_format {
> >
> >    my $class = shift;
> >    my $arg   = shift;
> >
> >
> > return unless defined($arg);
> >    return 'ace'
> >  if ($arg =~ /\.ace\.\d+$/i);
> >    return 'phrap'
> >  if ($arg =~ /\.phrap\.out$/i);
> >
> > }
> >
> > So it looks like 'ace' and 'phrap' are the two assembly formats that are
> > supported.
> >
> > The other place where the question of formats often comes up is with
> > sequence formats. Those are better documented, in the SeqIO HOWTO:
> >
> > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
> >
> >
> > Dave
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From jason at bioperl.org  Wed Oct 24 18:18:09 2007
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Oct 2007 18:18:09 -0400
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
Message-ID: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>

I'm pretty sure we fixed this problem after 1.4 so current "unstable"  
code a try first and let us know nif that solves the problem.

also - copy+paste of BLAST files on mailing list doesn't work so well  
so either a link to  URL or posting the file in a bugzilla bug  
(bugzilla.open-bio.org) make it easier for someone to try this at home.

-jason
On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:

> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what  
> you find.
>
> Joe
>
[SNIP]
--
Jason Stajich
jason at bioperl.org


From joseph.fass at gmail.com  Wed Oct 24 18:53:41 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 15:53:41 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
Message-ID: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>

I just updated to 1.5.2 via CPAN, and verified that that worked, and re-ran
my code ... same problem: it's still picking up "unfiltered+1" as the first
->next_hit result from wu-blast output.  This is a different issue than the
fixed bug (ID: 1649) I just found on bugzilla; that bug concerned the hit
sequences.  I'll post a report on bugzilla along with some files to try it
with (please let me know if what I upload there is incomplete).

Thanks for the quick attention, all!

~joe




On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I'm pretty sure we fixed this problem after 1.4 so current "unstable" code
> a try first and let us know nif that solves the problem.
>
> also - copy+paste of BLAST files on mailing list doesn't work so well so
> either a link to  URL or posting the file in a bugzilla bug (
> bugzilla.open-bio.org) make it easier for someone to try this at home.
>
> -jason
> On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
>
> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what you find.
>
> Joe
>
> [SNIP]
> --
> Jason Stajich
> jason at bioperl.org
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From joseph.fass at gmail.com  Wed Oct 24 19:25:50 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 16:25:50 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
	<195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
Message-ID: <195e25cb0710241625o8b92fe0y65925025fc9144c0@mail.gmail.com>

There's a script and sample input file to demonstrate this in Bugzilla, bug#
2388 <http://bugzilla.open-bio.org/show_bug.cgi?id=2388>

~joe



On 10/24/07, Joseph Fass <joseph.fass at gmail.com> wrote:
>
> I just updated to 1.5.2 via CPAN, and verified that that worked, and
> re-ran my code ... same problem: it's still picking up "unfiltered+1" as the
> first ->next_hit result from wu-blast output.  This is a different issue
> than the fixed bug (ID: 1649) I just found on bugzilla; that bug concerned
> the hit sequences.  I'll post a report on bugzilla along with some files to
> try it with (please let me know if what I upload there is incomplete).
>
> Thanks for the quick attention, all!
>
> ~joe
>
>
>
>
> On 10/24/07, Jason Stajich <jason at bioperl.org > wrote:
> >
> >  I'm pretty sure we fixed this problem after 1.4 so current "unstable"
> > code a try first and let us know nif that solves the problem.
> >
> > also - copy+paste of BLAST files on mailing list doesn't work so well so
> > either a link to  URL or posting the file in a bugzilla bug (
> > bugzilla.open-bio.org) make it easier for someone to try this at home.
> >
> > -jason
> > On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
> >
> > Hi Dave,
> >
> > here's my code, followed by a sample wu-blast report (below).
> > I'm using bioperl version 1.4
> > Thanks for looking into it, and I'd be very curious to know what you
> > find.
> >
> > Joe
> >
> > [SNIP]
> > --
> > Jason Stajich
> > jason at bioperl.org
> >
> >
>
>
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
>



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From simona_bazzocchi at yahoo.it  Wed Oct 24 23:46:53 2007
From: simona_bazzocchi at yahoo.it (simona bazzocchi)
Date: Thu, 25 Oct 2007 05:46:53 +0200 (CEST)
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
Message-ID: <594278.55585.qm@web27710.mail.ukl.yahoo.com>

Hi all, 
I'd like to parse my blast file to outuput in a html file filtering on percent identity, (75% identical or better). So I've just copied and pasted to create my perl file.
I launched this command:
perl searchIO.pl blast_file.txt
But it returned this error: "t
Bareword found where operator expected at searchIO.pl line 26, near "->length E"
        (Missing operator before E?)
syntax error at searchIO.pl line 26, near "->length E"
syntax error at searchIO.pl line 30, near "<gt"
Execution of searchIO.pl aborted due to compilation errors."
Here below you can find searchIO.pl
thanks



#!/usr/bin/perl
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);


# to filter your output
my $MinLength = 100; # need a variable with scope outside the method
sub hsp_filter { 
      my $hsp = shift;
      return 1 if $hsp->length('total') > $MinLength;
  }
sub result_filter { 
      my $result = shift;
      return $hsp->num_hits > 0;
  }

  sub hit_filter { 
      my $hit = shift;
      return $hit->length E<gt> 100; # test if length of the hit sequence
                                     # long enough    
  }
  my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HIT' =E<gt> \&hit_filter }  
      );


my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);

# can also set the filter via the writer object
$writer->filter('RESULT', \&result_filter);


 		
---------------------------------
Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3

From torsten.seemann at infotech.monash.edu.au  Thu Oct 25 00:20:13 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 25 Oct 2007 14:20:13 +1000
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
In-Reply-To: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
References: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
Message-ID: <a79f6a4b0710242120g13e9a55dq710d004745b7e68b@mail.gmail.com>

Simona

> So I've just copied and pasted to create my perl file.
> syntax error at searchIO.pl line 26, near "->length E"
> syntax error at searchIO.pl line 30, near "<gt"
>   sub hit_filter {
>       my $hit = shift;
>       return $hit->length E<gt> 100; # test if length of the hit sequence

You have a Perl syntax error due to cutting and pasting from code in
PerlDoc format. It should read:

  return $hit->length > 100;  # not "E<gt>

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010

From forrest_zhang at 163.com  Thu Oct 25 02:35:19 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 14:35:19 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>	<000101c815ed$bdafb2e0$390f18a0$@com>	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>	<000001c81657$0067fd40$0137f7c0$@com>
	<D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
Message-ID: <000001c816d1$38d70250$aa8506f0$@com>

Dear Chris,
	I try you protocol, but the taxonomy problem is still existent. And the new problem about " The table 'comment' is full" is coming.
The error example like below:
	
Could not store Q6DA52: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp. atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium | Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria | Proteobacteria | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Species::classification /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("-!- CATALYTIC ACTIVITY: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
-!- PATHWAY: Metabolic intermediate biosynthesis; chorismate
    biosynthesis; chorismate from D-erythrose 4-phosphate and PEP:
    step 3/7.
-!- PATHWAY: Context: Aromatic amino acids biosynthesis.
-!- SUBUNIT: Homodimer (By similarity).
-!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
","1") FKs (12352)
The table 'comment' is full
---------------------------------------------------
Could not store Q723F8: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Comment) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

 at load_seqdatabase.pl line 643
	

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:16:34 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:34 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000101c816df$600c5c40$202514c0$@com>



-----Original Message-----
From: Forrest Zhang [mailto:forrest_zhang at 163.com] 
Sent: Thursday, October 25, 2007 4:16 PM
To: 'Chris Fields'
Subject: RE: [Bioperl-l] ??: load_seqdatabase.pl error

Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:16:58 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:58 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000201c816df$6c956fb0$45c04f10$@com>


Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:06:27 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:06:27 +0800
Subject: [Bioperl-l] FW:  problem parsing WU-blast output
Message-ID: <000201c816dd$f5c5e5f0$e151b1d0$@com>

Hi, Joe
	My this script(wublast.pl) maybe is useful for you. You can get the
subsequence by using query range and hit range.
	The script is below, and the file name is wublast.pl.

use strict;
use Bio::SearchIO;

die "Usage:perl wublast <File>\n"
      unless @ARGV==1;
my $inputfile = $ARGV[0];
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => $inputfile);
print "query","\t","hit","\t","total_length","\t",
      "query_lenth","\t","hit_length","\t",
      "percent_identity","\t","score","\t","evalue","\t","rank",
      "\t","query range","\t","hit range","\n";

while( my $result = $in->next_result ) {
    my $image=$result->query_name;

    while( my $hit = $result->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {

	print $image,"\t",$hit->name,"\t",$hsp->length('total'),"\t",
	      $hsp->length('query'),"\t",$hsp->length('hit'),"\t",
	    $hsp->percent_identity,"\t",$hsp->score,"\t",$hsp->evalue,"\t",
 
$hsp->rank,"\t",$hsp->start('query'),",",$hsp->end('query'),"\t",
            $hsp->start('hit'),",",$hsp->end('hit'),"\n";

	}  
    }
}


Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
Sent: Thursday, October 25, 2007 5:43 AM
To: Dave Messina
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] problem parsing WU-blast output

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
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From David.Messina at sbc.su.se  Thu Oct 25 04:52:14 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 25 Oct 2007 10:52:14 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
	<195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
Message-ID: <628aabb70710250152l6218fa1as78b9ab23731f1530@mail.gmail.com>

Ah, wonderful -- thanks Florent! Man, that Deobfuscator sure is useful. :)

Dave

From cjfields at uiuc.edu  Thu Oct 25 09:07:23 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 25 Oct 2007 08:07:23 -0500
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
 =?utf-8?q?=2Epl_error?=
In-Reply-To: <000201c816df$6c956fb0$45c04f10$@com>
References: <000201c816df$6c956fb0$45c04f10$@com>
Message-ID: <F7F03A54-34F1-45A8-8141-7E785F0FB555@uiuc.edu>

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From joseph.fass at gmail.com  Thu Oct 25 17:50:02 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Thu, 25 Oct 2007 14:50:02 -0700
Subject: [Bioperl-l] what's the optimal way to search a fasta file for
	matching ID's?
Message-ID: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>

I would appreciate any advice, big or small, on this ...

I've got a decent-sized database ... 90,000 sequences or so in a single
fasta-format file.  Then, I've got sequence ID's from that database that
show up in blast reports.  I want to collect those ID's and their sequences
(for the purposes of exploring possible contigs).  Since the blast report
only includes sub-sequences (from alignments) of my sequences, I want to
parse the report, then match each hit ID against an ID in the database, so I
can pull out its full sequence.  Is there a faster way to do this than
opening the database file each time I have a new hit ID, so I can search it
from beginning to end?  If I push each sequence onto a list or hash, it's
liable to chew up a lot of RAM, I'm guessing.  Any suggestions?

Thanks in advance,
~joe

-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)

From MEC at stowers-institute.org  Thu Oct 25 18:17:04 2007
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Thu, 25 Oct 2007 17:17:04 -0500
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
Message-ID: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>

If you have the fasta database already indexed for blast searching, then
you should use fastacmd, which comes with the blast package, for
extracting (sub)sequences based on ID (and indices).

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
> Sent: Thursday, October 25, 2007 4:50 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] what's the optimal way to search a fasta 
> file formatching ID's?
> 
> I would appreciate any advice, big or small, on this ...
> 
> I've got a decent-sized database ... 90,000 sequences or so 
> in a single fasta-format file.  Then, I've got sequence ID's 
> from that database that show up in blast reports.  I want to 
> collect those ID's and their sequences (for the purposes of 
> exploring possible contigs).  Since the blast report only 
> includes sub-sequences (from alignments) of my sequences, I 
> want to parse the report, then match each hit ID against an 
> ID in the database, so I can pull out its full sequence.  Is 
> there a faster way to do this than opening the database file 
> each time I have a new hit ID, so I can search it from 
> beginning to end?  If I push each sequence onto a list or 
> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any 
> suggestions?
> 
> Thanks in advance,
> ~joe
> 
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


From jason at bioperl.org  Fri Oct 26 00:57:52 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 00:57:52 -0400
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
	<CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
Message-ID: <8F627E8A-EE44-4953-9A90-F82BC69C15D9@bioperl.org>

or see Bio::DB::Fasta if you want a bioperl soln.

On Oct 25, 2007, at 6:17 PM, Cook, Malcolm wrote:

> If you have the fasta database already indexed for blast searching,  
> then
> you should use fastacmd, which comes with the blast package, for
> extracting (sub)sequences based on ID (and indices).
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph  
>> Fass
>> Sent: Thursday, October 25, 2007 4:50 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] what's the optimal way to search a fasta
>> file formatching ID's?
>>
>> I would appreciate any advice, big or small, on this ...
>>
>> I've got a decent-sized database ... 90,000 sequences or so
>> in a single fasta-format file.  Then, I've got sequence ID's
>> from that database that show up in blast reports.  I want to
>> collect those ID's and their sequences (for the purposes of
>> exploring possible contigs).  Since the blast report only
>> includes sub-sequences (from alignments) of my sequences, I
>> want to parse the report, then match each hit ID against an
>> ID in the database, so I can pull out its full sequence.  Is
>> there a faster way to do this than opening the database file
>> each time I have a new hit ID, so I can search it from
>> beginning to end?  If I push each sequence onto a list or
>> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any
>> suggestions?
>>
>> Thanks in advance,
>> ~joe
>>
>> --
>> Joseph Fass
>> joseph.fass at gmail.com  ||  joefass at hotmail.com
>> 970.227.5928 (c)  ||  530.754.7978 (w)
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org


From forrest_zhang at 163.com  Fri Oct 26 04:21:56 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Fri, 26 Oct 2007 16:21:56 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICBGVzogIOetlOWkjTogIGxvYWRfc2VxZGF0?=
	=?utf-8?q?abase=2Epl_error?=
Message-ID: <000701c817a9$4733fb40$d59bf1c0$@com>

Chris,
	I am using --safe to loading sequence. Maybe I would load species data one by one.
It seem be OK now.

	Thanks for your help so much Chris.

Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 9:07 PM
To: Forrest Zhang; BioSQL
Cc: bioperl-l at bioperl.org BioPerl
Subject: Re: [Bioperl-l] FW: ??: load_seqdatabase.pl error

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l





From avilella at gmail.com  Fri Oct 26 05:33:09 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 10:33:09 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
Message-ID: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>

Hi all,

I was looking at the Gumby runnable, which is pretty cool. But I got an
error
when running the tests (see below). Can other people reproduce this?

It seems to me that the runnable is expecting a tree object, not the
filename for a tree...

avilella at magneto:~/bioperl/vanilla/bioperl-run$ perl t/Gumby.t
1..124
ok 1 - use Bio::Tools::Run::Phylo::Gumby;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::TreeIO;
ok 4 - use Bio::DB::Taxonomy;
ok 5 - use Bio::Tools::GFF;
ok 6 - Found input alignment file
ok 7 - Found input tree file
ok 8 - Found input gff file
ok 9 - The object isa Bio::Tools::Run::Phylo::Gumby
ok 10 - has a created method not in args
ok 11 - quiet was set
ok 12 - program_dir returned correct default
ok 13 - Correct exe default name
Can't call method "value" without a package or object reference at
/home/avilella/bioperl/vanilla/bioperl-live/Bio/Tools/Phylo/Gumby.pm line
136, <GEN2> line 6.
# Looks like you planned 124 tests but only ran 13.
# Looks like your test died just after 13.

From bix at sendu.me.uk  Fri Oct 26 06:10:41 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 11:10:41 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <4721BD21.9060805@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got
> an error when running the tests (see below). Can other people
> reproduce this?
> 
> It seems to me that the runnable is expecting a tree object, not the 
> filename for a tree...

No, most likely this is another thing broken by the SeqFeature changes.
I'm going to go ahead and try out some of my proposals in the
'Bio::SeqFeature::Annotated API change' thread.

From Rohit.Ghai at mikrobio.med.uni-giessen.de  Fri Oct 26 07:30:43 2007
From: Rohit.Ghai at mikrobio.med.uni-giessen.de (Rohit Ghai)
Date: Fri, 26 Oct 2007 13:30:43 +0200
Subject: [Bioperl-l] cannot run emboss from bioperl on windows
Message-ID: <4721CFE3.4060805@mikrobio.med.uni-giessen.de>

Dear all,

I have emboss installed on a windows machine. (Embosswin). I can run
this from the dos command line and the path is present. However, when I 
try to call
an emboss application from bioperl I get a "Application not found error"


   my $f = Bio::Factory::EMBOSS->new();
   # get an EMBOSS application  object from the factory
   my $fuzznuc = $f->program('fuzznuc');
     $fuzznuc->run(
                   { -sequence  => $infile,
                         -pattern   => $motif,
                        -outfile   => $outfile                       
               });
  gives the following error

-------------------- WARNING ---------------------
MSG: Application [fuzznuc] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at searchPatterns.pl line 
102.

Can somebody help me fix this ?

best regards
Rohit

-- 

Dr. Rohit Ghai
Institute of Medical Microbiology
Faculty of Medicine
Justus-Liebig University
Frankfurter Strasse 107
35392 - Giessen
GERMANY

Tel  :	0049 (0)641-9946413
Fax  :	0049 (0)641-9946409
Email:  Rohit.Ghai at mikrobio.med.uni-giessen.de


From cjfields at uiuc.edu  Fri Oct 26 08:51:26 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 07:51:26 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <4721BD21.9060805@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<4721BD21.9060805@sendu.me.uk>
Message-ID: <D2A5B64D-9534-4421-A6B5-6EA607F3D649@uiuc.edu>


On Oct 26, 2007, at 5:10 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I got
>> an error when running the tests (see below). Can other people
>> reproduce this?
>>
>> It seems to me that the runnable is expecting a tree object, not the
>> filename for a tree...
>
> No, most likely this is another thing broken by the SeqFeature  
> changes.
> I'm going to go ahead and try out some of my proposals in the
> 'Bio::SeqFeature::Annotated API change' thread.

I was able to repeat it on my end.  If you have a fix for it  
involving B::SF::A then definitely go ahead.

chris

From bix at sendu.me.uk  Fri Oct 26 10:48:27 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 15:48:27 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
Message-ID: <4721FE3B.2080507@sendu.me.uk>

Hilmar Lapp wrote:
> 
> On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:
> 
>> seq_id()
>>   Usage   : $obj->seq_id($newval)
>>   Function: holds a string corresponding to the unique
>>             seq_id of the sequence underlying the feature
>>             (e.g. database accession or primary key).
>>   Returns : a Bio::Annotation::SimpleValue object representing the
>>             seq_id.
> 
> type() and source() should be ontology-typed in a TypedSeqFeatureI (and 
> therefore be instances of Bio::Annotation::OntologyTerm, not 
> Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't 
> understand what the benefit of typing seq_id() any stronger than a 
> string would be.

Would there be any problem with having source() return a string, but 
still allow access to the OntologyTerm object via 
get_Annotations('source')? (Ditto with type?)

I think that's the way I'm going to go for now.

From bix at sendu.me.uk  Fri Oct 26 12:52:59 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:52:59 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
 problem with Genewise.t
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <47221B6B.5000604@sendu.me.uk>

Sendu Bala wrote:
> Following Chris's changes to SF::Annotated et al., lots of existing user 
> code breaks. Also, at least some Bioperl code breaks, notably 
> Bio::DB::SeqFeature::Store, which in mysql mode calls 
> _get_location_and_bin() which calls $feature->seq_id which ends up 
> storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
> the database, instead of an actual sequence id (which completely breaks 
> searching by seq_id).
> 
> I propose its API be changed to be more consistent with 
> Bio::SeqFeatureI, eg. instead of:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> we have:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> This would apply to seq_id(), name(), type(), source(), phase() and 
> frame(). Internally the implementation could store the string value in a 
> SimpleValue object.

I've now done this except for type() and source(), since these aren't in 
Generic. Instead we have source_tag() and primary_tag() accepting and 
returning strings.

source() and type() return objects as before, but now only accept 
objects when setting for consistency.


One test that pops up with an error is t/Genewise.t
I don't understand what's causing the problem. Can anyone help?

From bix at sendu.me.uk  Fri Oct 26 12:53:43 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:53:43 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <47221B97.10209@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got an
> error

This should now be fixed (update live and run). If you run into any 
other problems please let me know.

From cjfields at uiuc.edu  Fri Oct 26 13:48:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 12:48:55 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <47221B97.10209@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
Message-ID: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>


On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I  
>> got an
>> error
>
> This should now be fixed (update live and run). If you run into any
> other problems please let me know.

Works now!

chris

From jason at bioperl.org  Fri Oct 26 14:22:42 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 14:22:42 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
	problem with Genewise.t
In-Reply-To: <47221B6B.5000604@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk> <47221B6B.5000604@sendu.me.uk>
Message-ID: <053BEEDD-9C6A-4FE8-BCFD-6FD9C70537DB@bioperl.org>

fixed

> One test that pops up with an error is t/Genewise.t
> I don't understand what's causing the problem. Can anyone help?

--
Jason Stajich
jason at bioperl.org


From avilella at gmail.com  Fri Oct 26 14:29:37 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:29:37 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
	<34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
Message-ID: <358f4d650710261129v13758f55g2dbc6d788f0e7618@mail.gmail.com>

for me too, thanks Sendu :)

On 10/26/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:
>
> > Albert Vilella wrote:
> >> Hi all,
> >>
> >> I was looking at the Gumby runnable, which is pretty cool. But I
> >> got an
> >> error
> >
> > This should now be fixed (update live and run). If you run into any
> > other problems please let me know.
>
> Works now!
>
> chris
>

From avilella at gmail.com  Fri Oct 26 14:45:29 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:45:29 +0100
Subject: [Bioperl-l] problems to use parsing of rst in
	Bio::Tools::Run::Phylo::PAML::Codeml
In-Reply-To: <41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
References: <471CD625.7090605@rennes.inra.fr>
	<41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
Message-ID: <358f4d650710261145k3e174c5aj94cd69b9ef9a356f@mail.gmail.com>

Hi Claude,

Did you submit the bug in bugzilla?

Or if you want, can you attach me a tar.gz with your script and input file
so I can have a look at this?

Cheers,

    Albert.

On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Claude - Will try and take a look when I have time, but pretty overwhelmed
> with other things for the time being - best bet is to also submit this as a
> bug to bugzilla.open-bio.org
>
> -jason
> On Oct 22, 2007, at 12:56 PM, Claude Rispe wrote:
>
> Dear Dr Stajich
> We have difficulty using this bioperl module to run Paml, when we try to
> parse the reconstruction of ancestral sites (rst). I send a workable extract
> of our program,  and two example fasta files (alignments). The program
> seems to work fine (at least for running codeml) and generates a correct rst
> file (by visual inspection) but we have two problems when we try to parse
> the results.
>
> 1/ we have 36 taxa and 11 internal nodes (see attached .nwk file).
> However, when we use the functions of "get_rst_persite", they do not work
> for node 36 (the last terminal node) and for node 47 (the last internal
> node): they return errors. However, inspecting visually the rst file, there
> are no problemes with these sequences.
>
> 2/ if alignments contain gaps (as eg. the file b1630.fas-GBL), the
> get_rst_persite returns wrong values.It seems the references are not
> correct (gaps being ignored ?) and so we obtain codons which are different
> from those actually expected for most sequences!
>
> May be you will have a bit of time to have a glance at our code and
> example files. We might have not written the code correctly (I am not an
> expert at this task). Thanks a lot in advance for any advice or feedback,
> Claude Rispe
> #!usr/bin/perl -w
>
> use Bio::SeqIO;
> use Bio::AlignIO;
> use Bio::Tools::Phylo::PAML;
> use Bio::Tools::Run::Phylo::PAML::Codeml;
> use Bio::TreeIO;
> use Bio::Tree::TreeI;
>
> use strict;
>
>
> my $treeio=Bio::TreeIO->new(-file =>"entero_topo.nwk", -format=>"newick");
> my $tree=$treeio->next_tree();
>
>
>    # runs PAML and gets encestral sequences (for internal nodes)
> ------------------------------------------------------------
>       my $in=Bio::AlignIO->new(-file => "b3298.fas-GBL",-format  =>
> 'fasta');
>       while ( my $aln=$in->next_aln() ) {
>          my $kaks_factory=new Bio::Tools::Run::Phylo::PAML::Codeml (
> -tree=> $tree, -save_tempfiles=> 'TRUE', -dir=>'/tmp', -params=>
> {'runmode'=>0,'seqtype'=>1,'model'=>0,'RateAncestor'=>1} );
>          $kaks_factory->alignment($aln);
>          my($rc,$parser)= $kaks_factory->run();
>  my $result=$parser->next_result;
>
>
>          # parsing of ancestral states and of mutations along branches
> ------------------------------------------------------------
>  my @trees = $result->get_rst_trees;
>  my $persite = $result->get_rst_persite;
>  my $nbsites=scalar(@$persite)-1;
>  print "$nbsites\n";
>     for my $t ( @trees ) {
>                for my $node ( $t->get_nodes ) {
>                    next unless $node->ancestor; # skip root node
>    printf "node:%s     ancestor: %s  node is leaf?
> %s\n",$node->id,$node->ancestor->id,$node->is_Leaf;
>    if ($node->id=~/^(\d*)/) {
>        for( my $i=1;$i<=$nbsites;$i++) {
>          print " $i ",$persite->[$i]->[$1]->{'codon'}, '
> ',$persite->[$i]->[$1]->{'aa'}," ";
>          unless ($node->is_Leaf) {print "
> ",$persite->[$i]->[$1]->{'prob'}," ";}
>
>
>        }
>    }
>            print "\n";
>                }
>
>
>            }
>
>
>
>
>       }
>
> Eco3
>
> GTCGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Erwca
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCGTTAACG
> TCAATTTTCG GTATCGGTAA AACTCGGTCG CAGGCTATTT GTGCTGCAAC GGAGATTGCC
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG ATAAGCTGCG TGACGAAGTT
> GCCAAGTTTG TTGTAGAAGG TGATCTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTT
> ATGGACCTTG GTACTTATCG TGGTTTGCGT CATCGTCGTG GTCTGCCGGT TCGCGGTCAG
> CGTACCAAGA CTAACGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGTCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Klebs
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCACAAAC ATACCGTTAT CGCTTTAACC
> GCTATTTTCG GTATCGGCAA AACCCGTTCT AAAGCCATCT GCGCTGAAAC GGGCATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATTG ATATTCTGCG TGAAGCAGTA
> GGTAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GTTGCTACCG TGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yent
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCGTTAACT
> GCGATCTACG GCATCGGTAA GACCCGTTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Eco10
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Styphim
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Enterob
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAAAAAC ATGCTGTGAT CGCATTAACT
> TCGATCTATG GCGTCGGCAA GACCCGTTCC AAAGCCATTT TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAGTTA GCATGAGCAT CAAGCGCCTT
> ATGGACCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGCCAG
> CGCACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Eco5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco7
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Serrp
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTAAT CGCCTTAACG
> TCGATCTTCG GAATCGGTAA AACCCGCTCA CAGTCTATCT GTGCGTCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATTG AACAGCTGCG TGAAGCAGTC
> GCCAAATTCA CTGTAGAAGG TGATTTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTG
> ATGGATCTTG GTACTTACCG TGGTTTGCGT CATCGTCGTG GTCTGCCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCAATCAA GAAA
>
> Sodalis
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCCCTAACG
> TCAATCTACG GTATCGGCAA AACCCGCTCG CAGCACATCT GCGCGGCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAGATTG ACACGCTGCG TGAAGCAGTT
> ACCAAGTTTG TTGTCGAAGG CGATCTGCGC CGTGAAGTCA CCCTGAGTAT CAAGCGTCTG
> ATGGACCTTG GTACCTATCG TGGTTTGCGT CATCGTCGTG GTCTTCCGGT TCGCGGTCAG
> CGTACCAAGA CCAATGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGCCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Pholu
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAGC ATACCGTGAT CGCTTTAACA
> TCGATCTACG GAATTGGCAA AACTCGCTCC CAAGCCATTT GTGCTGCGGC GGGTATTGCT
> GAGCATGTTA AGATCAGCGA GCTGTCTGAA GAGCAAATTG ATAAGCTGCG TGACGAAGTT
> GCCAAATACG TTGTAGAAGG CGATTTGCGT CGTGAAGTAA CCCTGAGCAT CAAACGTCTG
> ATGGATCTTG GTACTTATCG TGGTTTACGT CACCGTCGTG GTCTACCTGT TCGCGGCCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCACGTA AGCCGATCAA GAAA
>
> Eco9
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco8
>
> GTAGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTAT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TTCTGGCCGA AGCTCTCGTC
> CTCAAACTAC GCAAGCAGTC GGTAGCTGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGT
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGT TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TGTGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTGGCGGG CTTATTAGTC TGGATGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTTG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig6
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig4
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig5
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig2
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGCT GATATGAACA CACTACACTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Erwca
>
> ATGGCTTTTA TTGCGAGTTC ACCGTTCACA CATAACCAGC AGCGCACGCA GCGCATCATG
> CTGTGGGTTA TTCTGGCCTG CCTGCCGGGC ATGTTGGCGC AGGTCTATTT CTTTGGCTAC
> GGCAACCTGA TTCAGGTCGG GCTGGCGTCT GCCACCGCAC TCATTGCGGA AGGCGTGACG
> CTGTCACTGA GGAAATTTGC GGTTCGTACC ACCCTGGCTG ATAATTCCGC GTTACTGACC
> GCCGTGCTGC TCGGAATCAG TCTACCGCCA TTAGCGCCCT GGTGGATGGT GGTCATGGCA
> ACCGTCTTCG CTATCATTAT CGCTAAACAG CTGTATGGCG GATTAGGGCA AAATCCCTTT
> AACCCCGCGA TGATTGGTTA TGTGGTGTTG CTGATCTCTT TCCCTGTCCA GATGACGAGC
> TGGCTGCCAC CCGAGCCGCT GCAAACCATC TCGCTTAGTT TCCATGACTC GCTAGTCATC
> ATTTTTACCG GACACACGCC TGACGGGCAT ACCATGCAGC AGCTGATGCA CAATGTTGAT
> GGCGTGAGTC AGGCCACCCC GCTGGATACG TTTAAAACCA GCTTACGTTC CGGCCAAACG
> CCACAGAACA TCCTGCAACA GCCGATGTTT GCACAATCAC TGTCTGGTAT TGGCTGGCAG
> TGGGTTAATA TCGGTTTTCT CATCGGCGGG CTGTTCTTGC TGATGCGCGG CACGATTCGC
> TGGCATATTC CAGTCAGTTT CCTGCTGTCG CTGATGTTCT GCGCCCTGCT AAGCTGGATC
> ATCGCGCCGG ATAAATTTGC CCAACCGATG TTACATCTGT TGTCCGGTGC GACCATGCTC
> GGCGCATTTT TCATCGCCAC AGATCCCGTT ACAGCATCAA CCACGAACCG GGGCCGTCTG
> ATTTTCGGTG CGTTGATTGG GTTACTGGTG TGGCTGATTC GCACCTATGG CGGCTACCCA
> GACGGCGTTG CCTTTGCCGT TCTACTGGCG AACATCACCG TCCCGCTGAT CGACTATTAC
> ACCAAGCCAC GTGCTTACGG CCACCATCGC
>
> Shig3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGGT GATATGAACA CACTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig1
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAACAGTC GGTAGCCGCC ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTATATGGCG GTCTGGGACA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCTTGGTT TTATCGACGC CATCCAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Yep2
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep3
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Klebs
>
> ATGGTTTTCA TCGCAAGCTC CCCCTATACC CATAACCAGC GGCAGACCTC GCGTATTATG
> CTGCTGGTGC TGCTCGCCGC TGTGCCTGGC ATTGTGGTCC AGACCTGGTT TTTCGGCTGG
> GGCACCGTAC TGCAGATTGT CCTCGCCGCC CTGACGGCCT GGGCGACCGA AGCCGCTATT
> CTCAAACTGC GTAAACAGCC TGTTGCTGCC ACGCTGAAAG ATAATTCCGC CCTGCTCACC
> GGCCTGCTGC TGGCGGTGAG TATTCCGCCA CTGGCCCCGT GGTGGATGGT GGTGCTCGGC
> ACTGCCTTTG CCGTAGTCAT TGCCAAGCAG TTGTACGGAG GCCTGGGCCA TAACCCCTTC
> AACCCGGCAA TGATCGGCTA TGTCGTGCTG CTGATTTCGT TCCCGGTGCA GATGACCTCC
> TGGCTGCCTT CCTATGAGAT AGCCGCCCAT ATCCCGGCAT TCAGCGACGC GCTGCAGATG
> ATCTTCACCG GTCATACCGC CGCCGGAGGC GACATGGCCA GTCTGCGGCT GGGTATCGAC
> GGCGTCAGCC AGGCCACCCC GCTGGATACC TTTAAAACCT CCCTGCATGC CGGACATAGC
> GTTCAGCAGG TGCTGCAATT GCCGGTCTAC GGCGGCGTGC TGGCAGGTCT GGGCTGGCAG
> TGGGTGAATA TCGCCTGGCT GGCAGGCGGC CTTTTCCTGC TGTGGCAGAA GGCGATCCGC
> TGGCATATCC CGGTCAGCTT CCTTGTTAGC CTCGGCCTGT GCGCCACCCT CGGCTGGATT
> TTTTCGCCGC AGAGCCTGGC CTCACCGCAG ATGCATTTGC TCTCCGGGGC GACCATGCTT
> GGCGCCTTCT TTATCCTGAC CGATCCGGTG ACGGCCTCAA CAACCAACCG CGGCCGTCTG
> ATCTTTGGCG CCCTCGCTGG CCTGCTGGTC TGGCTCATCC GCAGCTTCGG TGGTTATCCG
> GACGGCGTGG CGTTTGCCGT TCTGCTGGCG AATATTACCG TGCCGCTGAT CGATTACTAC
> ACGCGCCCGC GCGTATATGG CCACCGT---
>
> Yep1
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yent
>
> ---------A TAGCCAGTTC CCCTTTTACG CATAATCAAC GTAGCACCCG CAGTATTATG
> CTGCTGGTTA TTTTAGCCTG CATTCCGGGG ATTATCGCCC AGACTTACTT CTTTGGTTAT
> GGCAGCCTAA TCCAAGTTGC ACTGGCTATA ATGACCGCCG TGCTGGCCGA AGGCGCTGTC
> TTGCATTTAC GTAAACAGCC GGTACTGACA CGATTACAGG ATAACTCTGC CCTGCTCACT
> GGCTTATTGT TAGGTATCAG TCTGCCGCCA CTTGCCCCTT GGTGGATGAT TGTTCTGGGT
> ACGGCATTTG CCATTATTAT TGCCAAACAA CTTTACGGCG GTTTAGGTCA GAATCCGTTT
> AATCCTGCCA TGGTCGGCTA TGTTGTACTA CTGATTTCAT TCCCAGTACA AATGACCAGT
> TGGCTTCCTC CTCTGCCATT ACAGGGAACG CCGGTTGGAT TCTATGACAG CTTATTAACT
> ATTTTCACCG GATTCACCCA AAATGGTGCC GATATTCACC AACTGCAGAT TGGCTATGAT
> GGGATAAGTC AGGCCACGCC TCTCGATAAC TTTAAAACCT CACTGCGCTC C---CAACCC
> GTGGAACAGA TTCTGCAACA ACCGATTTTT ACCGCGGGGC TGGCGGGTAT TGGTTGGCAA
> TGGATTAACC TCGGTTTTCT GGCGGGCGGT CTGTTGCTGC TATGGCGTAA AGCCATCCAC
> TGGCATATTC CGGTGAGTTT CCTATTGGCT TTGGCAGGTT GTGCTGCTAT CAGTTGGATG
> ATTGCGCCAC ACAGCTTCGC CCCCCCTATG TTGCATCTGT TTTCCGGTGC CACCATGTTG
> GGTGCTTTCT TTATTGCCAC CGATCCGGTC AGCGCCTCGA CAACACCTCG TGGTCGGCTG
> ATTTTCGGCG CATTGATTGG TATTTTGGTG TGGCTGATTC GCGTTTACGG CGGTTATCCC
> GATGGGGTAG CATTTGCGGT GCTGCTGGCC AACATCTGTG TTCCACTGAT TGATCACTAC
> ACTCAACCAC GCGTTTATGG TCATCAGCGC
>
> Yep4
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep5
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yeps2
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTGCTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATC TCGGCTTTCT GGTTGGCGGT TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
>
> ...
>
> [Message clipped]

From hlapp at gmx.net  Fri Oct 26 19:32:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 26 Oct 2007 19:32:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4721FE3B.2080507@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
Message-ID: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>


On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:

> Would there be any problem with having source() return a string,  
> but still allow access to the OntologyTerm object via  
> get_Annotations('source')? (Ditto with type?)

Do I interpret your second email that you abandoned this plan? I.e.,  
source() and type() return objects? I think that's the right way.  
(Otherwise source() is redundant with source_tag().)

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================






From bix at sendu.me.uk  Fri Oct 26 19:47:11 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 00:47:11 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
Message-ID: <47227C7F.9010709@sendu.me.uk>

Hilmar Lapp wrote:
> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
> 
>> Would there be any problem with having source() return a string,  
>> but still allow access to the OntologyTerm object via  
>> get_Annotations('source')? (Ditto with type?)
> 
> Do I interpret your second email that you abandoned this plan? I.e.,  
> source() and type() return objects? I think that's the right way.  
> (Otherwise source() is redundant with source_tag().)

Yes, I abandoned the above plan. I've left source() as a SimpleValue, at 
least until issues with DB::Store are resolved wrt ontologies (it stores 
the entire ontology for each feature in the database, increasing storage 
requirments > 800x).

From cjfields at uiuc.edu  Fri Oct 26 23:39:09 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 22:39:09 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <47227C7F.9010709@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
Message-ID: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>


On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
>>
>>> Would there be any problem with having source() return a string,
>>> but still allow access to the OntologyTerm object via
>>> get_Annotations('source')? (Ditto with type?)
>>
>> Do I interpret your second email that you abandoned this plan? I.e.,
>> source() and type() return objects? I think that's the right way.
>> (Otherwise source() is redundant with source_tag().)
>
> Yes, I abandoned the above plan. I've left source() as a  
> SimpleValue, at
> least until issues with DB::Store are resolved wrt ontologies (it  
> stores
> the entire ontology for each feature in the database, increasing  
> storage
> requirments > 800x).

Do you mean SeqFeature::Store or OntologyStore (I'm guessing the  
latter)?

chris

From bix at sendu.me.uk  Sat Oct 27 03:03:12 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 08:03:12 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
Message-ID: <4722E2B0.3050503@sendu.me.uk>

Chris Fields wrote:
> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>> I've left source() as a SimpleValue, at least until issues with
>> DB::Store are resolved wrt ontologies (it stores the entire
>> ontology for each feature in the database, increasing storage 
>> requirments > 800x).
> 
> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the 
> latter)?

Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you 
set the type() as well of course; the only reason I don't suffer from 
that is that I deliberately avoid setting the type on my features.

From cjfields at uiuc.edu  Sat Oct 27 10:53:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sat, 27 Oct 2007 09:53:59 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4722E2B0.3050503@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
	<4722E2B0.3050503@sendu.me.uk>
Message-ID: <C69BF9A1-1B61-4CE6-80F2-0941D6DB31AB@uiuc.edu>


On Oct 27, 2007, at 2:03 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>>> I've left source() as a SimpleValue, at least until issues with
>>> DB::Store are resolved wrt ontologies (it stores the entire
>>> ontology for each feature in the database, increasing storage
>>> requirments > 800x).
>>
>> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the
>> latter)?
>
> Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you
> set the type() as well of course; the only reason I don't suffer from
> that is that I deliberately avoid setting the type on my features.

Makes sense if you're using $store->add_SeqFeatures (it stores a  
serializized SF along with the data via Storable, so the  
OntologyStore probably goes along for the ride).  If we make type  
checking optional and lazily create the OntologyStore singleton it  
would probably reduce the space, as you wouldn't create it unless  
needed.  Or you could map it over to a DB::SeqFeature after  
validating the type.

Just noticed something: DB::SeqFeature uses type() and source() as  
synonyms of primary_tag() and source_tag(); both use strings instead  
of SimpleValues.

chris

From snaphit at planet.nl  Thu Oct 25 04:07:00 2007
From: snaphit at planet.nl (Jelle86)
Date: Thu, 25 Oct 2007 01:07:00 -0700 (PDT)
Subject: [Bioperl-l]  get_Stream_by_gi: Memory going up every call.
Message-ID: <13401838.post@talk.nabble.com>


Hi, 
I have a problem when using Bio::DB::GenBank->get_Stream_by_gi . My usage
memory for the perl script keeps going up each time a piece of the list is
downloaded. 
I have a gilist, that consist of about 1300 gi's, and i split it in pieces
of 100gi's since get_stream_by_gi doesn't work on more than 300 or so (don't
know why..). 
But either way, using this constructing makes the script take more and more
memory each time 100entries are downloaded. For 1300 gi's not a problem, but
i'm planning on doing it for at least 200.000 gi's.
How can i solve it. At the end of the end of the loops and end of the usage
of the package genbankQuery I empty all the used objects with undef. 
Below are some snippets of my code. Is there a way to find out what actually
causes the problem and more how to solve it?


I use:
perl 5.8.8.822
bioper1.5.2
winxp
behind a proxy


=========
ESTdownload;
makeChunks(){
  while (@small_list = splice(@{$gilist_ref->{gilist}}, 0, 100)) {
        $self->callStream(\@small_list);
 }
}
callStream(){
  $smallref=shift;#contains @small_list ref.
  my $query = genbankQuery->new(ids=>$smallref);
  my $part_result = $query->streamQuery();
}
=========
genbankQuery;
new{
  
  my $self = {
			ids => '',			
			@_,					
		    };
  $self->{gb}=Bio::DB::GenBank->new();
}
streamQuery(){
  my $stream_obj = $self->{gb}->get_Stream_by_gi(\@ids);
  my $seq_obj;       
  #Step through the results 
  while ($seq_obj = $stream_obj->next_seq) {
    #make lines from features and return them in an array ref
  }
}
_____________
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13401838
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From snaphit at planet.nl  Fri Oct 26 08:42:13 2007
From: snaphit at planet.nl (Jelle86)
Date: Fri, 26 Oct 2007 05:42:13 -0700 (PDT)
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13401838.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com>
Message-ID: <13426480.post@talk.nabble.com>


Ok I stripped a lot. And this is causing the problem:

use Bio::DB::Genbank;
sub new(){
  my $invocant = shift;
  my $class = ref($invocant) || $invocant;
  my $self = {@_};
  $self->{gb} = Bio::DB::GenBank->new();
  bless $self, $class;
  return $self;
}

sub streamQuery(){
	my $self = shift;        
	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
        while (my $seq_obj = $stream_obj->next_seq) {
                
        }
}

Both subs (new and streamQuery) are called several times with a new
accessionlist. 
Removing the while loop, will use a bit less memory. But the memory usage is
still going up.
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13426480
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From wgallin at ualberta.ca  Mon Oct 29 00:03:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Sun, 28 Oct 2007 22:03:24 -0600
Subject: [Bioperl-l] Not catching an error in EUtilities
Message-ID: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>

I've been having an intermittent problem, when the NCBI service that  
is accessed by EUtilities (in particular efetch) is not available.

I have the calls enclosed in eval statements, but an exception is not  
thrown.  Instead I find that the  file that should contain the  
results of the efetch only has the following text:

Error: The resource is temporarily unavailable

So it appears that this is not generating an exception (maybe that is  
not desireable in general, but it would be useful in my case).

The result is that my script tries to access the file using  
Bio::Seq::IO, and the expected text is not there.

The relevant snippet of code and the output are copied below.

The only way that I can think of to catch this outcome is to open the  
file and check the firt three lines for this text, and then go back  
and redo the efetch if this particular text is found.

Is this behaviour considered a bug, or just an outcome that needs to  
be checked for when code is written using efetch?

If so, is there a standard way of checking for this?

Thanks,

Warren Gallin

[Code that successfully executes an epost and retrieves the history]

   RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
         -eutil   => 'efetch',
         -rettype => 'genbank',
         -db      => 'protein',
         -history => $history
     );};
     if ($@){
     	print "efetch error trapped\n$@\n";
     	goto RETRIEVE_LIST;

     }

     $file1 = ">" . $file1;
     $retry = 0;
     eval { $prot_eutil->get_Response( -file => $file1 ); };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++;
         sleep(5);
         goto RETRIEVE_LIST;
     }
     else {
         print "efetch ran on $loop_bottom through $loop_top.\n";
     }

The output to the terminal from this part of the code is:

efetch ran on 0 through 300.


From cjfields at uiuc.edu  Mon Oct 29 11:42:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 10:42:43 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <5AEAE8C4-2E18-4BBE-A470-8CB398949BEA@uiuc.edu>


On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
>
> Error: The resource is temporarily unavailable
>
> So it appears that this is not generating an exception (maybe that is
> not desireable in general, but it would be useful in my case).
>
> The result is that my script tries to access the file using
> Bio::Seq::IO, and the expected text is not there.
>
> The relevant snippet of code and the output are copied below.
>
> The only way that I can think of to catch this outcome is to open the
> file and check the firt three lines for this text, and then go back
> and redo the efetch if this particular text is found.
>
> Is this behaviour considered a bug, or just an outcome that needs to
> be checked for when code is written using efetch?
...
> If so, is there a standard way of checking for this?

I may have already mentioned this (it is mentioned in the POD), but  
it's worth repeating: if you running a script to post more than 100  
requests you should be running it btwn 9pm and 5am ET per NCBI's rules:

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

I have built in a way to pass in an LWP::UserAgent-related callback  
to get_Response() using the -cb parameter, primarily to allow piping  
data to a child process for instance.  This could also be used for  
checking the initial data retrieved and throwing if an error is  
returned.  I haven't extensively tested this yet; I can try running a  
stress test to see if I can trigger an efetch error and catch it in  
the callback.  If I can get something working I'll post it later  
today and may incorporate it into EUtilities in CVS.

A bit of background: efetch is the only eutil that doesn't have a  
specific parser (Bio::Tools::EUtilities) attached to it, primarily b/ 
c the data retrieved is very diverse (seq/pubmed/snp/etc data in XML,  
asn.1, text, HTML).  All other eutils besides efetch generate error  
codes via the HTTP::Response header (the norm) or in the XML  
returned; both of the previous types are errors that EUtilities  
catches and throws, so an eval{} works.  efetch errors seen to be  
atypical and may be related to the server load or specific database  
availability.

chris

> Thanks,
>
> Warren Gallin
>
> [Code that successfully executes an epost and retrieves the history]
>
>    RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
>          -eutil   => 'efetch',
>          -rettype => 'genbank',
>          -db      => 'protein',
>          -history => $history
>      );};
>      if ($@){
>      	print "efetch error trapped\n$@\n";
>      	goto RETRIEVE_LIST;
>
>      }
>
>      $file1 = ">" . $file1;
>      $retry = 0;
>      eval { $prot_eutil->get_Response( -file => $file1 ); };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++;
>          sleep(5);
>          goto RETRIEVE_LIST;
>      }
>      else {
>          print "efetch ran on $loop_bottom through $loop_top.\n";
>      }
>
> The output to the terminal from this part of the code is:
>
> efetch ran on 0 through 300.


From cjfields at uiuc.edu  Mon Oct 29 12:06:24 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 11:06:24 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13426480.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
Message-ID: <8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>

It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From cjfields at uiuc.edu  Mon Oct 29 16:45:53 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 15:45:53 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <A5708C31-CA39-43D8-ADE2-E1791D3332C7@uiuc.edu>

Warren,

For efetch the following works for me; it include a simple callback  
to check the initial data chunk (note the die in the callback and the  
extra call to check the header) and prints to the file if no error is  
detected, otherwise it retries.  I'll see if there is an easy way to  
integrate this into EUtilities.


# after eutil calls

open (my $SEQFILE, '>', $file) || die "Can't write to file:$!";
my $expected;
my $bytes = 0;

RETRIEVE_SEQS:
while ($retstart < $count) {
      $gpeptfactory->set_parameters(
		-retmax => $retmax,
                 -retstart => $retstart,
                              );
      my $response;
      eval{
         $response= $gpeptfactory->get_Response(-cb => sub {
            my ($chunk, $res) = @_;
             if ($bytes == 0 && $chunk =~ m{^Error:(.*)}i) {
                 die "$1\n";
             }
             $bytes += length($chunk);
             print $SEQFILE $chunk;
         });
      };
      if ($@ || $response->header('x-died')) {
          my $error = $@ || $response->header('x-died');
          die "Server error: $error.  Try again later" if $retry == 5;
          print STDERR "$error\n";
          print STDERR "Server error, redo #$retry\n";
          $retry++ && redo RETRIEVE_SEQS;
      } else  {
      	my $retend = $retstart + $retmax;
      	print "Loaded entries ",$retstart+1," through $retend on retry  
# $retry.\n";
      	$retstart += $retmax;
      	$retry = 0;
         $bytes = 0; # important!
         undef $expected ;
      }
}

close $SEQFILE;

chris

On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
> ...
> If so, is there a standard way of checking for this?
>
> Thanks,
>
> Warren Gallin
...

From wenbinye at gmail.com  Tue Oct 30 07:46:55 2007
From: wenbinye at gmail.com (Ye Wenbin)
Date: Tue, 30 Oct 2007 19:46:55 +0800
Subject: [Bioperl-l] console version of Deobfuscator
Message-ID: <op.t00dohrc52p72k@tsinghua-64dc66>

Hi, all.
I wrote a console version of Deobfuscator. I think it is easy to
use and more efficient to query and search.
Hope it is helpful!
You can download it from:
http://search.cpan.org/CPAN/authors/id/Y/YE/YEWENBIN/deob-0.02.tar.gz

-- 
Best regards.
Ye Wenbin

From cjfields at uiuc.edu  Tue Oct 30 08:10:41 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 07:10:41 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
Message-ID: <2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>

What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From snaphit at planet.nl  Tue Oct 30 04:51:40 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 09:51:40 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>

This doesn't seem to work. It still keeps using more memory. I already tried it once and didn't seem to make a difference. But gave it another try. But as I said, it doesn't solve the problem.


-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Mon 10/29/2007 5:06 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From jason at bioperl.org  Tue Oct 30 11:16:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Oct 2007 11:16:59 -0400
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>

Denis -
Not sure - the list members will know more.

-jason
Begin forwarded message:

> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
> Date: October 30, 2007 7:41:29 AM EDT
> To: <jason at bioperl.org>
> Subject: Pairwaise_kaks.pl
>
> Good morning,
>
> I'm attempting to set up the pairwise_kaks script here.
>
> I have successfully used an older version in a previous position so  
> I am
> somewhat familiar with it.
>
> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
> And have bioperl             in /usr/local/bioperl-1.5.2_100
>
>
> When I try to run the script I get the following
>
> Can't locate object method "_set_from_args" via package
> "Bio::Tools::Run::Alignment::Clustalw" at
> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>
> I'm not sure how to resolve this so I refer to a higher authority
>
> Merci
>
> Dennis Prickett
>
> Institute for Animal Health
> Compton nr Newbury
> Berkshire
> RG20 7NN
>
> Switchboard: +44  (0)1635 578411
> Central Fax: +44  (0)1635 57723
>

--
Jason Stajich
jason at bioperl.org


From cjfields at uiuc.edu  Tue Oct 30 11:33:34 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 10:33:34 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
Message-ID: <2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>

It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




From bix at sendu.me.uk  Tue Oct 30 12:10:42 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Tue, 30 Oct 2007 16:10:42 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
Message-ID: <47275782.2010200@sendu.me.uk>

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably 
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the 
same place. Ie. 1.5.2 release packages or CVS, not both.

From bix at sendu.me.uk  Wed Oct 31 07:36:09 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 31 Oct 2007 11:36:09 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
	<8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <472868A9.2090706@sendu.me.uk>

dennis prickett (IAH-C) wrote:
> Sendu
> 
> Thanks for the quick response.  
> 
> Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
> the bioperl core package.
> 
> But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

No, that's still 1.5.2 with minor installation-related patches ( 
http://www.bioperl.org/wiki/Release_1.5.2#Updates ). You'll need to 
install bioperl-live from CVS, or bioperl-run-1.5.2_100.

From dennis.prickett at bbsrc.ac.uk  Wed Oct 31 07:32:35 2007
From: dennis.prickett at bbsrc.ac.uk (dennis prickett (IAH-C))
Date: Wed, 31 Oct 2007 11:32:35 -0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <47275782.2010200@sendu.me.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>

Sendu

Thanks for the quick response.  

Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
the bioperl core package.

But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

Thanks 

Dennis Prickett

-----Original Message-----
From: Sendu Bala [mailto:bix at sendu.me.uk] 
Sent: 30 October 2007 16:11
To: Jason Stajich
Cc: bioperl-l list; dennis prickett (IAH-C)
Subject: Re: [Bioperl-l] Fwd: Pairwaise_kaks.pl

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package 
>> "Bio::Tools::Run::Alignment::Clustalw" at 
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the
same place. Ie. 1.5.2 release packages or CVS, not both.


From snaphit at planet.nl  Tue Oct 30 10:56:10 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 15:56:10 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>

I just made a test script which shows the problem.
The second while loop will cause the program to use more and more memory without releasing it.

I will post the bug later today.

Jelle

code:
use Bio::DB::GenBank;
use strict;
use warnings;
my @arraylist = (157043286,157043285,157043189); #use couple of hundreds gi's to see the issue
while (my @small_list = splice(@arraylist, 0, 100)) {
        my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
        my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);        
        while (my $seq_obj = $stream_obj->next_seq) {
            #this is what causes the problem...
        }        
}

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 1:10 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From snaphit at planet.nl  Wed Oct 31 06:07:38 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Wed, 31 Oct 2007 11:07:38 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
	<2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F1A@CPEXBE-EML18.kpnsp.local>

I installed S/SE/SENDU/bioperl-1.5.2_102.tar.gz using cpan -force -notest.
And now running the script doesn't use that much memory. Although it keeps going up, but just a little bit every call. For 14000 +/-20mb (starts at 16mb).

Before I used this bioperl version (only one I was able to install using PPM):
Bioinformatics Toolkit 1.5.2 RC2
Version:	1.5.1.9992
Released:	2006-10-02

I first replaced the modules you mentioned, but it didn't help. So I thought before I report the bug, I will try to install the package with cpan. It gave some errors at first, so I used force and notest. And now it seems to work. I get the output I expect and a lot less memory usage. 

So if you don't see anything on your windows machine, I won't report the bug.

Thanks,
Jelle



-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 4:33 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From swapnatbhat at gmail.com  Wed Oct 31 17:34:38 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 14:34:38 -0700 (PDT)
Subject: [Bioperl-l]  BLAST output parsing
Message-ID: <13519112.post@talk.nabble.com>


Hi all,

I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
it.  I did use -m 9 option to get a tabular information of the blast data. 
But it does not include the gene names or the names of the organisms of each
hit.  Are there any parsers that can do this job ??

I would really appreciate if anybody can help me with this.

Swapna
-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13519112
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From torsten.seemann at infotech.monash.edu.au  Wed Oct 31 21:27:29 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 1 Nov 2007 12:27:29 +1100
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <13519112.post@talk.nabble.com>
References: <13519112.post@talk.nabble.com>
Message-ID: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>

Swapna,

> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
> it.  I did use -m 9 option to get a tabular information of the blast data.
> But it does not include the gene names or the names of the organisms of each
> hit.  Are there any parsers that can do this job ??

The -m 9 tabular output does not include gene descriptions and
organisms. It only includes the "gene id" that was present immediately
after the ">" sign in the FASTA file that was used to create the BLAST
database you specified with the -d option when you ran BLAST.

Hence, no parser will help you. You either have to re-do the BLAST
with a different -m value that includes the information you desire, or
write code to convert your gene IDs into what you want.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University

From swapnatbhat at gmail.com  Wed Oct 31 23:49:45 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 20:49:45 -0700 (PDT)
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
References: <13519112.post@talk.nabble.com>
	<a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
Message-ID: <13523150.post@talk.nabble.com>


which -m option do you think will be helpful.  

swapna

Torsten Seemann wrote:
> 
> Swapna,
> 
>> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to
>> parse
>> it.  I did use -m 9 option to get a tabular information of the blast
>> data.
>> But it does not include the gene names or the names of the organisms of
>> each
>> hit.  Are there any parsers that can do this job ??
> 
> The -m 9 tabular output does not include gene descriptions and
> organisms. It only includes the "gene id" that was present immediately
> after the ">" sign in the FASTA file that was used to create the BLAST
> database you specified with the -d option when you ran BLAST.
> 
> Hence, no parser will help you. You either have to re-do the BLAST
> with a different -m value that includes the information you desire, or
> write code to convert your gene IDs into what you want.
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Monash University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13523150
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.


From outaleb at web.de  Mon Oct  1 07:46:08 2007
From: outaleb at web.de (issam outaleb)
Date: Mon, 01 Oct 2007 13:46:08 +0200
Subject: [Bioperl-l] help about Fasta file???
Message-ID: <2005673060@web.de>



hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;

all 



#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht m?glich zum ?ffnen!!" ;open (OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;        if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {        #print OUT $1."\n"; #print this IPIs in this file.


 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new file with the description


#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    


		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){


$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien  geschlossen, Kopiervorgang 


. 


	
Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate 
kostenlos testen. *http://www.pc-sicherheit.web.de/startseite/?mc=022220* [http://www.pc-sicherheit.web.de/startseite/?mc=022220]



From shameer at ncbs.res.in  Mon Oct  1 12:57:15 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Mon, 1 Oct 2007 22:27:15 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>

Dear All,

Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
 My input file are in phylip  treefile format. Any Modules / codes in
Bio::Graphics / Phylogeny sections ?

Input file :
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);

-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 14:03:00 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:03:00 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
Message-ID: <1191261780.47013654cb81b@webmail.sas.upenn.edu>

I think you'll have better luck using some of already available programs to do
that, you'll get better looking trees. If you just have one tree to draw I
recommend you use:
http://itol.embl.de/

Lucia


Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear All,
>
> Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
>  My input file are in phylip  treefile format. Any Modules / codes in
> Bio::Graphics / Phylogeny sections ?
>
> Input file :
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
> 
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
> 
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From shameer at ncbs.res.in  Mon Oct  1 14:39:05 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Tue, 2 Oct 2007 00:09:05 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191263834.47013e5a6af93@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
Message-ID: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>

Dear Lucia,

Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
methods. Some how missed this excellent HOWTO :
http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
tried that and it worked very nicely. I have to work around to beautify
the tree and I am just going to do that.

Thanks & Cheers,
Shameer

> OK
>
> you can use the implementations in Bio::TreeIO
>
> you can basically read the tree in newick format and out as an svg graph
> something like this:
>
> my $in = new Bio::TreeIO(-file => 'input',
>                          -format => 'newick');
> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>                           -format => 'svggraph');
> while( my $tree = $in->next_tree ) {
>     $out->write_tree($tree);
> }
>
> you can also use Bio::Tree::Draw
>
> hope that helps
>
> Lucia
>
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Hi,
>>
>> Thanks for your mail. I have to create these trees as a part of a
>> webserver. i need to generate them dynamically using users input
>> sequence.
>> I think ITOL is not the stuff best suited for my purpose.
>>
>> > I think you'll have better luck using some of already available
>> programs
>> > to do
>> > that, you'll get better looking trees. If you just have one tree to
>> draw I
>> > recommend you use:
>> > http://itol.embl.de/
>> >
>> > Lucia
>> >
>> >
>> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
>> >
>> >> Dear All,
>> >>
>> >> Is it possible to draw a phylogeny tree file in PNG format using
>> Bioperl
>> >> ?
>> >>  My input file are in phylip  treefile format. Any Modules / codes in
>> >> Bio::Graphics / Phylogeny sections ?
>> >>
>> >> Input file :
>> >>
>> >
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
>>  3.
>> >>
>> >
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>  5
>> >>
>> >
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>> >>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
>


-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 14:48:51 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:48:51 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
Message-ID: <1191264531.47014113f2b54@webmail.sas.upenn.edu>

Yes,
that's the issue about those commands, trees are not pretty at all
that's why for a one tree only kind of thing I rather use ITOL
other thing to try is the tree drawer of the Mesquite package
glad I could help

Lucia

Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear Lucia,
>
> Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
> methods. Some how missed this excellent HOWTO :
> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
> tried that and it worked very nicely. I have to work around to beautify
> the tree and I am just going to do that.
>
> Thanks & Cheers,
> Shameer
>
> > OK
> >
> > you can use the implementations in Bio::TreeIO
> >
> > you can basically read the tree in newick format and out as an svg graph
> > something like this:
> >
> > my $in = new Bio::TreeIO(-file => 'input',
> >                          -format => 'newick');
> > my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >                           -format => 'svggraph');
> > while( my $tree = $in->next_tree ) {
> >     $out->write_tree($tree);
> > }
> >
> > you can also use Bio::Tree::Draw
> >
> > hope that helps
> >
> > Lucia
> >
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Hi,
> >>
> >> Thanks for your mail. I have to create these trees as a part of a
> >> webserver. i need to generate them dynamically using users input
> >> sequence.
> >> I think ITOL is not the stuff best suited for my purpose.
> >>
> >> > I think you'll have better luck using some of already available
> >> programs
> >> > to do
> >> > that, you'll get better looking trees. If you just have one tree to
> >> draw I
> >> > recommend you use:
> >> > http://itol.embl.de/
> >> >
> >> > Lucia
> >> >
> >> >
> >> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >> >
> >> >> Dear All,
> >> >>
> >> >> Is it possible to draw a phylogeny tree file in PNG format using
> >> Bioperl
> >> >> ?
> >> >>  My input file are in phylip  treefile format. Any Modules / codes in
> >> >> Bio::Graphics / Phylogeny sections ?
> >> >>
> >> >> Input file :
> >> >>
> >> >
> >>
> >
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
> >>  3.
> >> >>
> >> >
> >>
> >
>
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>  5
> >> >>
> >> >
> >>
> >
>
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
> >> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> >
>
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From jason at bioperl.org  Mon Oct  1 15:32:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 1 Oct 2007 12:32:38 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191264531.47014113f2b54@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
	<1191264531.47014113f2b54@webmail.sas.upenn.edu>
Message-ID: <F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>

I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
for prettier trees - you get postscript out but you can render this  
to png or jpg with unix tools.  If there is a better stand alone tree  
drawing engine we're happy to try and integrate it into bioperl - the  
modules here are native Perl only and you can use the bioperl-run  
modules that wrap DrawTree and DrawGram from EMBOSS to get other PS  
rendering output.

Mesquite, TreeView or other tools are usually much better but not  
always an option if you want to auto-render these images for a  
website, etc.

-jason


On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:

> Yes,
> that's the issue about those commands, trees are not pretty at all
> that's why for a one tree only kind of thing I rather use ITOL
> other thing to try is the tree drawer of the Mesquite package
> glad I could help
>
> Lucia
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Dear Lucia,
>>
>> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
>> Tree::Draw
>> methods. Some how missed this excellent HOWTO :
>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as  
>> well. I
>> tried that and it worked very nicely. I have to work around to  
>> beautify
>> the tree and I am just going to do that.
>>
>> Thanks & Cheers,
>> Shameer
>>
>>> OK
>>>
>>> you can use the implementations in Bio::TreeIO
>>>
>>> you can basically read the tree in newick format and out as an  
>>> svg graph
>>> something like this:
>>>
>>> my $in = new Bio::TreeIO(-file => 'input',
>>>                          -format => 'newick');
>>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>>>                           -format => 'svggraph');
>>> while( my $tree = $in->next_tree ) {
>>>     $out->write_tree($tree);
>>> }
>>>
>>> you can also use Bio::Tree::Draw
>>>
>>> hope that helps
>>>
>>> Lucia
>>>
>>>
>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>
>>>> Hi,
>>>>
>>>> Thanks for your mail. I have to create these trees as a part of a
>>>> webserver. i need to generate them dynamically using users input
>>>> sequence.
>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>
>>>>> I think you'll have better luck using some of already available
>>>> programs
>>>>> to do
>>>>> that, you'll get better looking trees. If you just have one  
>>>>> tree to
>>>> draw I
>>>>> recommend you use:
>>>>> http://itol.embl.de/
>>>>>
>>>>> Lucia
>>>>>
>>>>>
>>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>> Bioperl
>>>>>> ?
>>>>>>  My input file are in phylip  treefile format. Any Modules /  
>>>>>> codes in
>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>
>>>>>> Input file :
>>>>>>
>>>>>
>>>>
>>>
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> 1.51514,_H_255_263:6.20895):0.83877, 
> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> 0.92645,_H_520_534:7.97418):0.15279, 
> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> 1.52226,_H_463_464:5.42226):0.94093, 
> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> 1.64489,_L_336_343:8.00808):0.88402, 
> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> (((((_E_470_474:3.85000,_E_344_348:
>>>>  3.
>>>>>>
>>>>>
>>>>
>>>
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107, 
> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> 0.71112,_L_513_519:6.65273):0.67204, 
> ((_L_296_304:5.00000,_H_292_295:5.00000): 
> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> 1.08193,_H_229_243:7.93459):0.18730, 
> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> 0.07448,_L_120_122:7.07448):1.59389, 
> ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>>>  5
>>>>>>
>>>>>
>>>>
>>>
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> 0.88488,_E__40__48:5.79344):0.60814, 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> 1.25080):0.17461):6.94325);
>>>>>>
>>>>
>>>> --
>>>> Shameer Khadar
>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>> National Centre for Biological Sciences (TIFR)
>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>> T - 91-080-23666001 EXT - 6251
>>>> W - http://www.ncbs.res.in
>>>>
>>>
>>>
>>> Lucia Peixoto
>>> Department of Biology,SAS
>>> University of Pennsylvania
>>>
>>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From outaleb at web.de  Mon Oct  1 22:37:26 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 04:37:26 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
Message-ID: <4701AEE6.6070506@web.de>

Hi every body,
i have some AccNum in a file-> IPI67675
                                                 IPI98976.
                                                 ...

what i want is how can i look in the fasta file (db fasta) if there is 
some match
if yes then copy the entire entry into a new fasta file.
i tried with bioperl but cause i m noob:-(( i don t get it.
thx all



From ULNJUJERYDIX at spammotel.com  Tue Oct  2 02:21:31 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Tue, 2 Oct 2007 14:21:31 +0800
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
Message-ID: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>

Hi!
I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
sequence)
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in
bioperl.

I found similar solutions like
http://www.bio.davidson.edu/projects/DAB/DAB.html
divide and blast (but I need to specify coords)

there also this from the bioperl archives
http://bioinformatics.org/pipermail/bioclusters/2002-August/000375.html

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?


From n.haigh at sheffield.ac.uk  Tue Oct  2 03:56:57 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 08:56:57 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701AEE6.6070506@web.de>
References: <4701AEE6.6070506@web.de>
Message-ID: <4701F9C9.4050808@sheffield.ac.uk>

outaleb Issame wrote:
> Hi every body,
> i have some AccNum in a file-> IPI67675
>                                                  IPI98976.
>                                                  ...
>
> what i want is how can i look in the fasta file (db fasta) if there is 
> some match
> if yes then copy the entire entry into a new fasta file.
> i tried with bioperl but cause i m noob:-(( i don t get it.
> thx all
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   

Can you state clearly, what is in the "AccNum" file exactly, some sample
text from the actual file would be good. Is the FASTA file containing
the sequences in raw FASTA format or has it been processed using
somthing like formatdb from the BLAST software?

A few more details will help people understand and in turn help you with
a swift solution.

Cheers
Nath


From outaleb at web.de  Tue Oct  2 05:22:17 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 11:22:17 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701F9C9.4050808@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
Message-ID: <47020DC9.8040401@web.de>

hi,
with this file i mean, i picked out this Accession Number from IPI-Human 
Dbase,they come from a fasta file,
so they re under eachother like a i a table in separate file now.
what i want is how how can i check it in the fasta File (so in the 
IPI-Human FAsta File), i they re really there;
if yes please copy the entire entry of this Number (>....the sequence 
also)in new fasta file.so that i get at the end a new
FASTA file with jus this IPI Accession Number.
thx and hope was clearly.

Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>Hi every body,
>>i have some AccNum in a file-> IPI67675
>>                                                 IPI98976.
>>                                                 ...
>>
>>what i want is how can i look in the fasta file (db fasta) if there is 
>>some match
>>if yes then copy the entire entry into a new fasta file.
>>i tried with bioperl but cause i m noob:-(( i don t get it.
>>thx all
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>  
>>    
>>
>
>Can you state clearly, what is in the "AccNum" file exactly, some sample
>text from the actual file would be good. Is the FASTA file containing
>the sequences in raw FASTA format or has it been processed using
>somthing like formatdb from the BLAST software?
>
>A few more details will help people understand and in turn help you with
>a swift solution.
>
>Cheers
>Nath
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From n.haigh at sheffield.ac.uk  Tue Oct  2 05:56:49 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 10:56:49 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47020DC9.8040401@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de>
Message-ID: <470215E1.4080901@sheffield.ac.uk>

outaleb Issame wrote:
> hi,
> with this file i mean, i picked out this Accession Number from
> IPI-Human Dbase,they come from a fasta file,
> so they re under eachother like a i a table in separate file now.
> what i want is how how can i check it in the fasta File (so in the
> IPI-Human FAsta File), i they re really there;
> if yes please copy the entire entry of this Number (>....the sequence
> also)in new fasta file.so that i get at the end a new
> FASTA file with jus this IPI Accession Number.
> thx and hope was clearly.

Ok, first of all, I'd read the contents of your Accession numbers into a
hash, something like the following (this could be written in a shorter
form, but since you're a newbie I'll leave it in a longer form so you
can follow easier).

-- start script --
use strict;
use Bio::SeqIO;

# change the following three lines to point to the relevant paths
# of your list of accessions file, your fasta file and your output
# fasta file
my $acc_file = "/path/to/your/file";
my $fasta_file_in = "/path/to/your/fasta/file";
my $fasta_file_out = "/path/to/your/fasta/output/file";

# Use a hash to keep a record of accessions we want to find
my %hash_of_req_acc;

# read all the required accessions from the file into the hash as keys
open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
while (<ACC_FILE>) {
  my $line = $_;
  chomp $line;
  $hash_of_req_acc{$_} = 1;
}
close ACC_FILE;

my $seqio_object_in = Bio::SeqIO->new(
  -file => $fasta_file_in,
  -format => 'fasta'
);
my $seqio_object_out = Bio::SeqIO->new(
  -file => $fasta_file_out,
  -format => 'fasta'
);

# loop through all the sequences in the fasta file
while (my $seq_object = $seqio_object_in->next_seq) {
  # get the sequence accession for easy matching
  my $seq_acc = $seq_object->accession_number;

  # write the sequence object to the output fasta file if we have a
matching accession
  $seqio_object_out->write_seq($seq_object) if exists
$hash_of_req_acc{$seq_acc};
}
-- end script --

I haven't tested this, but it should at least get you started. Also, the
fasta description line in the output file may not be exactly as it was
in the input fasta file - if this really matters, you may need to get
back to us. Also, if the input fasta file is huge (many thousands of
sequences) it may be wise to create an index of the fasta file in order
to speed up retrieval.

You may find this page helpful:
http://www.bioperl.org/wiki/HOWTO:SeqIO

Anyway, hope this helps to get you started.
Nath




From outaleb at web.de  Tue Oct  2 06:50:32 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 12:50:32 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <470215E1.4080901@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk>
Message-ID: <47022278.7010700@web.de>

thx for the help, but i got a empty output file,
i think its problem with matching the acc number, my fasta file look like:

*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU...
 >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU..
 >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
MMMMM..*

and my i Accnum File look like:
*IPI00177321
IPI00453473

*i hopt it helps to understand.*
*.


Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>hi,
>>with this file i mean, i picked out this Accession Number from
>>IPI-Human Dbase,they come from a fasta file,
>>so they re under eachother like a i a table in separate file now.
>>what i want is how how can i check it in the fasta File (so in the
>>IPI-Human FAsta File), i they re really there;
>>if yes please copy the entire entry of this Number (>....the sequence
>>also)in new fasta file.so that i get at the end a new
>>FASTA file with jus this IPI Accession Number.
>>thx and hope was clearly.
>>    
>>
>
>Ok, first of all, I'd read the contents of your Accession numbers into a
>hash, something like the following (this could be written in a shorter
>form, but since you're a newbie I'll leave it in a longer form so you
>can follow easier).
>
>-- start script --
>use strict;
>use Bio::SeqIO;
>
># change the following three lines to point to the relevant paths
># of your list of accessions file, your fasta file and your output
># fasta file
>my $acc_file = "/path/to/your/file";
>my $fasta_file_in = "/path/to/your/fasta/file";
>my $fasta_file_out = "/path/to/your/fasta/output/file";
>
># Use a hash to keep a record of accessions we want to find
>my %hash_of_req_acc;
>
># read all the required accessions from the file into the hash as keys
>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>while (<ACC_FILE>) {
>  my $line = $_;
>  chomp $line;
>  $hash_of_req_acc{$_} = 1;
>}
>close ACC_FILE;
>
>my $seqio_object_in = Bio::SeqIO->new(
>  -file => $fasta_file_in,
>  -format => 'fasta'
>);
>my $seqio_object_out = Bio::SeqIO->new(
>  -file => $fasta_file_out,
>  -format => 'fasta'
>);
>
># loop through all the sequences in the fasta file
>while (my $seq_object = $seqio_object_in->next_seq) {
>  # get the sequence accession for easy matching
>  my $seq_acc = $seq_object->accession_number;
>
>  # write the sequence object to the output fasta file if we have a
>matching accession
>  $seqio_object_out->write_seq($seq_object) if exists
>$hash_of_req_acc{$seq_acc};
>}
>-- end script --
>
>I haven't tested this, but it should at least get you started. Also, the
>fasta description line in the output file may not be exactly as it was
>in the input fasta file - if this really matters, you may need to get
>back to us. Also, if the input fasta file is huge (many thousands of
>sequences) it may be wise to create an index of the fasta file in order
>to speed up retrieval.
>
>You may find this page helpful:
>http://www.bioperl.org/wiki/HOWTO:SeqIO
>
>Anyway, hope this helps to get you started.
>Nath
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From cjfields at uiuc.edu  Tue Oct  2 09:00:57 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 08:00:57 -0500
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
Message-ID: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>

There is a script that comes with the bioperl core distribution,  
bp_split_seq.pl, which does this.  Here's the CVS location:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
scripts/seq/?cvsroot=bioperl

chris

On Oct 2, 2007, at 1:21 AM, Kevin Lam wrote:

> Hi!
> I am trying to annotate a 200kb sequence by doing blastx to find  
> the protein
> seq location
> I need to split the sequence up so that I get the best hits for  
> each region
> (the top blast hits will mask the smaller proteins if i do it as a  
> whole
> sequence)
> if i were to do it manually i can set the subsequence in the web  
> gui for
> ncbi's blast.
> this way, the blast hits coords are based on the whole 200kb.
>
> but I can't find this option in blast or a straightforward way to  
> do it in
> bioperl.
>
> I found similar solutions like
> http://www.bio.davidson.edu/projects/DAB/DAB.html
> divide and blast (but I need to specify coords)
>
> there also this from the bioperl archives
> http://bioinformatics.org/pipermail/bioclusters/2002-August/ 
> 000375.html
>
> but isn't there an easier way like i can specify blast subsequence  
> 200-900
> of fasta file and it will return the blastx hits in coords in terms  
> of the
> whole 200kb?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From rrc22 at cam.ac.uk  Tue Oct  2 09:38:45 2007
From: rrc22 at cam.ac.uk (Roy Chaudhuri)
Date: Tue, 02 Oct 2007 14:38:45 +0100
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <470249E5.6050206@cam.ac.uk>

> but isn't there an easier way like i can specify blast subsequence 200-900
> of fasta file and it will return the blastx hits in coords in terms of the
> whole 200kb?

Once you have split up your sequence (as Chris suggested), and run your 
BLAST, then you can add the hits to each subsequence as features. The 
subsequences can then be re-assembled using the cat method from 
Bio::SeqUtils, which will adjust the coordinates of the features 
appropriately.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.


From cjfields at uiuc.edu  Tue Oct  2 11:03:29 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 10:03:29 -0500
Subject: [Bioperl-l] exonerate
In-Reply-To: <29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
Message-ID: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>

One option is to try running $run->cleanup() after you finish  
parsing, which gets rid of the tempfiles on each run.

chris

On Sep 30, 2007, at 8:53 PM, alan wrote:

> Hi,
>
>
>>> I am calling exonerate.pm within my script while attempting to
>>> align cDNA  to multiple genomic fragments. After processing about
>>> 120+ genomic fragments my code crashes with the following error:
>>>
>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>> aborting...
>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>
>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>> routine yet I get the error message about "too many open files".
>>> Any suggestions on how I should be closing these files?
>>>
>>>
>>> Extract from my code that runs exonerate is listed below.
>>>
>>> foreach my $f(@files) {
>>>   next unless (-f  "$dir/$f");
>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>   my $query_obj = $q_in->next_seq();
>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>> format=>"Fasta");
>>>   my $target_obj = $target_in->next_seq();
>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>
>>>   [code for parsing the data.......]
>>>
>>>   $exonerate_io->close; #tried this line out of desperation but it
>>> did not help :-)
>>> }
>>>
>>> thanks
>>> alan




From outaleb at web.de  Tue Oct  2 10:51:05 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 16:51:05 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47022278.7010700@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de>
Message-ID: <47025AD9.1090105@web.de>

hi again,
i think i can resolve this problem with the method : id_parser();
how can i do that?
any suggestion .or experience??
ehx again



outaleb Issame wrote:

>thx for the help, but i got a empty output file,
>i think its problem with matching the acc number, my fasta file look like:
>
>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU...
> >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU..
> >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>MMMMM..*
>
>and my i Accnum File look like:
>*IPI00177321
>IPI00453473
>
>*i hopt it helps to understand.*
>*.
>
>
>Nathan S. Haigh wrote:
>
>  
>
>>outaleb Issame wrote:
>> 
>>
>>    
>>
>>>hi,
>>>with this file i mean, i picked out this Accession Number from
>>>IPI-Human Dbase,they come from a fasta file,
>>>so they re under eachother like a i a table in separate file now.
>>>what i want is how how can i check it in the fasta File (so in the
>>>IPI-Human FAsta File), i they re really there;
>>>if yes please copy the entire entry of this Number (>....the sequence
>>>also)in new fasta file.so that i get at the end a new
>>>FASTA file with jus this IPI Accession Number.
>>>thx and hope was clearly.
>>>   
>>>
>>>      
>>>
>>Ok, first of all, I'd read the contents of your Accession numbers into a
>>hash, something like the following (this could be written in a shorter
>>form, but since you're a newbie I'll leave it in a longer form so you
>>can follow easier).
>>
>>-- start script --
>>use strict;
>>use Bio::SeqIO;
>>
>># change the following three lines to point to the relevant paths
>># of your list of accessions file, your fasta file and your output
>># fasta file
>>my $acc_file = "/path/to/your/file";
>>my $fasta_file_in = "/path/to/your/fasta/file";
>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>
>># Use a hash to keep a record of accessions we want to find
>>my %hash_of_req_acc;
>>
>># read all the required accessions from the file into the hash as keys
>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>while (<ACC_FILE>) {
>> my $line = $_;
>> chomp $line;
>> $hash_of_req_acc{$_} = 1;
>>}
>>close ACC_FILE;
>>
>>my $seqio_object_in = Bio::SeqIO->new(
>> -file => $fasta_file_in,
>> -format => 'fasta'
>>);
>>my $seqio_object_out = Bio::SeqIO->new(
>> -file => $fasta_file_out,
>> -format => 'fasta'
>>);
>>
>># loop through all the sequences in the fasta file
>>while (my $seq_object = $seqio_object_in->next_seq) {
>> # get the sequence accession for easy matching
>> my $seq_acc = $seq_object->accession_number;
>>
>> # write the sequence object to the output fasta file if we have a
>>matching accession
>> $seqio_object_out->write_seq($seq_object) if exists
>>$hash_of_req_acc{$seq_acc};
>>}
>>-- end script --
>>
>>I haven't tested this, but it should at least get you started. Also, the
>>fasta description line in the output file may not be exactly as it was
>>in the input fasta file - if this really matters, you may need to get
>>back to us. Also, if the input fasta file is huge (many thousands of
>>sequences) it may be wise to create an index of the fasta file in order
>>to speed up retrieval.
>>
>>You may find this page helpful:
>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>
>>Anyway, hope this helps to get you started.
>>Nath
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> 
>>
>>    
>>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From rvos at interchange.ubc.ca  Tue Oct  2 13:00:36 2007
From: rvos at interchange.ubc.ca (rvos at interchange.ubc.ca)
Date: Tue, 02 Oct 2007 10:00:36 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <405453b66e.3b66e40545@interchange.ubc.ca>

An alternative is to explore the Bio::Phylo treedrawer:

http://search.cpan.org/~rvosa/Bio-Phylo-0.17_RC6/lib/Bio/Phylo/Treedrawer.pm

This is a separate install (in the interest of full disclosure: I'm the author).

Rutger

----- Original Message -----
From: Jason Stajich <jason at bioperl.org>
Date: Monday, October 1, 2007 12:32 pm
Subject: Re: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?

> I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
> for prettier trees - you get postscript out but you can render this 
> 
> to png or jpg with unix tools.  If there is a better stand alone 
> tree  
> drawing engine we're happy to try and integrate it into bioperl - 
> the  
> modules here are native Perl only and you can use the bioperl-run  
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS 
> 
> rendering output.
> 
> Mesquite, TreeView or other tools are usually much better but not  
> always an option if you want to auto-render these images for a  
> website, etc.
> 
> -jason
> 
> 
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
> 
> > Yes,
> > that's the issue about those commands, trees are not pretty at all
> > that's why for a one tree only kind of thing I rather use ITOL
> > other thing to try is the tree drawer of the Mesquite package
> > glad I could help
> >
> > Lucia
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Dear Lucia,
> >>
> >> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
> >> Tree::Draw
> >> methods. Some how missed this excellent HOWTO :
> >> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as 
> 
> >> well. I
> >> tried that and it worked very nicely. I have to work around to  
> >> beautify
> >> the tree and I am just going to do that.
> >>
> >> Thanks & Cheers,
> >> Shameer
> >>
> >>> OK
> >>>
> >>> you can use the implementations in Bio::TreeIO
> >>>
> >>> you can basically read the tree in newick format and out as an  
> >>> svg graph
> >>> something like this:
> >>>
> >>> my $in = new Bio::TreeIO(-file => 'input',
> >>>                          -format => 'newick');
> >>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >>>                           -format => 'svggraph');
> >>> while( my $tree = $in->next_tree ) {
> >>>     $out->write_tree($tree);
> >>> }
> >>>
> >>> you can also use Bio::Tree::Draw
> >>>
> >>> hope that helps
> >>>
> >>> Lucia
> >>>
> >>>
> >>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>
> >>>> Hi,
> >>>>
> >>>> Thanks for your mail. I have to create these trees as a part 
> of a
> >>>> webserver. i need to generate them dynamically using users input
> >>>> sequence.
> >>>> I think ITOL is not the stuff best suited for my purpose.
> >>>>
> >>>>> I think you'll have better luck using some of already available
> >>>> programs
> >>>>> to do
> >>>>> that, you'll get better looking trees. If you just have one  
> >>>>> tree to
> >>>> draw I
> >>>>> recommend you use:
> >>>>> http://itol.embl.de/
> >>>>>
> >>>>> Lucia
> >>>>>
> >>>>>
> >>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>>>
> >>>>>> Dear All,
> >>>>>>
> >>>>>> Is it possible to draw a phylogeny tree file in PNG format 
> using>>>> Bioperl
> >>>>>> ?
> >>>>>>  My input file are in phylip  treefile format. Any Modules / 
> 
> >>>>>> codes in
> >>>>>> Bio::Graphics / Phylogeny sections ?
> >>>>>>
> >>>>>> Input file :
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> > (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> > 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> > 1.51514,_H_255_263:6.20895):0.83877, 
> > (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> > 0.92645,_H_520_534:7.97418):0.15279, 
> > (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> > 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> > ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> > 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> > (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> > 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> > 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> > 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> > 1.52226,_H_463_464:5.42226):0.94093, 
> > (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> > 1.64489,_L_336_343:8.00808):0.88402, 
> > (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> > (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> > (((((_E_470_474:3.85000,_E_344_348:
> >>>>  3.
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 85000):0.89054,_L_475_478:4.74054):1.20107, 
> > (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> > 0.71112,_L_513_519:6.65273):0.67204, 
> > ((_L_296_304:5.00000,_H_292_295:5.00000): 
> > 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> > 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> > 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> > 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> > 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> > 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> > 1.08193,_H_229_243:7.93459):0.18730, 
> > (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> > ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> > 0.07448,_L_120_122:7.07448):1.59389, 
> > ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> > 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> > 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> > ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> > (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> > 0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>>>  5
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> > (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> > ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> > 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> > 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> > ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> > (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> > 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> > 0.88488,_E__40__48:5.79344):0.60814, 
> > 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> > 1.25080):0.17461):6.94325);
> >>>>>>
> >>>>
> >>>> --
> >>>> Shameer Khadar
> >>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >>>> National Centre for Biological Sciences (TIFR)
> >>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >>>> T - 91-080-23666001 EXT - 6251
> >>>> W - http://www.ncbs.res.in
> >>>>
> >>>
> >>>
> >>> Lucia Peixoto
> >>> Department of Biology,SAS
> >>> University of Pennsylvania
> >>>
> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From Russell.Smithies at agresearch.co.nz  Tue Oct  2 17:34:20 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 10:34:20 +1300
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>

I know this is the Bioperl list but how about just doing it with grep?

	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of outaleb Issame
> Sent: Wednesday, 3 October 2007 3:51 a.m.
> To: outaleb Issame
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> 
> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
> 
> 
> 
> outaleb Issame wrote:
> 
> >thx for the help, but i got a empty output file,
> >i think its problem with matching the acc number, my fasta file look
like:
> >
> >*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU...
> > >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU..
> > >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >MMMMM..*
> >
> >and my i Accnum File look like:
> >*IPI00177321
> >IPI00453473
> >
> >*i hopt it helps to understand.*
> >*.
> >
> >
> >Nathan S. Haigh wrote:
> >
> >
> >
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>
> >>>hi,
> >>>with this file i mean, i picked out this Accession Number from
> >>>IPI-Human Dbase,they come from a fasta file,
> >>>so they re under eachother like a i a table in separate file now.
> >>>what i want is how how can i check it in the fasta File (so in the
> >>>IPI-Human FAsta File), i they re really there;
> >>>if yes please copy the entire entry of this Number (>....the
sequence
> >>>also)in new fasta file.so that i get at the end a new
> >>>FASTA file with jus this IPI Accession Number.
> >>>thx and hope was clearly.
> >>>
> >>>
> >>>
> >>>
> >>Ok, first of all, I'd read the contents of your Accession numbers
into a
> >>hash, something like the following (this could be written in a
shorter
> >>form, but since you're a newbie I'll leave it in a longer form so
you
> >>can follow easier).
> >>
> >>-- start script --
> >>use strict;
> >>use Bio::SeqIO;
> >>
> >># change the following three lines to point to the relevant paths
> >># of your list of accessions file, your fasta file and your output
> >># fasta file
> >>my $acc_file = "/path/to/your/file";
> >>my $fasta_file_in = "/path/to/your/fasta/file";
> >>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>
> >># Use a hash to keep a record of accessions we want to find
> >>my %hash_of_req_acc;
> >>
> >># read all the required accessions from the file into the hash as
keys
> >>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>while (<ACC_FILE>) {
> >> my $line = $_;
> >> chomp $line;
> >> $hash_of_req_acc{$_} = 1;
> >>}
> >>close ACC_FILE;
> >>
> >>my $seqio_object_in = Bio::SeqIO->new(
> >> -file => $fasta_file_in,
> >> -format => 'fasta'
> >>);
> >>my $seqio_object_out = Bio::SeqIO->new(
> >> -file => $fasta_file_out,
> >> -format => 'fasta'
> >>);
> >>
> >># loop through all the sequences in the fasta file
> >>while (my $seq_object = $seqio_object_in->next_seq) {
> >> # get the sequence accession for easy matching
> >> my $seq_acc = $seq_object->accession_number;
> >>
> >> # write the sequence object to the output fasta file if we have a
> >>matching accession
> >> $seqio_object_out->write_seq($seq_object) if exists
> >>$hash_of_req_acc{$seq_acc};
> >>}
> >>-- end script --
> >>
> >>I haven't tested this, but it should at least get you started. Also,
the
> >>fasta description line in the output file may not be exactly as it
was
> >>in the input fasta file - if this really matters, you may need to
get
> >>back to us. Also, if the input fasta file is huge (many thousands of
> >>sequences) it may be wise to create an index of the fasta file in
order
> >>to speed up retrieval.
> >>
> >>You may find this page helpful:
> >>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>Anyway, hope this helps to get you started.
> >>Nath
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >>
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From thiago.venancio at gmail.com  Tue Oct  2 17:41:06 2007
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Tue, 2 Oct 2007 18:41:06 -0300
Subject: [Bioperl-l] frac_* methods
Message-ID: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>

Hi all,

This topic was discussed before, but I would like to put it on the list
again, maybe someone has an update.

The methods frac_identical, frac_conserved, frac_aligned_query and
frac_aligned_hit can also be used in the hit context, after HSP tilling. In
my point of view, it is better to use it just in HSPs individually, because
there are some rare/strange kinds of alignments. However, we frequently need
to get one measure of the whole alignment.

Any of the BioPerl masters has an update on this topic ? What is the best
current usage ?

Best.

Thiago

-- 
"Innovation distinguishes between a leader and a follower."
    Steve Jobs

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================


From outaleb at web.de  Tue Oct  2 17:47:07 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 23:47:07 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
Message-ID: <4702BC5B.7040407@web.de>

thx for this, but i want just create new fasta file with my accNumbers 
which i search in the FASTA file(localdbase).
so --> just search this Numbers in the FASTA file, if yes then copy the 
Header and Sequence to other new fasta file .
i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
i get crazy guys.
common some expert in this area??
 


Smithies, Russell wrote:

>I know this is the Bioperl list but how about just doing it with grep?
>
>	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
>
>
>
>  
>
>>-----Original Message-----
>>From: bioperl-l-bounces at lists.open-bio.org
>>    
>>
>[mailto:bioperl-l-bounces at lists.open-
>  
>
>>bio.org] On Behalf Of outaleb Issame
>>Sent: Wednesday, 3 October 2007 3:51 a.m.
>>To: outaleb Issame
>>Cc: bioperl-l at lists.open-bio.org
>>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
>>
>>hi again,
>>i think i can resolve this problem with the method : id_parser();
>>how can i do that?
>>any suggestion .or experience??
>>ehx again
>>
>>
>>
>>outaleb Issame wrote:
>>
>>    
>>
>>>thx for the help, but i got a empty output file,
>>>i think its problem with matching the acc number, my fasta file look
>>>      
>>>
>like:
>  
>
>>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>      
>>>
>>protein
>>    
>>
>>>DDHHHU...
>>>      
>>>
>>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>DDHHHU..
>>>      
>>>
>>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>MMMMM..*
>>>
>>>and my i Accnum File look like:
>>>*IPI00177321
>>>IPI00453473
>>>
>>>*i hopt it helps to understand.*
>>>*.
>>>
>>>
>>>Nathan S. Haigh wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>outaleb Issame wrote:
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>hi,
>>>>>with this file i mean, i picked out this Accession Number from
>>>>>IPI-Human Dbase,they come from a fasta file,
>>>>>so they re under eachother like a i a table in separate file now.
>>>>>what i want is how how can i check it in the fasta File (so in the
>>>>>IPI-Human FAsta File), i they re really there;
>>>>>if yes please copy the entire entry of this Number (>....the
>>>>>          
>>>>>
>sequence
>  
>
>>>>>also)in new fasta file.so that i get at the end a new
>>>>>FASTA file with jus this IPI Accession Number.
>>>>>thx and hope was clearly.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Ok, first of all, I'd read the contents of your Accession numbers
>>>>        
>>>>
>into a
>  
>
>>>>hash, something like the following (this could be written in a
>>>>        
>>>>
>shorter
>  
>
>>>>form, but since you're a newbie I'll leave it in a longer form so
>>>>        
>>>>
>you
>  
>
>>>>can follow easier).
>>>>
>>>>-- start script --
>>>>use strict;
>>>>use Bio::SeqIO;
>>>>
>>>># change the following three lines to point to the relevant paths
>>>># of your list of accessions file, your fasta file and your output
>>>># fasta file
>>>>my $acc_file = "/path/to/your/file";
>>>>my $fasta_file_in = "/path/to/your/fasta/file";
>>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>>
>>>># Use a hash to keep a record of accessions we want to find
>>>>my %hash_of_req_acc;
>>>>
>>>># read all the required accessions from the file into the hash as
>>>>        
>>>>
>keys
>  
>
>>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>>>while (<ACC_FILE>) {
>>>>my $line = $_;
>>>>chomp $line;
>>>>$hash_of_req_acc{$_} = 1;
>>>>}
>>>>close ACC_FILE;
>>>>
>>>>my $seqio_object_in = Bio::SeqIO->new(
>>>>-file => $fasta_file_in,
>>>>-format => 'fasta'
>>>>);
>>>>my $seqio_object_out = Bio::SeqIO->new(
>>>>-file => $fasta_file_out,
>>>>-format => 'fasta'
>>>>);
>>>>
>>>># loop through all the sequences in the fasta file
>>>>while (my $seq_object = $seqio_object_in->next_seq) {
>>>># get the sequence accession for easy matching
>>>>my $seq_acc = $seq_object->accession_number;
>>>>
>>>># write the sequence object to the output fasta file if we have a
>>>>matching accession
>>>>$seqio_object_out->write_seq($seq_object) if exists
>>>>$hash_of_req_acc{$seq_acc};
>>>>}
>>>>-- end script --
>>>>
>>>>I haven't tested this, but it should at least get you started. Also,
>>>>        
>>>>
>the
>  
>
>>>>fasta description line in the output file may not be exactly as it
>>>>        
>>>>
>was
>  
>
>>>>in the input fasta file - if this really matters, you may need to
>>>>        
>>>>
>get
>  
>
>>>>back to us. Also, if the input fasta file is huge (many thousands of
>>>>sequences) it may be wise to create an index of the fasta file in
>>>>        
>>>>
>order
>  
>
>>>>to speed up retrieval.
>>>>
>>>>You may find this page helpful:
>>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>>
>>>>Anyway, hope this helps to get you started.
>>>>Nath
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>
>=======================================================================
>Attention: The information contained in this message and/or attachments
>from AgResearch Limited is intended only for the persons or entities
>to which it is addressed and may contain confidential and/or privileged
>material. Any review, retransmission, dissemination or other use of, or
>taking of any action in reliance upon, this information by persons or
>entities other than the intended recipients is prohibited by AgResearch
>Limited. If you have received this message in error, please notify the
>sender immediately.
>=======================================================================
>
>  
>



From jason at bioperl.org  Tue Oct  2 18:22:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 15:22:59 -0700
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>

I think my answer before was something to the tune of:

Use an alignment algorithm that finds a single best alignment like  
FASTA or Smith-Waterman (SW) if what you want is a single number that  
represents the alignment.  BLAST is great for fast searching but  
FASTA or SW/SSEARCH are going to be better at creating an alignment.   
Consider the -postsw option in WUBLAST as well as it will realign the  
HSPs with SW.

I personally never use the frac alignment summary stats for the Hit  
object for this reason unless I know I am going to have a single HSP.

-jason

On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago
>
> -- 
> "Innovation distinguishes between a leader and a follower."
>     Steve Jobs
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct  2 18:32:30 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 17:32:30 -0500
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <B9E32251-2A8E-4079-B256-9665D9987B02@uiuc.edu>

I think their use is based on what you are trying to accomplish.  For  
instance I am currently running a lot of small BLASTN queries  
(limiting by normalized bit score), so I tend to look at the HSP data  
more.  However, in other circumstances I might want the overall  
frac_identical for all HSPs ($hit->frac_identical).  YMMV.

chris

On Oct 2, 2007, at 4:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago




From razi.khaja at gmail.com  Tue Oct  2 19:46:12 2007
From: razi.khaja at gmail.com (Razi Khaja)
Date: Tue, 2 Oct 2007 19:46:12 -0400
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4702BC5B.7040407@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de> <470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
	<4702BC5B.7040407@web.de>
Message-ID: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>

Here is the easiest non-bioperl solution using executables provided
with ncbi's blast:

(1) format your multifasta file into a blast database

> /usr/local/ncbi/blast-2.2.16/bin/formatdb -i yourmultifastafile -t yourblastdb

(2) extract sequences from the newly created blast database with a
file containing a list of accession numbers (one on each line)

> /usr/local/ncib/blast-2.2.16/bin/fastacmd -d yourblastdb -i inputfilewithaccessionnumbers -o outputfile

Your outputfile should be a multifasta file of your list of accession numbers

blast executables are available from
http://www.ncbi.nlm.nih.gov/blast/download.shtml

Hope that helps.
Razi Khaja

On 10/2/07, outaleb Issame <outaleb at web.de> wrote:
> thx for this, but i want just create new fasta file with my accNumbers
> which i search in the FASTA file(localdbase).
> so --> just search this Numbers in the FASTA file, if yes then copy the
> Header and Sequence to other new fasta file .
> i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
> i get crazy guys.
> common some expert in this area??
>
>
>
> Smithies, Russell wrote:
>
> >I know this is the Bioperl list but how about just doing it with grep?
> >
> >       grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
> >
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: bioperl-l-bounces at lists.open-bio.org
> >>
> >>
> >[mailto:bioperl-l-bounces at lists.open-
> >
> >
> >>bio.org] On Behalf Of outaleb Issame
> >>Sent: Wednesday, 3 October 2007 3:51 a.m.
> >>To: outaleb Issame
> >>Cc: bioperl-l at lists.open-bio.org
> >>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> >>
> >>hi again,
> >>i think i can resolve this problem with the method : id_parser();
> >>how can i do that?
> >>any suggestion .or experience??
> >>ehx again
> >>
> >>
> >>
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>>thx for the help, but i got a empty output file,
> >>>i think its problem with matching the acc number, my fasta file look
> >>>
> >>>
> >like:
> >
> >
> >>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>
> >>>
> >>protein
> >>
> >>
> >>>DDHHHU...
> >>>
> >>>
> >>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>DDHHHU..
> >>>
> >>>
> >>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>MMMMM..*
> >>>
> >>>and my i Accnum File look like:
> >>>*IPI00177321
> >>>IPI00453473
> >>>
> >>>*i hopt it helps to understand.*
> >>>*.
> >>>
> >>>
> >>>Nathan S. Haigh wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>outaleb Issame wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>hi,
> >>>>>with this file i mean, i picked out this Accession Number from
> >>>>>IPI-Human Dbase,they come from a fasta file,
> >>>>>so they re under eachother like a i a table in separate file now.
> >>>>>what i want is how how can i check it in the fasta File (so in the
> >>>>>IPI-Human FAsta File), i they re really there;
> >>>>>if yes please copy the entire entry of this Number (>....the
> >>>>>
> >>>>>
> >sequence
> >
> >
> >>>>>also)in new fasta file.so that i get at the end a new
> >>>>>FASTA file with jus this IPI Accession Number.
> >>>>>thx and hope was clearly.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>Ok, first of all, I'd read the contents of your Accession numbers
> >>>>
> >>>>
> >into a
> >
> >
> >>>>hash, something like the following (this could be written in a
> >>>>
> >>>>
> >shorter
> >
> >
> >>>>form, but since you're a newbie I'll leave it in a longer form so
> >>>>
> >>>>
> >you
> >
> >
> >>>>can follow easier).
> >>>>
> >>>>-- start script --
> >>>>use strict;
> >>>>use Bio::SeqIO;
> >>>>
> >>>># change the following three lines to point to the relevant paths
> >>>># of your list of accessions file, your fasta file and your output
> >>>># fasta file
> >>>>my $acc_file = "/path/to/your/file";
> >>>>my $fasta_file_in = "/path/to/your/fasta/file";
> >>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>>>
> >>>># Use a hash to keep a record of accessions we want to find
> >>>>my %hash_of_req_acc;
> >>>>
> >>>># read all the required accessions from the file into the hash as
> >>>>
> >>>>
> >keys
> >
> >
> >>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>>>while (<ACC_FILE>) {
> >>>>my $line = $_;
> >>>>chomp $line;
> >>>>$hash_of_req_acc{$_} = 1;
> >>>>}
> >>>>close ACC_FILE;
> >>>>
> >>>>my $seqio_object_in = Bio::SeqIO->new(
> >>>>-file => $fasta_file_in,
> >>>>-format => 'fasta'
> >>>>);
> >>>>my $seqio_object_out = Bio::SeqIO->new(
> >>>>-file => $fasta_file_out,
> >>>>-format => 'fasta'
> >>>>);
> >>>>
> >>>># loop through all the sequences in the fasta file
> >>>>while (my $seq_object = $seqio_object_in->next_seq) {
> >>>># get the sequence accession for easy matching
> >>>>my $seq_acc = $seq_object->accession_number;
> >>>>
> >>>># write the sequence object to the output fasta file if we have a
> >>>>matching accession
> >>>>$seqio_object_out->write_seq($seq_object) if exists
> >>>>$hash_of_req_acc{$seq_acc};
> >>>>}
> >>>>-- end script --
> >>>>
> >>>>I haven't tested this, but it should at least get you started. Also,
> >>>>
> >>>>
> >the
> >
> >
> >>>>fasta description line in the output file may not be exactly as it
> >>>>
> >>>>
> >was
> >
> >
> >>>>in the input fasta file - if this really matters, you may need to
> >>>>
> >>>>
> >get
> >
> >
> >>>>back to us. Also, if the input fasta file is huge (many thousands of
> >>>>sequences) it may be wise to create an index of the fasta file in
> >>>>
> >>>>
> >order
> >
> >
> >>>>to speed up retrieval.
> >>>>
> >>>>You may find this page helpful:
> >>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>>>
> >>>>Anyway, hope this helps to get you started.
> >>>>Nath
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l at lists.open-bio.org
> >>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>_______________________________________________
> >>>Bioperl-l mailing list
> >>>Bioperl-l at lists.open-bio.org
> >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >=======================================================================
> >Attention: The information contained in this message and/or attachments
> >from AgResearch Limited is intended only for the persons or entities
> >to which it is addressed and may contain confidential and/or privileged
> >material. Any review, retransmission, dissemination or other use of, or
> >taking of any action in reliance upon, this information by persons or
> >entities other than the intended recipients is prohibited by AgResearch
> >Limited. If you have received this message in error, please notify the
> >sender immediately.
> >=======================================================================
> >
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jason at bioperl.org  Tue Oct  2 20:50:37 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 17:50:37 -0700
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
Message-ID: <CF48176B-CE5B-40EC-81DE-8C3114502ADE@bioperl.org>

http://bioperl.open-bio.org/wiki/ 
FAQ#How_do_I_use_Bio::Index::Fasta_and_index_on_different_ids.3F

On Oct 2, 2007, at 7:51 AM, outaleb Issame wrote:

> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
>
>
>
> outaleb Issame wrote:
>
>> thx for the help, but i got a empty output file,
>> i think its problem with matching the acc number, my fasta file  
>> look like:
>>
>> *>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to  
>> NOD3 protein
>> DDHHHU...
>>> IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> DDHHHU..
>>> IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> MMMMM..*
>>
>> and my i Accnum File look like:
>> *IPI00177321
>> IPI00453473
>>
>> *i hopt it helps to understand.*
>> *.
>>
>>
>> Nathan S. Haigh wrote:
>>
>>
>>
>>> outaleb Issame wrote:
>>>
>>>
>>>
>>>
>>>> hi,
>>>> with this file i mean, i picked out this Accession Number from
>>>> IPI-Human Dbase,they come from a fasta file,
>>>> so they re under eachother like a i a table in separate file now.
>>>> what i want is how how can i check it in the fasta File (so in the
>>>> IPI-Human FAsta File), i they re really there;
>>>> if yes please copy the entire entry of this Number (>....the  
>>>> sequence
>>>> also)in new fasta file.so that i get at the end a new
>>>> FASTA file with jus this IPI Accession Number.
>>>> thx and hope was clearly.
>>>>
>>>>
>>>>
>>>>
>>> Ok, first of all, I'd read the contents of your Accession numbers  
>>> into a
>>> hash, something like the following (this could be written in a  
>>> shorter
>>> form, but since you're a newbie I'll leave it in a longer form so  
>>> you
>>> can follow easier).
>>>
>>> -- start script --
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> # change the following three lines to point to the relevant paths
>>> # of your list of accessions file, your fasta file and your output
>>> # fasta file
>>> my $acc_file = "/path/to/your/file";
>>> my $fasta_file_in = "/path/to/your/fasta/file";
>>> my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>
>>> # Use a hash to keep a record of accessions we want to find
>>> my %hash_of_req_acc;
>>>
>>> # read all the required accessions from the file into the hash as  
>>> keys
>>> open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>> while (<ACC_FILE>) {
>>> my $line = $_;
>>> chomp $line;
>>> $hash_of_req_acc{$_} = 1;
>>> }
>>> close ACC_FILE;
>>>
>>> my $seqio_object_in = Bio::SeqIO->new(
>>> -file => $fasta_file_in,
>>> -format => 'fasta'
>>> );
>>> my $seqio_object_out = Bio::SeqIO->new(
>>> -file => $fasta_file_out,
>>> -format => 'fasta'
>>> );
>>>
>>> # loop through all the sequences in the fasta file
>>> while (my $seq_object = $seqio_object_in->next_seq) {
>>> # get the sequence accession for easy matching
>>> my $seq_acc = $seq_object->accession_number;
>>>
>>> # write the sequence object to the output fasta file if we have a
>>> matching accession
>>> $seqio_object_out->write_seq($seq_object) if exists
>>> $hash_of_req_acc{$seq_acc};
>>> }
>>> -- end script --
>>>
>>> I haven't tested this, but it should at least get you started.  
>>> Also, the
>>> fasta description line in the output file may not be exactly as  
>>> it was
>>> in the input fasta file - if this really matters, you may need to  
>>> get
>>> back to us. Also, if the input fasta file is huge (many thousands of
>>> sequences) it may be wise to create an index of the fasta file in  
>>> order
>>> to speed up retrieval.
>>>
>>> You may find this page helpful:
>>> http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>
>>> Anyway, hope this helps to get you started.
>>> Nath
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From Russell.Smithies at agresearch.co.nz  Tue Oct  2 21:05:25 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 14:05:25 +1300
Subject: [Bioperl-l] coloring of HSPs in blast panel
In-Reply-To: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk><47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de><D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz><4702BC5B.7040407@web.de>
	<62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDC73@imail.agresearch.co.nz>

Hi all,
I'm using a modified version of Lincoln's tutorial
(http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output)
and I'm colouring the HSPs by setting the -bgcolor by score with a sub
to give a similar image to that from NCBI but for some reason, my
colours are coming out wrong (see attached example)
They seem to be off by one but I can't see why.

Any ideas?

I can't be certain but I think it's only started doing this since our
BLAST upgrade to 2.2.17 a few weeks ago.

Here's the colouring code:
------------------------------------------------------------------------
-------
my $track = $panel->add_track(
                              -glyph       => 'segments',
                              -label       => 1,
                              -connector   => 'dashed',
                              -bgcolor     => sub {
                                my $feature = shift;
                                my $score = $feature->score;
			return 'red'       if $score >= 200;
                                    return 'fuchsia' if $score >= 80;
                                    return 'lime'      if $score >= 50;
			return 'blue'      if $score >= 40;
                                    return 'black';
                               },
                              -font2color  => 'gray',
                              -sort_order  => 'high_score',
                              -description => sub {
                                my $feature = shift;
                                return unless
$feature->has_tag('description');
                                my ($description) =
$feature->each_tag_value('description');
                                my $score = $feature->score;
                                "$description, score=$score";
                               },
                             );
------------------------------------------------------------------------
---------


Thanx,

Russell Smithies




=======================================================================
Attention: The information contained in this message and/or attachments
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From aaron.j.mackey at gsk.com  Tue Oct  2 21:40:14 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Tue, 2 Oct 2007 21:40:14 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
Message-ID: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>

Let me second Jason's comment that while BLAST is a great search program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with the 
FASTA package) is now vector-parallelized on most i386 architectures, it 
is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run 
BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 10:50:47 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 10:50:47 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
References: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
	<OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>

I agree that BLAST is not a very good alignment algorithm but believe
there are plenty of reasons to run BLAST, especially when placing a
contig /BAC/PAC to a genome. In those cases, fully implementation of SW
requires an unpractical matrix of n X m.   

Currently we are developing an algorithm which will run global alignment
after BLAST. Hopefully a Perl wrapper will become available next year.


Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Tuesday, October 02, 2007 9:40 PM
To: Jason Stajich
Cc: bioperl-l list; Thiago Venancio
Subject: Re: [Bioperl-l] frac_* methods

Let me second Jason's comment that while BLAST is a great search
program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
the 
FASTA package) is now vector-parallelized on most i386 architectures, it

is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run

BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From aaron.j.mackey at gsk.com  Wed Oct  3 11:53:12 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Wed, 3 Oct 2007 11:53:12 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
Message-ID: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are expected 
to occur naturally (i.e. are not an artifact of the experiment that in an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very 
good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical significance)

Please don't get me wrong, I think BLAST is an invaluable tool that fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures, it
> 
> is only about 10 times slower than BLAST for complete database searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> > Consider the -postsw option in WUBLAST as well as it will realign the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the 
> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From vebaev at gmail.com  Wed Oct  3 12:44:35 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 19:44:35 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
Message-ID: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>

Hi,
What methods should I use to draw a CG plot of a sequence (with
bio::graphics)?

Thanks

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 13:37:51 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 13:37:51 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
References: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
	<OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C36@NIHCESMLBX8.nih.gov>

I agree what you said. 

One of the reasons that we introduce 'BLAST-guided-global alignment
(NW)' is that a significant amount of clones are either of low quality,
partially sequenced, erroneously assembled, or come from non reference
strain.   

Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Wednesday, October 03, 2007 11:53 AM
To: Cui, Wenwu (NIH/NLM/NCBI) [C]
Cc: bioperl-l list; Jason Stajich; Thiago Venancio
Subject: RE: [Bioperl-l] frac_* methods

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance
for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling
algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are
expected 
to occur naturally (i.e. are not an artifact of the experiment that in
an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very

good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical
significance)

Please don't get me wrong, I think BLAST is an invaluable tool that
fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of
SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global
alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with
so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures,
it
> 
> is only about 10 times slower than BLAST for complete database
searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even
run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number
that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment.

> > Consider the -postsw option in WUBLAST as well as it will realign
the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single
HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the

> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs
individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at uiuc.edu  Wed Oct  3 14:19:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 13:19:43 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
Message-ID: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>

You should look at Bio::Graphics::Glyph::dna.  From the POD:

---------------------------

This glyph draws DNA sequences.  At high magnifications, this glyph
will draw the actual base pairs of the sequence (both strands).  At
low magnifications, the glyph will plot the GC content.  By default,
the GC calculation will use non-overlapping bins, but this can be
changed by specifying the gc_window option, in which case, a
sliding window calculation will be used.

For this glyph to work, the feature must return a DNA sequence string
in response to the dna() method. For example, you can use a
Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
like this:
     my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
     my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end  
=> 800 );
     $feature->attach_seq($dna);
     $panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used.

---------------------------

chris

On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:

> Hi,
> What methods should I use to draw a CG plot of a sequence (with
> bio::graphics)?
>
> Thanks
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From vebaev at gmail.com  Wed Oct  3 14:31:49 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 21:31:49 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
Message-ID: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>

Thanks,
I will use Bio::Graphics::Glyph::dna for the classical CG%
(this type is for C+G % or CpG)?


and if I want to draw a similar plot but for example for a % of dinucleotide
(NpN) occurrances in a sliding windiw, what should I use?


Thanks!




2007/10/3, Chris Fields <cjfields at uiuc.edu>:
>
> You should look at Bio::Graphics::Glyph::dna.  From the POD:
>
> ---------------------------
>
> This glyph draws DNA sequences.  At high magnifications, this glyph
> will draw the actual base pairs of the sequence (both strands).  At
> low magnifications, the glyph will plot the GC content.  By default,
> the GC calculation will use non-overlapping bins, but this can be
> changed by specifying the gc_window option, in which case, a
> sliding window calculation will be used.
>
> For this glyph to work, the feature must return a DNA sequence string
> in response to the dna() method. For example, you can use a
> Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
> like this:
>      my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
>      my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end
> => 800 );
>      $feature->attach_seq($dna);
>      $panel->add_track( $feature, -glyph => 'dna' );
>
> A Bio::Graphics::Feature object may also be used.
>
> ---------------------------
>
> chris
>
> On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:
>
> > Hi,
> > What methods should I use to draw a CG plot of a sequence (with
> > bio::graphics)?
> >
> > Thanks
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From dave at davemessina.com  Wed Oct  3 14:22:23 2007
From: dave at davemessina.com (Dave Messina)
Date: Wed, 3 Oct 2007 20:22:23 +0200
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <37574C6D-98BA-47A5-875E-9255377133B8@sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the  
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Panel.html

I think the example code will help you to do what you want.


Dave



From cjfields at uiuc.edu  Wed Oct  3 15:10:46 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 14:10:46 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
	<a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
Message-ID: <7B62B534-2A8C-4EAE-B956-F0FADB726195@uiuc.edu>

On Oct 3, 2007, at 1:31 PM, Vesselin Baev wrote:

> Thanks,
> I will use Bio::Graphics::Glyph::dna for the classical CG%
> (this type is for C+G % or CpG)?
>
>
> and if I want to draw a similar plot but for example for a % of  
> dinucleotide
> (NpN) occurrances in a sliding windiw, what should I use?
>
>
> Thanks!

It would be GC content, not CpG.  Not sure what you would use for  
dinucleotide content; you could look at the Bio::Graphics::Glyph::dna  
code and either subclass it for your needs (probably the best option)  
or add an extra parameter and 'rewire' the appropriate methods to do  
what you want.

chris


From dmessina at sbc.su.se  Wed Oct  3 14:55:10 2007
From: dmessina at sbc.su.se (dmessina at sbc.su.se)
Date: Wed, 3 Oct 2007 20:55:10 +0200 (CEST)
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <61118.217.213.158.117.1191437710.squirrel@mail.sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html

I think the example code will help you to do what you want.


Dave




From lzhtom at hotmail.com  Wed Oct  3 18:30:43 2007
From: lzhtom at hotmail.com (zhihuali)
Date: Wed, 3 Oct 2007 22:30:43 +0000
Subject: [Bioperl-l] Loading Blast Report in a minimal way
Message-ID: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>


Hi netters,

I'm using SearchIO to parse my blast reports. They are extremely huge, and not surprisingly, it's extremely slow and sometimes the system crashed due to memmory problem. As I can handle small reports quickly, it seems like a problem related to the way SearchIO works: it slurps the whole report into the memory and builds millions of objects.

I've checked old posts and some people used FastHitEventBuilder to build hit objects without any hsp objects. And some people suggested using tabular output of blast. But in my case I need to go to each of the hsps of each hit, parse the alignment, and gather the information needed if that hsp fits certain criteria, and then move on to the next hsp/or jump over to the next hit/ or exit the processing, according to the information I have already got. An ideal way would be to read one hsp at a time from the report to the memory.  Is there some way to modify SearchIO (or build another Search Event) to do this?

Thanks a lot!


Zhihua Li
_________________________________________________________________
?? Live Search ??????????????
http://www.live.com/?searchOnly=true


From budd at embl-heidelberg.de  Thu Oct  4 09:43:57 2007
From: budd at embl-heidelberg.de (Aidan Budd)
Date: Thu, 4 Oct 2007 15:43:57 +0200 (CEST)
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
Message-ID: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>

Hi bioperlers,

I've been trying to add info to a feature in a RichSeq object so that when 
the Seq is written in swissprot format I can put information in the final
field of the feature

FT   DOMAIN      208    392       Helicase ATP-binding.

i.e. where it says "Helicase ATP-binding."

I can control what goes in the primary field, and set the location, but 
haven't been able to work out how to add info to go in this final field.

Thanks,

Aidan

-- 
----------------------------------------------------------------------
Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
Meyerhofstr. 1, 69117 Heidelberg, Germany

URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html



From cjfields at uiuc.edu  Thu Oct  4 10:32:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 09:32:43 -0500
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
In-Reply-To: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
References: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
Message-ID: <84A6CB47-6890-476B-A375-6FCF37655330@uiuc.edu>

Try adding it as a tag value with the name 'description','note', or  
'product' (the first two are probably the best to use for most  
purposes).  There is a quick explanation here:

http://www.bioperl.org/wiki/HOWTO:Feature- 
Annotation#Building_Your_Own_Sequences

You can also do something like:

$sf->add_tag_value('description', 'Helicase ATP-binding');

See Bio::SeqFeature::Generic POD for more.

chris

On Oct 4, 2007, at 8:43 AM, Aidan Budd wrote:

> Hi bioperlers,
>
> I've been trying to add info to a feature in a RichSeq object so  
> that when
> the Seq is written in swissprot format I can put information in the  
> final
> field of the feature
>
> FT   DOMAIN      208    392       Helicase ATP-binding.
>
> i.e. where it says "Helicase ATP-binding."
>
> I can control what goes in the primary field, and set the location,  
> but
> haven't been able to work out how to add info to go in this final  
> field.
>
> Thanks,
>
> Aidan
>
> -- 
> ----------------------------------------------------------------------
> Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
> Meyerhofstr. 1, 69117 Heidelberg, Germany
>
> URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cain.cshl at gmail.com  Thu Oct  4 11:08:52 2007
From: cain.cshl at gmail.com (Scott Cain)
Date: Thu, 04 Oct 2007 11:08:52 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
Message-ID: <1191510532.2787.16.camel@localhost.localdomain>

Hi Chris,

I think adding the type=MYISAM is the right thing to do; please go ahead
and commit it.

Scott



On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
> Just thought I would forward this on to the GBrowse list as well in  
> case anyone has run into the same problem.  The issue pops up when  
> using bioperl from CVS and appears to be related to a fix Lincoln  
> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using  
> FULLTEXT, which only works for MyISAM currently.
> 
> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE  
> queries does work when InnoDB is set to the default.  Should I go  
> ahead and commit?
> 
> chris
> 
> Begin forwarded message:
> 
> > I'm getting the following error on my local MySQL (v 5.0.41) with
> > bp_seqfeature_load:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: The used table type doesn't support FULLTEXT indexes
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /Library/
> > Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
> > STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
> > Bio/DB/SeqFeature/Store.pm:382
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
> > 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
> > STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
> > SeqFeature/Store.pm:345
> > STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
> > -------------------------------------------
> >
> > The default setting for storage is InnoDB; switching to MyISAM fixes
> > the issue.  Should we specify TYPE = MyISAM with the various CREATE
> > TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
> > safe side?
> >
> > chris
> 
> 
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



From cjfields at uiuc.edu  Thu Oct  4 11:14:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 10:14:37 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <1191510532.2787.16.camel@localhost.localdomain>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
	<1191510532.2787.16.camel@localhost.localdomain>
Message-ID: <9DEFB5C1-6F79-465B-8FB4-68305C53E427@uiuc.edu>

Done.  If we run into issues and need to roll back let me know.

chris

On Oct 4, 2007, at 10:08 AM, Scott Cain wrote:

> Hi Chris,
>
> I think adding the type=MYISAM is the right thing to do; please go  
> ahead
> and commit it.
>
> Scott
>
>
>
> On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
>> Just thought I would forward this on to the GBrowse list as well in
>> case anyone has run into the same problem.  The issue pops up when
>> using bioperl from CVS and appears to be related to a fix Lincoln
>> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using
>> FULLTEXT, which only works for MyISAM currently.
>>
>> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE
>> queries does work when InnoDB is set to the default.  Should I go
>> ahead and commit?
>>
>> chris
>>
>> Begin forwarded message:
>>
>>> I'm getting the following error on my local MySQL (v 5.0.41) with
>>> bp_seqfeature_load:
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: The used table type doesn't support FULLTEXT indexes
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database / 
>>> Library/
>>> Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
>>> STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
>>> Bio/DB/SeqFeature/Store.pm:382
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
>>> 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
>>> STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
>>> SeqFeature/Store.pm:345
>>> STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
>>> -------------------------------------------
>>>
>>> The default setting for storage is InnoDB; switching to MyISAM fixes
>>> the issue.  Should we specify TYPE = MyISAM with the various CREATE
>>> TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
>>> safe side?
>>>
>>> chris
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.net email is sponsored by: Microsoft
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>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
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>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Thu Oct  4 15:30:48 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 14:30:48 -0500
Subject: [Bioperl-l] blastxml oddity
Message-ID: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>

Just noticed an oddity from BLASTXML output from the NCBI server; I'm  
cc'ing this to NCBI so maybe they can explain.  BTW, the following  
doesn't occur via URLAPI.

When running a standard BLAST query using the NCBI web page, if  
requesting XML output after the run I get the entire query seq masked  
out and no midline.  This occurs with all default settings except  
output type (set to XML).  Can anyone replicate this?

Here's a sample:

<Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
               <Hsp_bit-score>320.472</Hsp_bit-score>
               <Hsp_score>820</Hsp_score>
               <Hsp_evalue>2.17708e-86</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>181</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
               <Hsp_hit-to>181</Hsp_hit-to>
               <Hsp_query-frame>0</Hsp_query-frame>
               <Hsp_hit-frame>0</Hsp_hit-frame>
               <Hsp_identity>0</Hsp_identity>
               <Hsp_positive>0</Hsp_positive>
               <Hsp_gaps>0</Hsp_gaps>
               <Hsp_align-len>181</Hsp_align-len>
                
<Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
                
<Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPV 
TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAV 
LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
                
<Hsp_midline>                                                            
                                                                         
                                                    </Hsp_midline>
             </Hsp>
           </Hit_hsps>



<notblast>chris</notblast>


From cjfields at uiuc.edu  Thu Oct  4 16:36:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 15:36:25 -0500
Subject: [Bioperl-l] blastxml oddity
In-Reply-To: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
References: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
Message-ID: <86D7D694-1ACF-4D91-9FEC-0FEA21C1B689@uiuc.edu>

NCBI's BLAST team is working on this; it occurs only if you use an GI/ 
accession instead of a full sequence, and only for XML.

chris

On Oct 4, 2007, at 2:30 PM, Chris Fields wrote:

> Just noticed an oddity from BLASTXML output from the NCBI server; I'm
> cc'ing this to NCBI so maybe they can explain.  BTW, the following
> doesn't occur via URLAPI.
>
> When running a standard BLAST query using the NCBI web page, if
> requesting XML output after the run I get the entire query seq masked
> out and no midline.  This occurs with all default settings except
> output type (set to XML).  Can anyone replicate this?
>
> Here's a sample:
>
> <Hit_hsps>
>              <Hsp>
>                <Hsp_num>1</Hsp_num>
>                <Hsp_bit-score>320.472</Hsp_bit-score>
>                <Hsp_score>820</Hsp_score>
>                <Hsp_evalue>2.17708e-86</Hsp_evalue>
>                <Hsp_query-from>1</Hsp_query-from>
>                <Hsp_query-to>181</Hsp_query-to>
>                <Hsp_hit-from>1</Hsp_hit-from>
>                <Hsp_hit-to>181</Hsp_hit-to>
>                <Hsp_query-frame>0</Hsp_query-frame>
>                <Hsp_hit-frame>0</Hsp_hit-frame>
>                <Hsp_identity>0</Hsp_identity>
>                <Hsp_positive>0</Hsp_positive>
>                <Hsp_gaps>0</Hsp_gaps>
>                <Hsp_align-len>181</Hsp_align-len>
>
> <Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
>
> <Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGN 
> PV
> TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQL 
> AV
> LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
>
> <Hsp_midline>
>
>                                                     </Hsp_midline>
>              </Hsp>
>            </Hit_hsps>
>
>
>
> <notblast>chris</notblast>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 15:35:25 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 14:35:25 -0500
Subject: [Bioperl-l] bp_search2gff.pl
Message-ID: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>

Hello,

I have been playing with the bp_search2gff.pl script (on HEAD of
bioperl-live).    There are a couple of issues I was wondering about.

One is the ID that gets generated for a match feature when the --match
option is set.   The ID is  set to the ID of the query sequence.  This
can be problematic if you are representing the query sequence and the
blast hit in the same gff file.  When using the resultant gff file for
loading into Chado, it also creates a problem if you have more than
one hit for a given query sequence, for example if you ran two
different analyses that each had a hit for a given query.  Would it be
possible to have an option to create a unique ID for match features.
One suggestion could be to create an ID based on the ID of the query +
the id of the hit + the source

As long as two different analyses were loaded as different sources,
this would ensure unique IDs for the match features.


Also, is there a reason for writing the Target string as

Target=Sequence:SOME_ID

as opposed to

Target=SOME_ID


The latter seems a little more in line with the gff3 spec and plays a
little nicer with the GMOD tools.

Thanks for looking into this.

Eric


From cjfields at uiuc.edu  Fri Oct  5 15:51:20 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 5 Oct 2007 14:51:20 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
Message-ID: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>

We might want to file this as a bug so we can track it.

The core devs have been mulling over the state of GFF/GFF3 in  
BioPerl; proper handling of any SearchIO data is certainly included  
in that.  I believe some road forward is to be planned soon (after  
Genome Informatics).

chris

On Oct 5, 2007, at 2:35 PM, Eric Just wrote:

> Hello,
>
> I have been playing with the bp_search2gff.pl script (on HEAD of
> bioperl-live).    There are a couple of issues I was wondering about.
>
> One is the ID that gets generated for a match feature when the --match
> option is set.   The ID is  set to the ID of the query sequence.  This
> can be problematic if you are representing the query sequence and the
> blast hit in the same gff file.  When using the resultant gff file for
> loading into Chado, it also creates a problem if you have more than
> one hit for a given query sequence, for example if you ran two
> different analyses that each had a hit for a given query.  Would it be
> possible to have an option to create a unique ID for match features.
> One suggestion could be to create an ID based on the ID of the query +
> the id of the hit + the source
>
> As long as two different analyses were loaded as different sources,
> this would ensure unique IDs for the match features.
>
>
> Also, is there a reason for writing the Target string as
>
> Target=Sequence:SOME_ID
>
> as opposed to
>
> Target=SOME_ID
>
>
> The latter seems a little more in line with the gff3 spec and plays a
> little nicer with the GMOD tools.
>
> Thanks for looking into this.
>
> Eric
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 16:06:48 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 15:06:48 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
	<54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
Message-ID: <fa1fe35c0710051306v1636d6er6f02133f4ecef91c@mail.gmail.com>

Thanks Chris, I'll enter it as a bug.  I'd also be glad to help on the
solution if there is an executive decision made at some point.



On 10/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
> We might want to file this as a bug so we can track it.
>
> The core devs have been mulling over the state of GFF/GFF3 in
> BioPerl; proper handling of any SearchIO data is certainly included
> in that.  I believe some road forward is to be planned soon (after
> Genome Informatics).
>
> chris
>
> On Oct 5, 2007, at 2:35 PM, Eric Just wrote:
>
> > Hello,
> >
> > I have been playing with the bp_search2gff.pl script (on HEAD of
> > bioperl-live).    There are a couple of issues I was wondering about.
> >
> > One is the ID that gets generated for a match feature when the --match
> > option is set.   The ID is  set to the ID of the query sequence.  This
> > can be problematic if you are representing the query sequence and the
> > blast hit in the same gff file.  When using the resultant gff file for
> > loading into Chado, it also creates a problem if you have more than
> > one hit for a given query sequence, for example if you ran two
> > different analyses that each had a hit for a given query.  Would it be
> > possible to have an option to create a unique ID for match features.
> > One suggestion could be to create an ID based on the ID of the query +
> > the id of the hit + the source
> >
> > As long as two different analyses were loaded as different sources,
> > this would ensure unique IDs for the match features.
> >
> >
> > Also, is there a reason for writing the Target string as
> >
> > Target=Sequence:SOME_ID
> >
> > as opposed to
> >
> > Target=SOME_ID
> >
> >
> > The latter seems a little more in line with the gff3 spec and plays a
> > little nicer with the GMOD tools.
> >
> > Thanks for looking into this.
> >
> > Eric
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


From bix at sendu.me.uk  Sun Oct  7 08:40:44 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sun, 07 Oct 2007 13:40:44 +0100
Subject: [Bioperl-l] Bio::FeatureIO::gff bug?
In-Reply-To: <5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
References: <46F784EB.9050507@sendu.me.uk>	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>	<46F7B9A1.9080206@sendu.me.uk>	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>	<46F8DC34.6020908@sendu.me.uk>	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
Message-ID: <4708D3CC.60909@sendu.me.uk>

Hilmar Lapp wrote:
> On Sep 28, 2007, at 5:34 PM, Chris Fields wrote:
> 
>> The section writing the gff header info in _initialize() checks the  
>> file specifically for '>' prior to output; I think Sendu planned on  
>> changing that to use mode() instead.
> 
> What if we pass in a file handle?

mode() is supposed to work in that instance as well: it sees if the file 
handle is writable.


From er at xs4all.nl  Sun Oct  7 10:13:45 2007
From: er at xs4all.nl (Erik)
Date: Sun, 7 Oct 2007 16:13:45 +0200 (CEST)
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <4708D3CC.60909@sendu.me.uk>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
Message-ID: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>


http://bioperl.org/
http://www.bioperl.org/wiki/Main_Page

seems to be having problems - I only receive an empty
screen...

regards,
Erik






From cjfields at uiuc.edu  Sun Oct  7 17:16:02 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 7 Oct 2007 16:16:02 -0500
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
	<12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
Message-ID: <EBD33439-22B4-44FC-A60C-D3EC653EC363@uiuc.edu>

Should be back up.  Jason was running some wiki updates.

chris

On Oct 7, 2007, at 9:13 AM, Erik wrote:

>
> http://bioperl.org/
> http://www.bioperl.org/wiki/Main_Page
>
> seems to be having problems - I only receive an empty
> screen...
>
> regards,
> Erik




From alan at tll.org.sg  Mon Oct  8 01:02:45 2007
From: alan at tll.org.sg (alan)
Date: Mon, 8 Oct 2007 13:02:45 +0800
Subject: [Bioperl-l] exonerate
In-Reply-To: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
	<73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
Message-ID: <F5563806-FCAE-46C6-8EE3-3C55FCDD906C@tll.org.sg>

Hi Chris,

On 02 Oct 2007, at 11:03 PM, Chris Fields wrote:

> One option is to try running $run->cleanup() after you finish  
> parsing, which gets rid of the tempfiles on each run.
>

I tried this option in the past but it did not change anything.

I found a temporary solution: I am using tcsh and the ulimit for open  
files (descriptors) was set to 256. I changed this limit to 2000 and  
I got my code to run to completion. This imply that I am  
circumventing the real problem of open files. I will continue to look  
at the file closing step in bioperl but the ulimit or limit option  
allows me to get a quick work around for now.

for bash shell (ulimit -n [number])

for tcsh shell (limit descriptors [number])

alan




> chris
>
> On Sep 30, 2007, at 8:53 PM, alan wrote:
>
>> Hi,
>>
>>
>>>> I am calling exonerate.pm within my script while attempting to
>>>> align cDNA  to multiple genomic fragments. After processing about
>>>> 120+ genomic fragments my code crashes with the following error:
>>>>
>>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>>> aborting...
>>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>>
>>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>>> routine yet I get the error message about "too many open files".
>>>> Any suggestions on how I should be closing these files?
>>>>
>>>>
>>>> Extract from my code that runs exonerate is listed below.
>>>>
>>>> foreach my $f(@files) {
>>>>   next unless (-f  "$dir/$f");
>>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>>   my $query_obj = $q_in->next_seq();
>>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>>> format=>"Fasta");
>>>>   my $target_obj = $target_in->next_seq();
>>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>>
>>>>   [code for parsing the data.......]
>>>>
>>>>   $exonerate_io->close; #tried this line out of desperation but it
>>>> did not help :-)
>>>> }
>>>>
>>>> thanks
>>>> alan
>
>



From bix at sendu.me.uk  Mon Oct  8 05:54:15 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Mon, 08 Oct 2007 10:54:15 +0100
Subject: [Bioperl-l] Loading Blast Report in a minimal way
In-Reply-To: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
References: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
Message-ID: <4709FE47.3040103@sendu.me.uk>

zhihuali wrote:
> Hi netters,
> 
> I'm using SearchIO to parse my blast reports. They are extremely 
> huge, and not surprisingly, it's extremely slow and sometimes the 
> system crashed due to memmory problem. As I can handle small reports 
> quickly, it seems like a problem related to the way SearchIO works: 
> it slurps the whole report into the memory and builds millions of 
> objects.
> 
> I've checked old posts and some people used FastHitEventBuilder to 
> build hit objects without any hsp objects. And some people suggested 
> using tabular output of blast. But in my case I need to go to each of
>  the hsps of each hit, parse the alignment, and gather the
> information needed if that hsp fits certain criteria, and then move
> on to the next hsp/or jump over to the next hit/ or exit the
> processing, according to the information I have already got. An ideal
> way would be to read one hsp at a time from the report to the memory.
> Is there some way to modify SearchIO (or build another Search Event)
> to do this?

Use Bio::SearchIO::blast_pull

(ie.
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                             -file =>
't/data/new_blastn.txt');
)

It doesn't yet support all kinds of Blast report, however. Let me know
how you get on.

Cheers,
Sendu.


From bix at sendu.me.uk  Wed Oct 10 10:09:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 15:09:24 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
Message-ID: <470CDD14.4000005@sendu.me.uk>

Once I store a feature like so:

$db = Bio::DB::SeqFeature::Store->new( # mysql );
$db->new_feature(-primary_tag  => 'X',
                  -seq_id       => 'Y',
                  #...
		 -source       => 'Z');

How do I search for it again? I could have sworn that in the past the 
source somehow became one of the feature's attributes so that I could do:

@feats = $db->features(-attributes => {source => 'Z'});

(Or does/did some other feature-related module store source as an 
attribute, and in the past I stored those features in my db?)

The obvious isn't implemented:

@feats = $db->features(-source => 'Z');

Looking at the code I see I can do type and source at the same time:

@feats = $db->features(-type => 'X:Z');

which works, but how do I just search for all Z, regardless of type?


From lstein at cshl.edu  Wed Oct 10 10:20:33 2007
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 10 Oct 2007 10:20:33 -0400
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <470CDD14.4000005@sendu.me.uk>
References: <470CDD14.4000005@sendu.me.uk>
Message-ID: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>

Hi Sendu,

This may be a glaring omission on my part. Try searching for:

 @feats = $db->get_features_by_type(":$source");

Remove the colon in front of $source.

This might not work, but give it a try.

Lincoln

On 10/10/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> Once I store a feature like so:
>
> $db = Bio::DB::SeqFeature::Store->new( # mysql );
> $db->new_feature(-primary_tag  => 'X',
>                   -seq_id       => 'Y',
>                   #...
>                  -source       => 'Z');
>
> How do I search for it again? I could have sworn that in the past the
> source somehow became one of the feature's attributes so that I could do:
>
> @feats = $db->features(-attributes => {source => 'Z'});
>
> (Or does/did some other feature-related module store source as an
> attribute, and in the past I stored those features in my db?)
>
> The obvious isn't implemented:
>
> @feats = $db->features(-source => 'Z');
>
> Looking at the code I see I can do type and source at the same time:
>
> @feats = $db->features(-type => 'X:Z');
>
> which works, but how do I just search for all Z, regardless of type?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


From bix at sendu.me.uk  Wed Oct 10 11:10:45 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 16:10:45 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
References: <470CDD14.4000005@sendu.me.uk>
	<6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
Message-ID: <470CEB75.7050804@sendu.me.uk>

Lincoln Stein wrote:
> Hi Sendu,
> 
> This may be a glaring omission on my part. Try searching for:
> 
>  @feats = $db->get_features_by_type(":$source");
> 
> Remove the colon in front of $source.

It doesn't, unfortunately, colon or not. get_features_by_type is 
implemented using _features(-type => ), just like features(). In any 
case, I'm searching for multiple things at the same time so need to use 
the features() method.


The following patch seems to do the job in my hands, allowing:

@feats = $db->features(-source => 'Z');
to work as expected.

Also, we now have:
@feats = $db->features(-type => 'X', -source => 'Z');
as a nicer (ie. matching the syntax the user used to create the feature 
in the first place) alternative to:
@feats = $db->features(-type => 'X:Y');

Of course, this patch is specific to the mysql implementation. You may 
want to check it over to see if it is sane, see if there is a cleaner 
way to do it, or see if there's a more general way to apply it to all 
implementations.


RCS file: 
/home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.33
diff -r1.33 mysql.pm
724c724,725
<       $iterator
---
 >       $iterator,
 >       $sources
731a733
 >             ['SOURCE','SOURCES']
760c762,785
<
---
 >
 >   if (defined($sources)) {
 >     my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources);
 >     if (defined($types)) {
 >         my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types);
 >         my @final_types;
 >         foreach my $type (@types) {
 >             # *** not sure what to do if user supplies both -source
 >             #     and -type where the type includes a source!
 >             if ($type =~ /:/) {
 >                 push(@final_types, $type);
 >             }
 >             else {
 >                 foreach my $source (@sources) {
 >                     push(@final_types, $type.':'.$source);
 >                 }
 >             }
 >         }
 >         $types = \@final_types;
 >     }
 >     else {
 >         $types = [map { ':'.$_ } @sources];
 >     }
 >   }
939,940c964,971
<       push @matches,"tl.tag=?";
<       push @args,"$primary_tag:$source_tag";
---
 >       if (length($primary_tag)) {
 >         push @matches,"tl.tag=?";
 >         push @args,"$primary_tag:$source_tag";
 >       }
 >       else {
 >         push @matches,"tl.tag LIKE ?";
 >         push @args,"%:$source_tag";
 >       }


From bix at sendu.me.uk  Thu Oct 11 06:40:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 11 Oct 2007 11:40:24 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
Message-ID: <470DFD98.4030603@sendu.me.uk>

Following Chris's changes to SF::Annotated et al., lots of existing user 
code breaks. Also, at least some Bioperl code breaks, notably 
Bio::DB::SeqFeature::Store, which in mysql mode calls 
_get_location_and_bin() which calls $feature->seq_id which ends up 
storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
the database, instead of an actual sequence id (which completely breaks 
searching by seq_id).

I propose its API be changed to be more consistent with 
Bio::SeqFeatureI, eg. instead of:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : a Bio::Annotation::SimpleValue object representing the
            seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

we have:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : string representing the seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

This would apply to seq_id(), name(), type(), source(), phase() and 
frame(). Internally the implementation could store the string value in a 
SimpleValue object.


However, I'm obviously missing something, because I have no idea what 
the justification for returning SimpleValue objects was in the first 
place (what other module needs them?), nor even what the point of 
SimpleValue objects is in the first place.


From ULNJUJERYDIX at spammotel.com  Thu Oct 11 07:32:33 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Thu, 11 Oct 2007 19:32:33 +0800
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>

wow thanks for the replies!
I have gotten the answer from the blast help

Subsequence range can be specified by the ?L parameter. Please refer
to this web document for more information:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node60.html



Other end-user oriented standalone blast documents are at:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/


but will try this method as well to see which works better.

cheers!
kevin

There is a script that comes with the bioperl core distribution,

> bp_split_seq.pl, which does this.  Here's the CVS location:
>
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
> scripts/seq/?cvsroot=bioperl
>
> chris
>



From cjfields at uiuc.edu  Thu Oct 11 09:49:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 08:49:59 -0500
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
	<5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
Message-ID: <F866A1FE-EBC7-4722-A3E6-2F4A10FD0373@uiuc.edu>

Yep, started using this myself for mapping old predicted CDS onto new  
assemblies using BLASTX.  Works very well, particularly since it  
retains the seq position on hits, where using bp_slit_seq would  
require mapping to the correct coordinates.

chris

On Oct 11, 2007, at 6:32 AM, Kevin Lam wrote:

> wow thanks for the replies!
> I have gotten the answer from the blast help
>
> Subsequence range can be specified by the ?L parameter. Please refer
> to this web document for more information:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ 
> blastall_node60.html
>
>
>
> Other end-user oriented standalone blast documents are at:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
>
>
> but will try this method as well to see which works better.
>
> cheers!
> kevin
>
> There is a script that comes with the bioperl core distribution,
>
>> bp_split_seq.pl, which does this.  Here's the CVS location:
>>
>> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
>> scripts/seq/?cvsroot=bioperl
>>
>> chris
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From cjfields at uiuc.edu  Thu Oct 11 10:19:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 09:19:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>


On Oct 11, 2007, at 5:40 AM, Sendu Bala wrote:

> Following Chris's changes to SF::Annotated et al., lots of existing  
> user
> code breaks. Also, at least some Bioperl code breaks, notably
> Bio::DB::SeqFeature::Store, which in mysql mode calls
> _get_location_and_bin() which calls $feature->seq_id which ends up
> storing something like 'Bio::Annotation::SimpleValue=HASH 
> (0x1f435d0)' in
> the database, instead of an actual sequence id (which completely  
> breaks
> searching by seq_id).
>
> I propose its API be changed to be more consistent with
> Bio::SeqFeatureI, eg. instead of:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> we have:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> This would apply to seq_id(), name(), type(), source(), phase() and
> frame(). Internally the implementation could store the string value  
> in a
> SimpleValue object.

Agreed.  It would be easy to change over but we need to also make  
sure FeatureIO fixes are in place.  In reality all FeatureIO methods  
should be changed over to recognize any SeqFeatureI or (if we retain  
it) the stricter TypedSeqFeatureI.  Using only Bio::SF::Annotated  
limits other more lightweight implementations.  I simply haven't had  
time to work on it yet due to $job; if you want to make the necessary  
changes you are more than welcome; the few tests I found I moved into  
SeqFeatAnnotated.t, which likely expects the wrong behavior.

> However, I'm obviously missing something, because I have no idea what
> the justification for returning SimpleValue objects was in the first
> place (what other module needs them?), nor even what the point of
> SimpleValue objects is in the first place.

I believe it was to ensure any data stored or retrieved was strongly  
typed (i.e. scalars in SimpleValue, dbxrefs in DBLink, comments in  
Comment, etc).  Since B::SF::Generic is also AnnotatableI, it can  
store a mix of scalars in methods as well as Bio::Annotation data;  
this class attempts to lump them all together as Bio::Annotation in a  
Collection in a strongly typed, uniform way.  Hilmar's  
Bio::SF::AnnotationAdaptor frankly does a better job of describing  
the reasoning behind this and is more flexible; I use that now for  
typing via feature(), though I just realized it should be changed to  
be a singleton instance per class (oops!).

B::SF::A violated the SeqFeatureI interface from the get-go by  
returning objects.  To trick it's way around the issue it used  
overloading so that calling it in some contexts (print, comparison)  
returned a string or value; removing the overloads unmasked that  
behavior.  To me an object returned (regardless of overloading) is  
still an object and not a scalar, and still violates the interface  
methods where scalars are expected.  I can't fault the authors  
involved completely since the idea was to radically change the way  
SFs/Annotation worked together, but the implementation was never  
completed so I rolled it back and limited typing to B::SF::A until  
something else can be worked out.

Personally I think it's too 'heavy' and other options should be  
explored, such as abstracting out the type checking into a separate  
utility class which FeatureIO can use on any SeqFeatureI (TypeMapper  
does something like this for the primary_tag()).

chris


From jaudall at gmail.com  Thu Oct 11 20:51:50 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 18:51:50 -0600
Subject: [Bioperl-l] Hsp_hit-from
Message-ID: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>

Bioperl -

I'm parsing an XML blast output using SearchIO and the usual fields seem to
work fine.

print $result->query_name . "\t" . $hit->name . "\n";

However, I'm curious as to the 5' position distribution of my hits.  So I'd
like to access this data field <Hsp_query-from> in the xml output file.  I
searched both the mailing lists and the Search docs including
*Bio::Search::Hit::HitI,
*but I can't seem to find an example of someone accessing this data field.
Perhaps, I missed it, but do any of you have any suggestions as to how I
might get at the <Hsp_query-from> for each hit?  Thanks.

Josh


From cjfields at uiuc.edu  Thu Oct 11 22:14:21 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 21:14:21 -0500
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
Message-ID: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>


On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:

> Bioperl -
>
> I'm parsing an XML blast output using SearchIO and the usual fields  
> seem to
> work fine.
>
> print $result->query_name . "\t" . $hit->name . "\n";
>
> However, I'm curious as to the 5' position distribution of my  
> hits.  So I'd
> like to access this data field <Hsp_query-from> in the xml output  
> file.  I
> searched both the mailing lists and the Search docs including
> *Bio::Search::Hit::HitI,
> *but I can't seem to find an example of someone accessing this data  
> field.
> Perhaps, I missed it, but do any of you have any suggestions as to  
> how I
> might get at the <Hsp_query-from> for each hit?  Thanks.
>
> Josh

That tag (as well as related tags) are mapped to start(), end(), and  
strand() in the HSP objects.  To access the relevant data pass  
'query' or 'hit' to the method, so for the query use: $hsp->start 
('query') or $hsp->end('query').

Note: in BioPerl all location starts are less than the end (strand  
determines the orientation for DNA).

chris


From hlapp at gmx.net  Thu Oct 11 23:25:22 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 11 Oct 2007 23:25:22 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>


On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:

> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.

type() and source() should be ontology-typed in a TypedSeqFeatureI  
(and therefore be instances of Bio::Annotation::OntologyTerm, not  
Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't  
understand what the benefit of typing seq_id() any stronger than a  
string would be.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From jaudall at gmail.com  Thu Oct 11 23:34:18 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 20:34:18 -0700
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
	<162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
Message-ID: <52cea20c0710112034k60f14241k8884a07d26939e86@mail.gmail.com>

Thanks!  For some reason I was stuck on the idea that it would be different
with an xml file.  I'm glad it's not ...

On 10/11/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:
>
> > Bioperl -
> >
> > I'm parsing an XML blast output using SearchIO and the usual fields
> > seem to
> > work fine.
> >
> > print $result->query_name . "\t" . $hit->name . "\n";
> >
> > However, I'm curious as to the 5' position distribution of my
> > hits.  So I'd
> > like to access this data field <Hsp_query-from> in the xml output
> > file.  I
> > searched both the mailing lists and the Search docs including
> > *Bio::Search::Hit::HitI,
> > *but I can't seem to find an example of someone accessing this data
> > field.
> > Perhaps, I missed it, but do any of you have any suggestions as to
> > how I
> > might get at the <Hsp_query-from> for each hit?  Thanks.
> >
> > Josh
>
> That tag (as well as related tags) are mapped to start(), end(), and
> strand() in the HSP objects.  To access the relevant data pass
> 'query' or 'hit' to the method, so for the query use: $hsp->start
> ('query') or $hsp->end('query').
>
> Note: in BioPerl all location starts are less than the end (strand
> determines the orientation for DNA).
>
> chris
>


From pellet at cervi-lyon.inserm.fr  Fri Oct 12 04:48:06 2007
From: pellet at cervi-lyon.inserm.fr (Johann PELLET)
Date: Fri, 12 Oct 2007 10:48:06 +0200
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
Message-ID: <470F34C6.9050800@cervi-lyon.inserm.fr>

Hi,
I have two questions:
First, I have problems for example with this genbank entry: NC_008210. 
Indeed, for one CDS, the location is : 
join(161990..162784,complement(88222..88806),complement(86666..87448))

When I parse a genbank file with this entry.

my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
                               -file => $input_file);

while( my $seq = $seq_in->next_seq() ) {
    my @features = $seq->get_SeqFeatures();
    for ( my $i =0; $i < scalar @features; $i++ ){
        my $feat = @features[$i];
         if ( $feat->primary_tag eq 'CDS' ){


             my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
             my $seq_CDS=$seq_CDS_obj->seq;


I have this error:
Can't call method "isa" without a package or object reference at ....

Secondly, When location is like: 
join(complement(AY421753.1:1..6),complement(3813..5699)) I know that we 
must use spliced_seq with the argument db, but it's not working.
      my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
How can we valid a Bio::DB::RandomAccessI?

Thanks

-- 
Johann Pellet
phone (work): +33(0)4 37282352
E-mail:    pellet at cervi-lyon.inserm.fr
Centre d'Etudes et de Recherche en Virologie et Immunologie
INSERM U503
21, Avenue Tony Garnier
69365 Lyon cedex 07 France 



From bix at sendu.me.uk  Fri Oct 12 09:04:25 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 14:04:25 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
Message-ID: <470F70D9.6030108@sendu.me.uk>

Chris Fields wrote:
> B::SF::A violated the SeqFeatureI interface from the get-go by returning 
> objects.

On that note, the other major change I'd propose is to make B::SF::A 
inherit from B::SeqFeatureI. I really need this for RangeI methods.

Or, heck, since it's such a mess, do we just want to drop Annotated 
entirely and recommend using AnnotationAdaptor with Generic? What does 
Annotated bring to the table?

(Since its one of the modules added in 1.5 I think it's fair to drop it 
from the 1.6 release: stuff that doesn't work can and should be moved 
out of the path of stable branches.)


From hlapp at gmx.net  Fri Oct 12 10:46:19 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 10:46:19 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>


On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

My recollection may be wrong since it's been quite a while, but I  
believe one of the main motivations was to reflect the ontology- 
typing of feature type and other annotation that GFF3 requires.

The motivation of AnnotationAdaptor was primarily to provide a view  
onto a SeqFeatureI that makes tag/value annotation transparently  
appear as B:AnnotatableI and B:AnnotationCollectionI compliant, mixed  
in with the annotation collection that B:S:Generic may hold already.

Although sometimes confused, these are not the same motivations.  
AnnotationAdaptor provides a view - you use it when that's the view  
you need on a SeqFeatureI object you have in hand. For example,  
bioperl-db uses it so it doesn't have to bother about how to de/ 
serialize tag/value pairs, when it knows how to de/serialize  
annotation collections already from sequence objects.  
AnnotationAdaptor doesn't care whether the primary_tag, or any other  
tag, is from an ontology.

>
> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
>> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

I agree with that unless someone steps up and makes it work.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From cjfields at uiuc.edu  Fri Oct 12 10:49:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 09:49:25 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>


On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> B::SF::A violated the SeqFeatureI interface from the get-go by  
>> returning
>> objects.
>
> On that note, the other major change I'd propose is to make B::SF::A
> inherit from B::SeqFeatureI. I really need this for RangeI methods.

It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,  
which itself is-a SeqFeatureI.  We might want to run the tests on  
that but a quick inheritance tree check on my ends seems to confirm  
that.  If the Range methods don't work there may be an issue within  
B::SF::A (which wouldn't surprise me).

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

I agree about getting rid of B::SF::A, but if we do we will need a  
reasonable replacement for SFs in FeatureIO, as it relies directly on  
B::SF::A.  As for AnnotationAdaptor, it runs a simple type check on  
the data within a SF but I don't think it checks the primary_tag  
against the current SO or other ontologies for GFF3.

My inclination is to hold back FeatureIO from 1.6 and retool it to  
use any SeqFeatureI, then find a way to optionally type a  
SeqFeatureI.  This is so we don't have to completely retool every  
Bio::Tools* class.  For instance:

# a SF::Generic with a few type-related methods added to SeqFeatureI
$sf->type(); # undef, not checked
$sf->ontology_term; # undef, not checked

# call proper methods to type check
# or use a utility class dedicated to this function

$sf->validate_sf_type(); # or...
$util->validate_sf_type($sf);

$sf->type(); # returns string
$sf->ontology_term; # returns Bio::Ontology::TermI

My feeling is that FeatureIO needs the ability to validate SFs and  
maybe have it turned on by default, but it should be optional.  The  
TermI would be a Bio::Annotation::OntologyTerm if we insist on using  
AnnotationAdaptor for richly typed SFs, which may not be necessary  
(Hilmar?).  As not all SeqFeatureI are also AnnotatableI that should  
probably be optional anyway.

> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

Agreed.  If anyone wants to use experimental stuff they can always  
use bioperl-live.

chris


From cjfields at uiuc.edu  Fri Oct 12 11:02:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 10:02:03 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
Message-ID: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>


On Oct 12, 2007, at 9:46 AM, Hilmar Lapp wrote:

>
> On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:
>
>> Or, heck, since it's such a mess, do we just want to drop Annotated
>> entirely and recommend using AnnotationAdaptor with Generic? What  
>> does
>> Annotated bring to the table?
>
> My recollection may be wrong since it's been quite a while, but I  
> believe one of the main motivations was to reflect the ontology- 
> typing of feature type and other annotation that GFF3 requires.
>
> The motivation of AnnotationAdaptor was primarily to provide a view  
> onto a SeqFeatureI that makes tag/value annotation transparently  
> appear as B:AnnotatableI and B:AnnotationCollectionI compliant,  
> mixed in with the annotation collection that B:S:Generic may hold  
> already.
>
> Although sometimes confused, these are not the same motivations.  
> AnnotationAdaptor provides a view - you use it when that's the view  
> you need on a SeqFeatureI object you have in hand. For example,  
> bioperl-db uses it so it doesn't have to bother about how to de/ 
> serialize tag/value pairs, when it knows how to de/serialize  
> annotation collections already from sequence objects.  
> AnnotationAdaptor doesn't care whether the primary_tag, or any  
> other tag, is from an ontology.

Ah, forgot it returns a Collection.  It doesn't modify the SF I assume?

>> (Since its one of the modules added in 1.5 I think it's fair to  
>> drop it
>>> from the 1.6 release: stuff that doesn't work can and should be  
>>> moved
>> out of the path of stable branches.)
>
> I agree with that unless someone steps up and makes it work.
>
> 	-hilmar

Making it work may be more trouble than it's worth.  Sincerest  
apologies to the authors of the module but we should probably  
deprecate it in favor of something more flexible when we can.  It's  
obvious anything reliant on it would also have to be dropped.

The GMOD meeting is a few weeks away, where I assume some things will  
be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth  
saving; maybe retooling it would be in our best interests, but it  
needs a decent roadmap to move forward.

chris


From bix at sendu.me.uk  Fri Oct 12 11:06:30 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 16:06:30 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
Message-ID: <470F8D76.8080101@sendu.me.uk>

Chris Fields wrote:
> 
> On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:
> 
>> Chris Fields wrote:
>>> B::SF::A violated the SeqFeatureI interface from the get-go by
>>> returning objects.
>> 
>> On that note, the other major change I'd propose is to make
>> B::SF::A inherit from B::SeqFeatureI. I really need this for RangeI
>> methods.
> 
> It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,
> which itself is-a SeqFeatureI.  We might want to run the tests on
> that but a quick inheritance tree check on my ends seems to confirm
> that.  If the Range methods don't work there may be an issue within
> B::SF::A (which wouldn't surprise me).

Sorry, I was looking at the docs on the website and for whatever reason
its failing to display all the inherited modules. If RangeI methods
don't work I'll post back, but for now assume they do (I'm not in a
position to test right now).


> My inclination is [snip]

I still don't really understand what the deal is with all these modules,
so I'll leave it your hands to make further recommendations and take action.

 From my limited understanding what you said seems reasonable, except for
excluding FeatureIO completely. At least, I'd really like to see it in
1.6; it would be a shame to miss it just because of Annotated. Worst
case, isn't Generic 'good enough' as a replacement?


> The GMOD meeting is a few weeks away, where I assume some things will
> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
> saving; maybe retooling it would be in our best interests, but it
> needs a decent roadmap to move forward.

Agreed. I guess we'll wait for the results of that meeting? Is anyone 
going planning to discuss this issue?


From cjfields at uiuc.edu  Fri Oct 12 12:15:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 11:15:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F8D76.8080101@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
	<470F8D76.8080101@sendu.me.uk>
Message-ID: <EAD0DE5B-3E55-453B-A57B-C478F2BB9AE4@uiuc.edu>


On Oct 12, 2007, at 10:06 AM, Sendu Bala wrote:
...

>
> I still don't really understand what the deal is with all these  
> modules,
> so I'll leave it your hands to make further recommendations and  
> take action.
>
> From my limited understanding what you said seems reasonable,  
> except for
> excluding FeatureIO completely. At least, I'd really like to see it in
> 1.6; it would be a shame to miss it just because of Annotated. Worst
> case, isn't Generic 'good enough' as a replacement?

It probably could work, but type checking, ontology_term(), and SF  
data validation wouldn't be implemented immediately as it would  
require additional code.  I'll try looking into it this weekend to  
see what needs to be done and work from there.

>> The GMOD meeting is a few weeks away, where I assume some things will
>> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
>> saving; maybe retooling it would be in our best interests, but it
>> needs a decent roadmap to move forward.
>
> Agreed. I guess we'll wait for the results of that meeting? Is  
> anyone going planning to discuss this issue?

Jason is going to be there and intends to bring it up as it affects  
GBrowse/GMOD/Chado.

chris



From jason at bioperl.org  Fri Oct 12 12:18:15 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 12 Oct 2007 09:18:15 -0700
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
In-Reply-To: <470F34C6.9050800@cervi-lyon.inserm.fr>
References: <470F34C6.9050800@cervi-lyon.inserm.fr>
Message-ID: <90E849A1-C5AB-40B3-9AB1-2DC79EBF5C4C@bioperl.org>

1.

Always 'use strict;' in your code - you'll see the bug more clearly  
that you should use $feat not $cds in the if stmt.


2.
You should pass in an actual Bio::DB::GenBank object to the -db  
argument.

my $db = Bio::DB::GenBank->new;
my $cds = $seq->spliced_seq(-db => $db);

-jason
On Oct 12, 2007, at 1:48 AM, Johann PELLET wrote:

> Hi,
> I have two questions:
> First, I have problems for example with this genbank entry: NC_008210.
> Indeed, for one CDS, the location is :
> join(161990..162784,complement(88222..88806),complement(86666..87448))
>
> When I parse a genbank file with this entry.
>
> my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
>                                -file => $input_file);
>
> while( my $seq = $seq_in->next_seq() ) {
>     my @features = $seq->get_SeqFeatures();
>     for ( my $i =0; $i < scalar @features; $i++ ){
>         my $feat = @features[$i];
>          if ( $feat->primary_tag eq 'CDS' ){
>
>
>              my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
>              my $seq_CDS=$seq_CDS_obj->seq;
>


>
> I have this error:
> Can't call method "isa" without a package or object reference at ....
>
> Secondly, When location is like:
> join(complement(AY421753.1:1..6),complement(3813..5699)) I know  
> that we
> must use spliced_seq with the argument db, but it's not working.
>       my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
> How can we valid a Bio::DB::RandomAccessI?
>
> Thanks
>
> -- 
> Johann Pellet
> phone (work): +33(0)4 37282352
> E-mail:    pellet at cervi-lyon.inserm.fr
> Centre d'Etudes et de Recherche en Virologie et Immunologie
> INSERM U503
> 21, Avenue Tony Garnier
> 69365 Lyon cedex 07 France
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From hlapp at gmx.net  Fri Oct 12 13:22:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 13:22:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
	<D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
Message-ID: <9762F1F9-68C8-42E2-8488-6656C76D36B8@gmx.net>


On Oct 12, 2007, at 11:02 AM, Chris Fields wrote:

>> Although sometimes confused, these are not the same motivations.  
>> AnnotationAdaptor provides a view - you use it when that's the  
>> view you need on a SeqFeatureI object you have in hand. For  
>> example, bioperl-db uses it so it doesn't have to bother about how  
>> to de/serialize tag/value pairs, when it knows how to de/serialize  
>> annotation collections already from sequence objects.  
>> AnnotationAdaptor doesn't care whether the primary_tag, or any  
>> other tag, is from an ontology.
>
> Ah, forgot it returns a Collection.  It doesn't modify the SF I  
> assume?

No, not if you only use getters. It does support adding annotation  
too, though.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From smwilson at hpc.unm.edu  Fri Oct 12 13:45:41 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Fri, 12 Oct 2007 11:45:41 -0600
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
	against latest Homo_sapiens.ags file
Message-ID: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>

Hi,

I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
memory.  I get a simple "Out of memory" output even with the  
following code:

#!/usr/bin/perl
use strict;
use Bio::ASN1::EntrezGene;
   my $parser = Bio::ASN1::EntrezGene->new('file' =>  
"Homo_sapiens.xml");
   while(my $result = $parser->next_seq)
   {
   }



Thanks.
Susan





From arareko at campus.iztacala.unam.mx  Fri Oct 12 14:10:44 2007
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 12 Oct 2007 14:10:44 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FB8A4.2050601@campus.iztacala.unam.mx>

Hi Susan,

Bio::ASN1::EntrezGene is not part of the BioPerl distribution, even 
though it shares the same namespace and is used by BP. Maybe you'd want 
to contact Mingyi Liu who is the author of the module. for more info 
take a look here:

http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene/

Regards,
Mauricio.

Susan Wilson wrote:
> Hi,
> 
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
> 
> 
> 
> Thanks.
> Susan
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM



From Kevin.M.Brown at asu.edu  Fri Oct 12 14:19:48 2007
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 12 Oct 2007 11:19:48 -0700
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>

> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> machine with 256GB of memory.  I get a simple "Out of memory" 
> output even with the following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }

I think most systems have a per process memory limit (either hardcoded
in the OS or configured depending on the OS) and IIRC most of the IO
handlers for BioPerl load entire file contents into memory to process
them.  Some of the IO parsers have been changed recently (a new one
added for blast) so that it only pulls into memory as much as it needs
to process the next result rather than the whole file in one shebang.



From stefan.kirov at bms.com  Fri Oct 12 14:34:49 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:34:49 -0400
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <470FBE49.7010703@bms.com>

Kevin Brown wrote:
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
>> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
>> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
>> machine with 256GB of memory.  I get a simple "Out of memory" 
>> output even with the following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>     
>
> I think most systems have a per process memory limit (either hardcoded
> in the OS or configured depending on the OS) and IIRC most of the IO
> handlers for BioPerl load entire file contents into memory to process
> them.  Some of the IO parsers have been changed recently (a new one
> added for blast) so that it only pulls into memory as much as it needs
> to process the next result rather than the whole file in one shebang.
>   
The file is approx. 6GB, so on a 256GB machine this is not going to
create any problem. I think this might be deep not well controlled
recursion problem.
Stefan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From mingyi.liu at gpc-biotech.com  Fri Oct 12 15:06:25 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 15:06:25 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <470FC5B1.3090606@gpc-biotech.com>

BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi


From j_martin at lbl.gov  Fri Oct 12 14:58:41 2007
From: j_martin at lbl.gov (Joel Martin)
Date: Fri, 12 Oct 2007 11:58:41 -0700
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FBE49.7010703@bms.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
	<470FBE49.7010703@bms.com>
Message-ID: <20071012185841.GE13838@eniac.jgi-psf.org>

Hello,
    Just a suggestion, is /usr/bin/perl a 64 bit perl?
Even on our sun machines with 72+ GB memory, for some reason they're
distributed with a 32 bit perl which can handle large files but would
probably have out of memory errrors if trying to read one into memory.

% file /usr/bin/perl 
/usr/bin/perl:  ELF 32-bit MSB executable SPARC Version 1, dynamically
linked, stripped

Joel

On Fri, Oct 12, 2007 at 02:34:49PM -0400, Stefan Kirov wrote:
> Kevin Brown wrote:
> >> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> >> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> >> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> >> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> >> machine with 256GB of memory.  I get a simple "Out of memory" 
> >> output even with the following code:
> >>
> >> #!/usr/bin/perl
> >> use strict;
> >> use Bio::ASN1::EntrezGene;
> >>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> >> "Homo_sapiens.xml");
> >>    while(my $result = $parser->next_seq)
> >>    {
> >>    }
> >>     
> >
> > I think most systems have a per process memory limit (either hardcoded
> > in the OS or configured depending on the OS) and IIRC most of the IO
> > handlers for BioPerl load entire file contents into memory to process
> > them.  Some of the IO parsers have been changed recently (a new one
> > added for blast) so that it only pulls into memory as much as it needs
> > to process the next result rather than the whole file in one shebang.
> >   
> The file is approx. 6GB, so on a 256GB machine this is not going to
> create any problem. I think this might be deep not well controlled
> recursion problem.
> Stefan
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >   
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From stefan.kirov at bms.com  Fri Oct 12 14:20:38 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:20:38 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FBAF6.1050509@bms.com>

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   
Susan,
Are you running the latest version of Bio::ASN1::EntrezGene? You may
have a better chance of getting a fast (and useful) answer if you
contact Mingyi Liu (see on CPAN) directly- the module is not part of
Bioperl. Just to mention- I have also seen similar problems and there
seems to be particular problematic records. I think NCBI made some
changes/additions to their format (might have to do something with the
number/structure of contigs). I will have to run my pipeline soon again
and if I run into the same problem I will probably create bug report for
Mingyi. I hope you do it before me- it is boring and long process.
Stefan



From mingyi.liu at gpc-biotech.com  Fri Oct 12 14:50:08 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 14:50:08 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FC1E0.4070708@gpc-biotech.com>

Hi, Susan,

Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, it's better to directly contact me.  I actually deleted a few messages of this discussion before one caught my eye. Nowadays I'm working in some other areas and not tracking bioperl mailing list closely, a direct email to me would usually work out better.

As for the problem you mentioned, there could be two reasons: 1. It 
seems that you converted the file to XML file instead of ASN file. My 
parser is designed for ASN file, so please use gene2xml to convert the 
downloaded file to ASN file instead of XML file.  It is likely the wrong 
syntax of the file caused my parser to attempt to read the entire file 
as a string (because it couldn't find the start/end).  However, there's 
another minor possibility (which you might have taken care of already): 
2. Perl 5.8 added 64 bit support, but I don't know if you have perl 5.8 
64 bit installed on your system to support the 256 GB system memory you 
have?  If not, your >5 GB file is over the 4 GB 32 bit Perl limit.

Let me know if my suggestions work out for you.

Best,

Mingyi

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   



From gyang at plantbio.uga.edu  Fri Oct 12 16:52:06 2007
From: gyang at plantbio.uga.edu (Guojun Yang)
Date: Fri, 12 Oct 2007 16:52:06 -0400
Subject: [Bioperl-l] hide XML display on web
In-Reply-To: 41A08079-6EEC-4B62-8104-C41E70C03083@uiuc.edu
Message-ID: <20071012205206.9105fd09@dogwood.plantbio.uga.edu>

Hi, All,  
I have a cgi script that uses remoteblast (xml output). Every time, before and after the blast is finished, a lot of information is displayed on the client's screen, it's a nuisance but I am wondering if anyone knows how to rid of these. See below for examples:  
   
Thanks  
Guojun Yang  
_______________________example_____________________  
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>NCBI Blast:</title>
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
<!--[if lte IE 6]>
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
<![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="js/results.js"></script>
</head>

<body id="type-a" class="noToggleCheck" >
<div id="wrap">
   <div id="header">
  <div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span class="desc"> Basic Local Alignment Search Tool</span>
  </div>
  <div id="search">
  <div><script language="JavaScript" type="text/javascript"><!--
    var myncbi_xo = 0;
    var myncbi_x = MyNCBI_find();
    var myncbi_cu = unescape('http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3F');
    function MyNCBI_find()
    {
        var cs = document.cookie.split('; ');
        for(var i = 0; i < cs.length; i++) {
            // a name/value pair (a crumb) is separated by an equal sign
            var c = cs[i].split('=');
            if(c[0] == 'WebCubbyUser') { return c[1]; }
        }
        return '';
    }
.........


From hlapp at gmx.net  Sat Oct 13 17:49:49 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 13 Oct 2007 17:49:49 -0400
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <F2EFD76D-AA02-4FF7-8CAA-86AAC58E2D2E@gmx.net>


On Oct 12, 2007, at 2:19 PM, Kevin Brown wrote:

> IIRC most of the IO handlers for BioPerl load entire file contents  
> into memory to process them

As was determined already this most likely isn't the issue here, but  
I'm still confused by your statement. Most BioPerl Bio::SeqIO,  
Bio::ClusterIO, and Bio::OntologyIO parsers read an input file line  
by line, or at least by chunk.

Did you possibly mean something else?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From mingyi.liu at gpc-biotech.com  Sat Oct 13 23:28:09 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Sat, 13 Oct 2007 23:28:09 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <47118CC9.8090807@gpc-biotech.com>

Hi, Susan,

Let us know how my suggestions worked for you.  I replied to both you 
and the bioperl mailing list last Friday in the hope that my answer 
could be helpful for the list discussion, but it seems that the mailing 
list server had serious problems and dropped both of my emails.  I'm 
therefore replying again and combined the content of my 2 emails 
together below. Hopefully the email gets sent out to the mailing list.  
If not, would one of you please forward it out?  Thanks.

Mingyi Liu wrote:
> Hi, Susan,
>
> Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, 
> it's better to directly contact me.  I actually deleted a few messages 
> of this discussion before one caught my eye. Nowadays I'm working in 
> some other areas and not tracking bioperl mailing list closely, a 
> direct email to me would usually work out better.
>
> As for the problem you mentioned, there could be two reasons: 1. It 
> seems that you converted the file to XML file instead of ASN file. My 
> parser is designed for ASN file, so please use gene2xml to convert the 
> downloaded file to ASN file instead of XML file.  It is likely the 
> wrong syntax of the file caused my parser to attempt to read the 
> entire file as a string (because it couldn't find the start/end).  
> However, there's another minor possibility (which you might have taken 
> care of already): 2. Perl 5.8 added 64 bit support, but I don't know 
> if you have perl 5.8 64 bit installed on your system to support the 
> 256 GB system memory you have?  If not, your >5 GB file is over the 4 
> GB 32 bit Perl limit.
>
> Let me know if my suggestions work out for you.
>
> Best,
>
> Mingyi
>
BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped 
binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus 
SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi

> Susan Wilson wrote:
>> Hi,
>>
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
>> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
>> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB 
>> of  memory.  I get a simple "Out of memory" output even with the  
>> following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>
>>
>>
>> Thanks.
>> Susan
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>   
>
>



From smwilson at hpc.unm.edu  Mon Oct 15 11:08:55 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 15 Oct 2007 09:08:55 -0600
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC5B1.3090606@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
	<470FC5B1.3090606@gpc-biotech.com>
Message-ID: <72C50125-E169-448C-8F25-AB13A8AD308D@hpc.unm.edu>

Mingyi,

Thank you very much for your advice.  The text ASN file 1/4 the size  
of the (evil, evil) XML file and parsing it ran just fine.  We are  
still pursuing a 64-bit perl on our 256GB server and I will let you  
know how it works.

Thanks.
Susan



On Oct 12, 2007, at 1:06 PM, Mingyi Liu wrote:

> BTW, here's the syntax in one of my messages last year about how to  
> convert the compressed binary ASN format NCBI provides to the text  
> ASN format my module (or Stefan's SeqIO::entrezgene) expects (the - 
> x switch does the trick, overwriting the default option to produce  
> XML output):
>
> my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i  
> Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the  
> gzipped binary file directly downloaded from NCBI
>
> Same syntax should be used when you're using SeqIO (thus  
> SeqIO::entrezgene).
>
> BTW, text ASN is both smaller and faster to parse than XML format.
>
> Best,
>
> Mingyi



From wgallin at ualberta.ca  Mon Oct 15 18:25:14 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 15 Oct 2007 16:25:14 -0600
Subject: [Bioperl-l] Capturing Joined Sequence from two records
Message-ID: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>

I have encountered a case of a protein sequence record for which the  
coding sequence is a join with ranges from two nucleotide sequence  
records:

gi # is 7648673

Relevant annotation is:

   CDS             1..630
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"


Is there any way using Bio::Seq objects to seamlessly get the CDS  
nucleic acid sequence, or do I need to just treat it as an oddity and  
cobble together something manually?

Warren Gallin


From esnyder at vbi.vt.edu  Mon Oct 15 16:38:06 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 16:38:06 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713CFAE.7020007@vbi.vt.edu>

Hello Again,

I think I've discovered the problem.  Apparently I've got an old version 
of BioPerl which expected an array of arguments rather than a named 
list.  When I cut-and-pasted the new code for translate() into my 
distribution, the problem went away.

So, the next question is: how can I be sure that I have the most 
up-to-date distribution available (or at least the one that matches the 
BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within 
the last year but I don't know where it actually came from.

Thanks,
eesnyder

-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"




From jason at bioperl.org  Mon Oct 15 18:54:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 15 Oct 2007 15:54:38 -0700
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
Message-ID: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>

pass in a db handle to spliced_seq. There was a question about this  
on the list a few days ago.
http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html

  - does anyone want to add this solution in more example to FAQ?

-jason

On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:

> I have encountered a case of a protein sequence record for which the
> coding sequence is a join with ranges from two nucleotide sequence
> records:
>
> gi # is 7648673
>
> Relevant annotation is:
>
>    CDS             1..630
>                       /gene="KCND2"
>                       /coded_by="join
> (AF166007.1:430..1544,AF166008.1:345..507,
>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>                        
> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>
>
> Is there any way using Bio::Seq objects to seamlessly get the CDS
> nucleic acid sequence, or do I need to just treat it as an oddity and
> cobble together something manually?
>
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org

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From torsten.seemann at infotech.monash.edu.au  Mon Oct 15 20:49:16 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Tue, 16 Oct 2007 10:49:16 +1000
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <a79f6a4b0710151749o240a5e72j697a1cff6bf39baf@mail.gmail.com>

>  pass in a db handle to spliced_seq. There was a question about this on the
> list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?

Done.

http://www.bioperl.org/wiki/FAQ#How_do_I_get_the_complete_spliced_sequence_when_the_coordinates_refer_to_Genbank_identifiers.3F

If anyone spots any errors or wants to improve it, please do so.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From cjfields at uiuc.edu  Mon Oct 15 21:02:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:02:25 -0500
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
In-Reply-To: <4713CFAE.7020007@vbi.vt.edu>
References: <4713CFAE.7020007@vbi.vt.edu>
Message-ID: <67EBC789-C27F-4918-941C-46E62ACFE934@uiuc.edu>

http://www.bioperl.org/wiki/ 
FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F

If you installed BioPerl via CPAN you more than likely have 1.4.  The  
most recent dev release is 1.5.2.

chris

On Oct 15, 2007, at 3:38 PM, Eric E. Snyder wrote:

> Hello Again,
>
> I think I've discovered the problem.  Apparently I've got an old  
> version
> of BioPerl which expected an array of arguments rather than a named
> list.  When I cut-and-pasted the new code for translate() into my
> distribution, the problem went away.
>
> So, the next question is: how can I be sure that I have the most
> up-to-date distribution available (or at least the one that matches  
> the
> BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within
> the last year but I don't know where it actually came from.
>
> Thanks,
> eesnyder
>
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0447
> USA
>
> Office:    (540) 231-5428
> Mobile:    (540) 230-5225
> Fax:    (540) 231-2606
> Email:    eesnyder at vbi.vt.edu
> JDAM:    N 37 12'01.6", W 80 24'26.9"
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Oct 15 21:39:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:39:37 -0500
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>

Would spliced_seq() work with a protein sequence this way?  The  
location string is in a tag 'coded_by', which would require a little  
more work to get the sequence.

chris

On Oct 15, 2007, at 5:54 PM, Jason Stajich wrote:

> pass in a db handle to spliced_seq. There was a question about this  
> on the list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?
>
> -jason
>
> On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:
>
>> I have encountered a case of a protein sequence record for which the
>> coding sequence is a join with ranges from two nucleotide sequence
>> records:
>>
>> gi # is 7648673
>>
>> Relevant annotation is:
>>
>>    CDS             1..630
>>                       /gene="KCND2"
>>                       /coded_by="join
>> (AF166007.1:430..1544,AF166008.1:345..507,
>>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>>                        
>> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>>
>>
>> Is there any way using Bio::Seq objects to seamlessly get the CDS
>> nucleic acid sequence, or do I need to just treat it as an oddity and
>> cobble together something manually?
>>
>> Warren Gallin
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From Russell.Smithies at agresearch.co.nz  Mon Oct 15 23:51:40 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 16 Oct 2007 16:51:40 +1300
Subject: [Bioperl-l] Parsing EMBL records
In-Reply-To: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca><EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
	<50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05EFC097@imail.agresearch.co.nz>

I've got some output from "newcpgreport" that looks like embl format but
I'm having trouble parsing it.
One of the reasons might be because of this warning but I'm not sure.
	-------------------- WARNING ---------------------
	MSG: Got a sequence with no letters in it cannot guess alphabet
[]
	---------------------------------------------------

I need to get it into gff or tabbed format and don't want to have to
resort to Perl regexes to do it.
Has anyone got some example code for parsing embl or swiss output I
could borrow?

The "newcpgreport " output looks like this:
-----------------------------------------------------
ID   BTA28  46084206 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       181953..182223
FT                    /size=271
FT                    /Sum C+G=162
FT                    /Percent CG=59.78
FT                    /ObsExp=0.75
FT   CpG island       222609..223040
FT                    /size=432
FT                    /Sum C+G=290
FT                    /Percent CG=67.13
FT                    /ObsExp=0.97
FT   CpG island       288537..288741
FT                    /size=205
FT                    /Sum C+G=112
FT                    /Percent CG=54.63
FT                    /ObsExp=0.85 
------------------------------------------------------


Any help greatly appreciated  :-)

Russell Smithies

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From esnyder at vbi.vt.edu  Mon Oct 15 14:50:54 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 14:50:54 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713B68E.2040804@vbi.vt.edu>

Hello,

I am having trouble with translate() when supplying parameters such as 
-frame, -codontable_id, etc.  I am working straight out of the tutorial 
with a very simple program-- which has me stumped!

use Bio::SeqIO;
foreach my $file ( @ARGV ){
     my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
                                     -format =>  "fasta" );
     my $seq_obj = $seqio_obj->next_seq;

     print "loaded one sequence:\n\tdisplay_id\t" .
	   $seq_obj->display_id() . "\n" .
     	   "\tdescription\t" . $seq_obj->description() . "\n";

     foreach my $frame ( 0 .. 2){
         $prot_obj = $seq_obj->translate( '-frame' => $frame );
         print "translation = " . $prot_obj->seq . "\n";
     }
}

Everything works as expected until calling translate.  The output I get 
is the translation of my FASTA sequence (in frame zero, repeated three 
times) in which every "stop" is replaced with "-frame" (!!).  However, 
with no parameters, translate works as advertised.

This is getting me down because by using the full complement of 
translate options, including specifying frame, genetic code, alternative 
start codons, etc., BioPerl will save me a huge amount of time... but 
only if I can figure out how to use it properly!

Any assistance would be greatly appreciated!!!

Sincerely,
eesnyder


-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"



From bosborne11 at verizon.net  Tue Oct 16 08:57:46 2007
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 16 Oct 2007 08:57:46 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
 parameters
In-Reply-To: <4713B68E.2040804@vbi.vt.edu>
Message-ID: <C33A2D8A.FF00%bosborne11@verizon.net>

Eric,

I took your code, unmodified, and ran it using a file in the distribution.
The output looks OK, different frames are used and I don't see "-frame" in
the output sequence (see below). This is using the latest bioperl-live -
what version Bioperl are you using?

Brian O.


269 ~/bioperl-live>./test.pl t/data/HUMBETGLOA.fa
loaded one sequence:
        display_id      HUMBETGLOA
        description     Human haplotype C4 beta-globin gene, complete cds.
translation = 
TSYLTPLITPLIVTLWVVSDFLFICIFDCIKRSLVFYLLFPKT**VTNAQSTLICIYSIFRHNLLACMSKLRKTTT
NECIYMYMYVCTYTHIYIYIFFLFLPEGFNPNKEKICLELR*SFHPFCPVSILHILETQEEIHLHIPKLNYGRQNS
STFSASTSYLCNKKIGKTIFNMLTKL*FQILRKYTCKGGCF**QFVLMVWGQEIYLRGRAEGLKSNS*ASARRAKD
RYGCHHLDLTLWSHTLGLANLLPGAGRAGARAGHKSQGRAIYCLHLLLTQLCSLATSNRHHGASDS*GEVCRYCPV
GQGERG*SWW*GPGQVGIKVTRQV*GDQ*KLGMWRQRRLLGF**ALTLSAYWSIFPPLGCWWSTLGPRGSLSPLGI
CPLLMLLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWILRTSG*VYGTLDVFFPLLFYG*VH
VIGRG*VTGYSLEWETDE*LHQCGSLRIVLVSFICCS*QLFSFV*FLLSFFFFSAIFTIILNALTLCITKGNISEI
H*VT*KKTLHSLPSTLLFGIYVCLFAYS*SPYFIFFYF*LIHNHYTYLWVKV*CFNMCTHIDQIRVILHL*F*KML
SSFNILFCLSYF*YFP*SLSFRAIMIQCIMPLCTILKNNSDNFWVKAIAISLHINISAYKL*LM*EVSYC**QLQS
SYHSAFILWLG*GWIILSPS*ALLLIMFIPLIFLPQLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHK
YH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHCNDVFKLFLNILLKRECGRSVHLKHKEMKS
*FKPWENTLYLKLHERR*GCKQLMHIGNSPDAYALFIPQKRIQVEA*FGG*SFAMLYFTLLIVLAVLMNVFSLPIC
LSCISQP*LHSVLLLRDTTFPLKCSFHVLRRDGFSSPGHSALVVSVVL*RST*RRKNRGHGLTVL*ALLPCLPHSQ
*PGICSASLPELS
translation = 
PPI*HH*LPH**SHFGL*VTFYLFVFLTALRGL*FFTSCFPKPNK*LMHRAH*FVFILFLDIIY*HA*AN*EKQQQ
MNAYICICMCVHIHIYIYIYFFFSYQKVLIQIRRRYA*N*GRVFIHSVL*VFCIFWRRRKRSIYISQS*IMVDKTL
PLLVHQLLICVIRKLGKRSSICLPSCDSKYYVNTLAKEDVFSSNLY*WYGAKRYILEGGLRV*SPTPKPVPEEPRT
GTAVIT*TSPCGATP*GWPIYSQEQGGQEPGLGIKVRAEPSIAYICF*HNCVH*QPQTDTMVHLTPEEKSAVTALW
GKVNVDEVGGEALGRLVSRLQDRFKETNRNWACGDREDSWVSDRH*LSLPIGLFSHP*AAGGLPLDPEVL*VLWGS
VHS*CCYGQP*GEGSWQESARCL**WPGSPGQPQGHLCHTE*AAL*QAARGS*ELQGESMGPLMFSFPFFSMVKFM
S*EGDK*QGTV*NGKQTNDCISVEVSGSF*FLLFAVHNNCFLLFNSCFLFFSSPQFLLLYLMP*HCV*QKEISLRY
IK*LKKKLYTVCLVHYYLEYMCAYLHIHNLPTLFSFIFN*YIIIIHIYGLKCNVLICVHILTKSG*FCICNFKKCF
LLLIYFFVYLISNTFPNLFLSGQ**YNVSCLFAPF*RITVIISGLRQ*QYLCI*IFLHINCN*CKRFHIANSSYNP
ATILLLFYGWDKAGLF*VQARPFC*SCSYLLSSSHSSWATCWSVCWPITLAKNSPHQCRLPIRKWWLVWLMPWPTS
ITKLAFLLSNFY*RFLCSLSPTTKLGDIMKGLEHLDSA**KTFIFIAMMYLNYF*IFY*KGNVGGQCI*NIKK*RA
SSNLGKIHYILNSMKEGEAANS*CTLATALMHMPYSSLRKGFK*RLDLEVKVLLCCILHYLLF*LSS*MSFHYPFA
YPASLSLDSTQFSCLEIPPFP*SVPSMFYGEMVSPRLATQP*LSLLSYRGLLEEGKTGVMV*LSCEPFFPASPTHS
DPESAVLVSRNY
translation = 
LLFDTTDYPIDSHTLGCK*LFIYLYF*LH*EVSSFLPLVSQNLISN*CTEHIDLYLFYF*T*FISMHEQIKKNNNK
*MHIYVYVCVYIYTYIYIYIFSFLTRRF*SK*GEDMLRTEVEFSSILSCKYFAYSGDAGRDPSTYPKAELW*TKLF
HF*CINFLFV**ENWENDLQYAYQAVIPNIT*IHLQRRMFLVAICTDGMGPRDIS*REG*GFEVQLLSQCQKSQGQ
VRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQSHLLLTFASDTTVFTSNLKQTPWCI*LLRRSLPLLPCG
AR*TWMKLVVRPWAGWYQGYKTGLRRPIETGHVETEKTLGFLIGTDSLCLLVYFPTLRLLVVYPWTQRFFESFGDL
STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRVSLWDP*CFLSPSFLWLSSC
HRKGISNRVQFRMGNRRMIASVWKSQDRFSFFYLLFITIVFFCLILAFFFFLLRNFYYYT*CLNIVYNKRKYL*DT
LSNLKKNFTQSA*YITIWNICVLICIFIISLLYFLLFLIDT*SLYIFMG*SVMF*YVYTY*PNQGNFAFVILKNAF
FF*YTFLFILFLILSLISFFQGNNDTMYHASLHHSKE*Q**FLG*GNSNISAYKYFCI*IVTDVRGFILLIAATIQ
LPFCFYFMVGIRLDYSESKLGPFANHVHTSYLPPTAPGQRAGLCAGPSLWQRIHPTSAGCLSESGGWCG*CPGPQV
SLSSLSCCPISIKGSFVP*VQLLNWGIL*RALSIWILPNKKHLFSLQ*CI*IISEYFTKKGMWEVSAFKT*RNEEL
VQTLGKYTIS*TP*KKVRLQTANAHWQQP*CICLIHPSEKDSSRGLIWRLKFCYAVFYITYCFSCPHECLFTTHLL
ILHLSALTPLSSLA*RYHLSPEVFLPCFTARWFLLAWPLSLSCLCCLIEVYLKKEKQGSWFDCPVSPSSLPPPLTV
TRNLQC*SPGTI



On 10/15/07 2:50 PM, "Eric E. Snyder" <esnyder at vbi.vt.edu> wrote:

> Hello,
> 
> I am having trouble with translate() when supplying parameters such as
> -frame, -codontable_id, etc.  I am working straight out of the tutorial
> with a very simple program-- which has me stumped!
> 
> use Bio::SeqIO;
> foreach my $file ( @ARGV ){
>      my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
>                                      -format =>  "fasta" );
>      my $seq_obj = $seqio_obj->next_seq;
> 
>      print "loaded one sequence:\n\tdisplay_id\t" .
>   $seq_obj->display_id() . "\n" .
>   "\tdescription\t" . $seq_obj->description() . "\n";
> 
>      foreach my $frame ( 0 .. 2){
>          $prot_obj = $seq_obj->translate( '-frame' => $frame );
>          print "translation = " . $prot_obj->seq . "\n";
>      }
> }
> 
> Everything works as expected until calling translate.  The output I get
> is the translation of my FASTA sequence (in frame zero, repeated three
> times) in which every "stop" is replaced with "-frame" (!!).  However,
> with no parameters, translate works as advertised.
> 
> This is getting me down because by using the full complement of
> translate options, including specifying frame, genetic code, alternative
> start codons, etc., BioPerl will save me a huge amount of time... but
> only if I can figure out how to use it properly!
> 
> Any assistance would be greatly appreciated!!!
> 
> Sincerely,
> eesnyder
> 




From sheris at berkeley.edu  Tue Oct 16 19:15:43 2007
From: sheris at berkeley.edu (Sheri Simmons)
Date: Tue, 16 Oct 2007 16:15:43 -0700
Subject: [Bioperl-l] what are the key features of genbank file recognized by
	SeqIO?
Message-ID: <200710161615.43420.sheris@berkeley.edu>

I'm hoping someone can help me with figuring out how to generate genbank files 
from scratch that can be interpreted with SeqIO. The problem is that genbank 
files generated via the artemis program are not recognized by SeqIO, so I am 
attempting to generate SeqIO-compatible genbank files so they can be 
converted to other formats later. 
I produced a file which looks by eye exactly like standard genbank files, but 
which is not recognized by SeqIO. Could anyone tell me or refer me to a 
source that explains the exact format that SeqIO::genbank requires? 
FYI here's a snippet of the file generated by my program:

########
LOCUS   Contig2406              66712 bp        dna     linear  UNK
FEATURES             Location/Qualifiers
     CDS                 83..1222
                            /gene="org_2406_0001"
     CDS                1259..1576
                           /gene="org_2406_0002"
     CDS                complement(1830..3284)
                           /gene="org_2406_0003c"
(more CDS)
BASE COUNT      14091 a         19796 c         18841 g         13747 t
ORIGIN
        1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
      61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
(more sequence)
###########

Thanks,
Sheri

-- 
Sheri Simmons
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
http://webfiles.berkeley.edu/~sheris


From barry.moore at genetics.utah.edu  Tue Oct 16 19:47:56 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 16 Oct 2007 17:47:56 -0600
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>

Hi Sheri,

You would need to look at the source code for Bio::SeqIO::genbank.pm  
specifically the next_seq method.  If you let us know what kind of  
errors you're getting, or what data is missing in your seq object  
perhaps we could help you narrow it down.  You could also send one of  
your GenBank style files that isn't working and someone might be  
willing to take a stab at running it.

Barry

On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:

> I'm hoping someone can help me with figuring out how to generate  
> genbank files
> from scratch that can be interpreted with SeqIO. The problem is  
> that genbank
> files generated via the artemis program are not recognized by  
> SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank  
> files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me  
> to a
> source that explains the exact format that SeqIO::genbank requires?
> FYI here's a snippet of the file generated by my program:
>
> ########
> LOCUS   Contig2406              66712 bp        dna     linear  UNK
> FEATURES             Location/Qualifiers
>      CDS                 83..1222
>                             /gene="org_2406_0001"
>      CDS                1259..1576
>                            /gene="org_2406_0002"
>      CDS                complement(1830..3284)
>                            /gene="org_2406_0003c"
> (more CDS)
> BASE COUNT      14091 a         19796 c         18841 g          
> 13747 t
> ORIGIN
>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta  
> acatacacaa
>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg  
> ccgatatcaa
> (more sequence)
> ###########
>
> Thanks,
> Sheri
>
> --
> Sheri Simmons
> Department of Earth and Planetary Sciences
> University of California, Berkeley
> Berkeley, CA 94720-4767
> http://webfiles.berkeley.edu/~sheris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Tue Oct 16 19:58:46 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Oct 2007 16:58:46 -0700
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
References: <200710161615.43420.sheris@berkeley.edu>
	<020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
Message-ID: <74393EF9-C4B9-4F3B-8150-E22BECE81587@bioperl.org>

I am sure we should also let the Artemis developers know what is  
going on so they can help fix the bug on their end as well.

Have you also tried dumping EMBL from Artemis, a format I assume they  
are more likely to use, and seeing if that parses fine in BioPerl?

-jason
On Oct 16, 2007, at 4:47 PM, Barry Moore wrote:

> Hi Sheri,
>
> You would need to look at the source code for Bio::SeqIO::genbank.pm
> specifically the next_seq method.  If you let us know what kind of
> errors you're getting, or what data is missing in your seq object
> perhaps we could help you narrow it down.  You could also send one of
> your GenBank style files that isn't working and someone might be
> willing to take a stab at running it.
>
> Barry
>
> On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:
>
>> I'm hoping someone can help me with figuring out how to generate
>> genbank files
>> from scratch that can be interpreted with SeqIO. The problem is
>> that genbank
>> files generated via the artemis program are not recognized by
>> SeqIO, so I am
>> attempting to generate SeqIO-compatible genbank files so they can be
>> converted to other formats later.
>> I produced a file which looks by eye exactly like standard genbank
>> files, but
>> which is not recognized by SeqIO. Could anyone tell me or refer me
>> to a
>> source that explains the exact format that SeqIO::genbank requires?
>> FYI here's a snippet of the file generated by my program:
>>
>> ########
>> LOCUS   Contig2406              66712 bp        dna     linear  UNK
>> FEATURES             Location/Qualifiers
>>      CDS                 83..1222
>>                             /gene="org_2406_0001"
>>      CDS                1259..1576
>>                            /gene="org_2406_0002"
>>      CDS                complement(1830..3284)
>>                            /gene="org_2406_0003c"
>> (more CDS)
>> BASE COUNT      14091 a         19796 c         18841 g
>> 13747 t
>> ORIGIN
>>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta
>> acatacacaa
>>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg
>> ccgatatcaa
>> (more sequence)
>> ###########
>>
>> Thanks,
>> Sheri
>>
>> --
>> Sheri Simmons
>> Department of Earth and Planetary Sciences
>> University of California, Berkeley
>> Berkeley, CA 94720-4767
>> http://webfiles.berkeley.edu/~sheris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From torsten.seemann at infotech.monash.edu.au  Tue Oct 16 21:31:03 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Wed, 17 Oct 2007 11:31:03 +1000
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <a79f6a4b0710161831x30efa062oacc64844706e8a96@mail.gmail.com>

On 17/10/2007, Sheri Simmons <sheris at berkeley.edu> wrote:
> I'm hoping someone can help me with figuring out how to generate genbank files
> from scratch that can be interpreted with SeqIO. The problem is that genbank
> files generated via the artemis program are not recognized by SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me to a
> source that explains the exact format that SeqIO::genbank requires?

Here is NCBI's documentation on the feature table format.
http://www.ncbi.nlm.nih.gov/collab/FT/

Regarding Artemis: if you load an EMBL file, then save as EMBL, it
seems to keep the header. If you save it as Genbank though, it
discards the header and only outputs the feature table and sequence.
Also, Artemis for many of its Save options only saves the feature
table. Both of these last two can't be read by BioPerl. At one stage I
had some code to whack in a fake header and empty sequence at the end
to get it to load.

Now, regarding your example output. I'm never sure if the first line
is LOCUS or ID, I guess one is deprecated. You also don't have a Date
at the end of the first line, but maybe it is optional. You are also
missing the "//" on the final line. Finally, Genbank is strict on
correct spacing etc, but I'm sure the Bioperl parser is written
relatively defensively here, so that might not be the problem.

Hope this helps,

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From wgallin at ualberta.ca  Wed Oct 17 21:42:54 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Wed, 17 Oct 2007 19:42:54 -0600
Subject: [Bioperl-l] Still trouble with remote joined records
Message-ID: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>

I must be missing something, but I can not get the procedure outlined  
in FAQ 5.5 to do what I think it should (maybe my expectations are  
incorrect.

I think I have an up-to-date release:

GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print  
$Bio::Root::Version::VERSION,"\n"'
1.005002102


If I run the following script (not that gi7648673 is a protein record):
___________________________________________________________
#! /usr/bin/perl

#071017 - Small script to test the method for getting the ORF sequence
#using dbh passing into the sequence method.


use strict;
use warnings;
use LWP::Simple;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::Seq;

#Create handles to GenBank and GenPept

my $gbh = Bio::DB::GenBank -> new;
my $gph = Bio::DB::GenPept -> new;

#This is the gi number of the entry being tested

my $test_gi = 7648673;

#Get the protein sequence file from GENBANK

my $test_na_record = $gph -> get_Seq_by_gi ($test_gi);

#Go through the features - when the CDS feature is found splice  
together the sequence and translate.


   for my $feat ( $test_na_record->get_SeqFeatures ) {
     if ( $feat->primary_tag eq 'CDS' ) {
        my $cds = $feat->spliced_seq(-db => $gbh, -nosort => 1);
        print $cds->translate->seq, "\n";
     }
   }


exit;
_______________________________________________________________________
I get an error that a protein sequence can not be translated.  I  
thought that by feeding the handle to GenBank into the spliced_seq  
method that it would retrieve the necessary nucleic acid sequence  
records and splice together the specified ranges.

So I tried using the corresponding nucleic acid record, gi7648671,  
which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).

That yielded the correct amino acid sequence for the first half the  
protein, encoded by the sequence in the record itself, but it did not  
retrieve the other nucleic acid record that is specified to contain  
the 3' end of the sequence.

So, as far as I can see, passing the DB handle isn't causing the  
spliced_seq method to go elsewhere for the nucleic acid sequence data.

I thought that was the purpose.

Can anyone enlighten me, or is this a bug?

Warren Gallin



From cjfields at uiuc.edu  Wed Oct 17 22:49:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 21:49:37 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
Message-ID: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>

On Oct 17, 2007, at 8:42 PM, Warren Gallin wrote:

> I must be missing something, but I can not get the procedure outlined
> in FAQ 5.5 to do what I think it should (maybe my expectations are
> incorrect.
>
> I think I have an up-to-date release:
>
> GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print
> $Bio::Root::Version::VERSION,"\n"'
> 1.005002102
> ...
> I get an error that a protein sequence can not be translated.  I
> thought that by feeding the handle to GenBank into the spliced_seq
> method that it would retrieve the necessary nucleic acid sequence
> records and splice together the specified ranges.

No, the error is expected:

MSG: Can't translate an amino acid sequence.

The record in question is a protein record, so you are retrieving a  
protein sequence, which can't be translated (the exception is valid,  
in other words).  Note that the 'CDS' feature in this case has a  
specified location of 1..630 (indicated by arrow):

      CDS             1..630   <---------
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"

The tag name 'coded_by' has the data you want; however it is stored  
as a string only.

> So I tried using the corresponding nucleic acid record, gi7648671,
> which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).
>
> That yielded the correct amino acid sequence for the first half the
> protein, encoded by the sequence in the record itself, but it did not
> retrieve the other nucleic acid record that is specified to contain
> the 3' end of the sequence.
> ...
> So, as far as I can see, passing the DB handle isn't causing the
> spliced_seq method to go elsewhere for the nucleic acid sequence data.
>
> I thought that was the purpose.
>
> Can anyone enlighten me, or is this a bug?
>
> Warren Gallin

This appears to be a bug.  The remote sequence is designated in the  
feature:

      CDS             join 
(430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
                      AF166008.1:9952..10044,AF166008.1:13222..13469,
                      AF166008.1:15123..15300)
                      /gene="KCND2"
                      /codon_start=1
                      /product="voltage-gated potassium channel Kv4.2"
                      /protein_id="AAF65618.1"
                      /db_xref="GI:7648673"

but the location is truncated when passed through SeqIO to genbank  
output, which explains the spliced_seq() problem:

      CDS             430..1544
                      /db_xref="GI:7648673"
                      /codon_start=1
                      /protein_id="AAF65618.1"
                      /gene="KCND2"

I'll try looking into this; if I can't get to it immediately I'll  
file a bug report.  Thanks!

chris


From cjfields at uiuc.edu  Wed Oct 17 23:45:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 22:45:55 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
	<8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
Message-ID: <872F9A22-AC32-4381-B7FE-4554943C8D75@uiuc.edu>


On Oct 17, 2007, at 9:49 PM, Chris Fields wrote:

> ...
>> So, as far as I can see, passing the DB handle isn't causing the
>> spliced_seq method to go elsewhere for the nucleic acid sequence  
>> data.
>>
>> I thought that was the purpose.
>>
>> Can anyone enlighten me, or is this a bug?
>>
>> Warren Gallin
>
> This appears to be a bug.  The remote sequence is designated in the
> feature:
>
>       CDS             join
> (430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
>                       AF166008.1:9952..10044,AF166008.1:13222..13469,
>                       AF166008.1:15123..15300)
>                       /gene="KCND2"
>                       /codon_start=1
>                       /product="voltage-gated potassium channel Kv4.2"
>                       /protein_id="AAF65618.1"
>                       /db_xref="GI:7648673"
>
> but the location is truncated when passed through SeqIO to genbank
> output, which explains the spliced_seq() problem:
>
>       CDS             430..1544
>                       /db_xref="GI:7648673"
>                       /codon_start=1
>                       /protein_id="AAF65618.1"
>                       /gene="KCND2"
>
> I'll try looking into this; if I can't get to it immediately I'll
> file a bug report.  Thanks!
>
> chris

Looked into it and there isn't a problem with BioPerl, but there  
appears to be an error on NCBI's end with some full GenBank seqs and  
remote locations.  The default return type for records using  
Bio::DB::GenBank is 'gbwithparts' (which retrieves full records for  
everything), but this particular record version has a truncated  
location.  You can see the truncated version here via eutils:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
db=nucleotide&retmode=text&id=7648671&rettype=gbwithparts

You can get around this in your script by changing the requested  
format to 'gb', which has the correct location string and returns the  
full protein seq:

my $gbh = Bio::DB::GenBank->new(-format => 'gb');

chris


From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From cjfields at uiuc.edu  Fri Oct 19 00:47:12 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 18 Oct 2007 23:47:12 -0500
Subject: [Bioperl-l] Bioperl DB RefSeq
In-Reply-To: <534058.73546.qm@web38804.mail.mud.yahoo.com>
References: <534058.73546.qm@web38804.mail.mud.yahoo.com>
Message-ID: <744D3248-EA8E-4832-847D-4434DFF258E6@uiuc.edu>

Use an eval {} block, described here:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Error_Handling

my $seq;
eval {
   $seq =  $seq = $seq_refseq->get_Seq_by_id("$acc");
};

print "ID does not exist!\n" if $@;

chris

On Oct 18, 2007, at 10:11 PM, Steven Mei wrote:

> Hi,
>
> I have a list of refseq accession  numbers and  wish  to get  their  
> sequences. I used Bio::DB:: RefSeq module
>
> However, if the $acc is bad (such as deleted accession), an  
> exception  would  printed out  and the script stops execution.
>
>
> ---------------EXCEPTION-------------------
> MSG: id does not exist
> ...
> ----------------------------------------------------
>
> my $seq = $seq_refseq->get_Seq_by_id("$acc");
>
>
> What I wish to happen is the script would handle the next accession  
> (bypass the bad accession) and continue until all the accessions  
> have been processed.
>
> Anyone have idea how to handle this issue? Thanks
>
> -- Mike



From j.s.soares at gmail.com  Fri Oct 19 08:45:25 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 05:45:25 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of the gene. This is the thing where the script goes weird. It doesn't
reset the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need to know how
many repetitions of the pattern there are in each gene, as above, it does
not reset the counting of repetitions and istead gives me the repitions in
the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;

#print "What is the pattern you're looking for?";
#chomp (my $pat = <>);# Taking the pattern input from the user and cuting
the new line character in the end

#print "How many letters in the pattern?";
#chomp (my $patlen = <>);# Taking the length of the pattern input from the
user and cuting the new line character in the end

print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";# Taking the file to analyse
input from the user and cuting the new line character in the end

print "Where do you want to store the rough file?";
chomp (my $rough = <>);# Taking the rough file input from the user and
cuting the new line character in the end

print "Where do you want to store the final file?";
chomp (my $final = <>);# Taking the clean file input from the user and
cuting the new line character in the end

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0,
0);#Initialization of the variables common to the whole script:
#$count_of_pat3 is used to count how many times the pattern appears in a DNA
sequence.
#$position states the location in number of bases from the start of the
sequence to the first base of the pattern. 
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');#A
BioPerl module was used here (Bio::Tools::SeqPattern in order to give the
program a better direction telling it what exactly the pattern is about. If
it's DNA, RNA or Protein. In this case it's DNA.

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {#Using
BioPerl module Bio::SeqIO to open the file that contains the sequences to be
analysed
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
#Using Perl's simple default function open to create the rough file and make
it writable

        while (my $seq_obj = $in->next_seq) {
#This while loop uses BioPerl objects: $seq_obj and next_seq. It basically
states that for each sequence in the Sequences file it will run the lines
that follow and after that it will pick up the next sequence

        	#my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE
=>'Dna');#A BioPerl module was used here (Bio::Tools::SeqPattern in order to
give the program a better direction telling it what exactly the pattern is
about. If it's DNA, RNA or Protein. In this case it's DNA.

                my $id1 = $seq_obj->display_id();
#We use the $seq_obj->display_id() object here to be able to chop the fasta
header from each sequence and store it as the variable $id1

                     
				foreach ($seq_obj->seq =~ m/$pat/g){#for each sequence that contains the
pattern we are looking for, we start the count of the times the pattern
repeats itself
								++$count_of_pat;
							
							print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",#The Fasta Header,
the number of pattern repitions and the position where each repition was
found in each sequence is printed on the rough file
							$position + $-[0] + 1, "\n"; #This resets the position for the next
repetition
							$position = $position + length($seq_obj) - $patlen + 1;
							#print $-;
							#print "$count_of_pat\n";
							#print "$position\n";
							#print $seq_obj->seq, "\n";
							}#The positon is set to start from 1 rather than the default Perl
start position 0.
				
							
					}
					
					
        close MOTIFCOUNT;#With the file completelly scanned, the rough file
is closed

        open (SYM, "+< $rough") or die "The file doesn't exist";#The rough
file is open again and if it hasn't been created it prints out that it
doesn't exist

        open (TAB, ">> $final") or die "The gene list wasn't
transformed";#Another file is created and made writable, the final file.
This is done as can be seen in the following lines in order to substitute
any space by a tab and to print, as a header in the file, the motif we were
looking for.

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;#The regexp that substitutes each space
for a tab 
        		print TAB "$line";
        	}
        }
        close (SYM);#Closing both files the rough and the final
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;


Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
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From j.s.soares at gmail.com  Fri Oct 19 09:10:18 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 06:10:18 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of each gene. This is where the script goes weird. It doesn't reset
the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need the
information on how many repetitions of the pattern there are in each gene,
as above, it does not reset the counting of repetitions and instead gives me
the repitions in the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Perl;
use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;




print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";
print "Where do you want to store the rough file?";
chomp (my $rough = <>);
print "Where do you want to store the final file?";
chomp (my $final = <>);

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";


        while (my $seq_obj = $in->next_seq) {

                #my $id1 = $seq_obj->display_id();
				my $seq_length = length($seq_obj);
				#print "$seq_length\n";
				foreach ($seq_obj->seq =~ m/$pat/g){
								++$count_of_pat;
								
								my $id1 = $seq_obj->display_id();
								print $seq_obj->seq, "\n";							
								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
								$position + $-[0] + 1, "\n";
								$position = $position + length($seq_obj) - $patlen + 1;
								#print "$id1\n";
								#print "$count_of_pat\n";
								#print "$position\n";
								
								}
					
					#print "$seq_length\n";
					print $seq_obj->seq, "\n";
					}
					
					
        close MOTIFCOUNT;

        open (SYM, "+< $rough") or die "The file doesn't exist";

        open (TAB, ">> $final") or die "The gene list wasn't transformed";

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;
        		print TAB "$line";
        	}
        }
        close (SYM);
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;



Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From chemmeri at cgb.indiana.edu  Fri Oct 19 09:40:22 2007
From: chemmeri at cgb.indiana.edu (Chris Hemmerich)
Date: Fri, 19 Oct 2007 09:40:22 -0400 (EDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <13293737.post@talk.nabble.com>
References: <13293737.post@talk.nabble.com>
Message-ID: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>



Djoja,

Perhaps this is a problem with scope. Since you declare $position outside 
of

         while (my $seq_obj = $in->next_seq) {

it will not be reset for each sequence.  The line

 		$position = $position + length($seq_obj) - $patlen + 1;

will continue to increase $position for each sequence processed. From a 
quick look, I don't think you need $position at all in this script and can 
just print $-[0]+1.

Hope this helps,

  Chris


On Fri, 19 Oct 2007, Djodja wrote:

>
> Hi all,
>
> This is my first post. I am very puzzeled about a script that i wrote last
> year, that was working fine, and all of sudden, with no change to the code
> it just stopped doing what it was supposed to do. Basically I'm searching
> for patterns on a whole genome database.
>
> The pattern that I'm searching for at the moment is AACAAAG.
>
> My script finds the pattern, no problem on regexps or anything. It also
> searches the whole genome divided in fasta headers for each gene. The
> problem is that I need to know the position of the pattern, relative to the
> start of each gene. This is where the script goes weird. It doesn't reset
> the counter to the start of each gene. It instead continues to count
> patterns as if the genes aren't separated at all. Also I need the
> information on how many repetitions of the pattern there are in each gene,
> as above, it does not reset the counting of repetitions and instead gives me
> the repitions in the whole genome.
>
> here is the code:
>
> #!/usr/lib/perl -w
>
> use Bio::Perl;
> use Bio::Seq ();
> use Bio::SeqIO ();
> use Bio::Tools::SeqPattern ();
> use strict;
> use warnings;
>
>
>
>
> print 'Where is the file that you want to analise?';
> chomp (my $Fasfile = <>) or die "No such file";
> print "Where do you want to store the rough file?";
> chomp (my $rough = <>);
> print "Where do you want to store the final file?";
> chomp (my $final = <>);
>
> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>
> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>
>
>        while (my $seq_obj = $in->next_seq) {
>
>                #my $id1 = $seq_obj->display_id();
> 				my $seq_length = length($seq_obj);
> 				#print "$seq_length\n";
> 				foreach ($seq_obj->seq =~ m/$pat/g){
> 								++$count_of_pat;
>
> 								my $id1 = $seq_obj->display_id();
> 								print $seq_obj->seq, "\n";
> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
> 								$position + $-[0] + 1, "\n";
> 								$position = $position + length($seq_obj) - $patlen + 1;
> 								#print "$id1\n";
> 								#print "$count_of_pat\n";
> 								#print "$position\n";
>
> 								}
>
> 					#print "$seq_length\n";
> 					print $seq_obj->seq, "\n";
> 					}
>
>
>        close MOTIFCOUNT;
>
>        open (SYM, "+< $rough") or die "The file doesn't exist";
>
>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>
> 	print TAB "Motif: $pat\n";
>        while (my $line = <SYM>){
>
>        	foreach ($line){
>                	$line =~ s/\|/\t/g;
>        		print TAB "$line";
>        	}
>        }
>        close (SYM);
>        close(TAB);
>
>        print "The gene list was created and transformed successfully.\n\a"
> }
> exit;
>
>
>
> Can anyone help me out? This is kind of in the way of my PhD progression.
>
> All the best,
>
> Djodja
> -- 
> View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From smei_26 at yahoo.com  Fri Oct 19 13:51:48 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Fri, 19 Oct 2007 10:51:48 -0700 (PDT)
Subject: [Bioperl-l] Please help: GenBank ID map
Message-ID: <560962.35266.qm@web38802.mail.mud.yahoo.com>

Hi, 

I have list of GenBank ID inlcuding ids for EST, gemonics sequence and UniGene. I wish to map these ids to RefSeq Ids using BioPerl. Anyone know how to do this? Thanks

example of the GenBank Id list: 

NM_000137
BC004558
BF939919
AL031588
AI673812
NM_006024
AK024914
AK026008
NM_014823
AA523958
NM_001677
AW291083
AL049246
AF116615
AI672084


-- Mike

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From j.s.soares at gmail.com  Sat Oct 20 03:11:17 2007
From: j.s.soares at gmail.com (Djodja)
Date: Sat, 20 Oct 2007 00:11:17 -0700 (PDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
References: <13293737.post@talk.nabble.com>
	<Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
Message-ID: <13307407.post@talk.nabble.com>


I will have to give you the credit here as well!

THank you so much Chris.

I have declared both $position and $count_of_pat inside the while loop.

Will rearrange the script and I'm going to make it a subroutine as I have
many other patterns to search for.

Thank you thank you thankyou.

Also, I am in England in Exeter. If you want I could look on ways to get you
here for a nice talk for you to expose your work.

Let me know.

Djodja

Chris Hemmerich wrote:
> 
> 
> 
> Djoja,
> 
> Perhaps this is a problem with scope. Since you declare $position outside 
> of
> 
>          while (my $seq_obj = $in->next_seq) {
> 
> it will not be reset for each sequence.  The line
> 
>  		$position = $position + length($seq_obj) - $patlen + 1;
> 
> will continue to increase $position for each sequence processed. From a 
> quick look, I don't think you need $position at all in this script and can 
> just print $-[0]+1.
> 
> Hope this helps,
> 
>   Chris
> 
> 
> On Fri, 19 Oct 2007, Djodja wrote:
> 
>>
>> Hi all,
>>
>> This is my first post. I am very puzzeled about a script that i wrote
>> last
>> year, that was working fine, and all of sudden, with no change to the
>> code
>> it just stopped doing what it was supposed to do. Basically I'm searching
>> for patterns on a whole genome database.
>>
>> The pattern that I'm searching for at the moment is AACAAAG.
>>
>> My script finds the pattern, no problem on regexps or anything. It also
>> searches the whole genome divided in fasta headers for each gene. The
>> problem is that I need to know the position of the pattern, relative to
>> the
>> start of each gene. This is where the script goes weird. It doesn't reset
>> the counter to the start of each gene. It instead continues to count
>> patterns as if the genes aren't separated at all. Also I need the
>> information on how many repetitions of the pattern there are in each
>> gene,
>> as above, it does not reset the counting of repetitions and instead gives
>> me
>> the repitions in the whole genome.
>>
>> here is the code:
>>
>> #!/usr/lib/perl -w
>>
>> use Bio::Perl;
>> use Bio::Seq ();
>> use Bio::SeqIO ();
>> use Bio::Tools::SeqPattern ();
>> use strict;
>> use warnings;
>>
>>
>>
>>
>> print 'Where is the file that you want to analise?';
>> chomp (my $Fasfile = <>) or die "No such file";
>> print "Where do you want to store the rough file?";
>> chomp (my $rough = <>);
>> print "Where do you want to store the final file?";
>> chomp (my $final = <>);
>>
>> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
>> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>>
>> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>>
>>
>>        while (my $seq_obj = $in->next_seq) {
>>
>>                #my $id1 = $seq_obj->display_id();
>> 				my $seq_length = length($seq_obj);
>> 				#print "$seq_length\n";
>> 				foreach ($seq_obj->seq =~ m/$pat/g){
>> 								++$count_of_pat;
>>
>> 								my $id1 = $seq_obj->display_id();
>> 								print $seq_obj->seq, "\n";
>> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
>> 								$position + $-[0] + 1, "\n";
>> 								$position = $position + length($seq_obj) - $patlen + 1;
>> 								#print "$id1\n";
>> 								#print "$count_of_pat\n";
>> 								#print "$position\n";
>>
>> 								}
>>
>> 					#print "$seq_length\n";
>> 					print $seq_obj->seq, "\n";
>> 					}
>>
>>
>>        close MOTIFCOUNT;
>>
>>        open (SYM, "+< $rough") or die "The file doesn't exist";
>>
>>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>>
>> 	print TAB "Motif: $pat\n";
>>        while (my $line = <SYM>){
>>
>>        	foreach ($line){
>>                	$line =~ s/\|/\t/g;
>>        		print TAB "$line";
>>        	}
>>        }
>>        close (SYM);
>>        close(TAB);
>>
>>        print "The gene list was created and transformed
>> successfully.\n\a"
>> }
>> exit;
>>
>>
>>
>> Can anyone help me out? This is kind of in the way of my PhD progression.
>>
>> All the best,
>>
>> Djodja
>> -- 
>> View this message in context:
>> http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13307407
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From avilella at gmail.com  Mon Oct 22 04:53:45 2007
From: avilella at gmail.com (Albert Vilella)
Date: Mon, 22 Oct 2007 09:53:45 +0100
Subject: [Bioperl-l] java runnables
Message-ID: <358f4d650710220153o4a941088qd5a109d546a1e140@mail.gmail.com>

Hi all,

A question related to java runnables in bioperl-run:

I would like to have a Pecan (http://www.bioperl.org/wiki/PECAN) runnable in
bioperl-run,
and there are a couple of java runnables already written, eponine and vista.

I was wondering if the current state of the java runnables satifies
everybody or if people
can think of a more clean or generic way of calling java from bioperl-run.

Comments?

Cheers,

    Albert.


From wgallin at ualberta.ca  Mon Oct 22 13:53:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 11:53:24 -0600
Subject: [Bioperl-l] Problem with EUtilities
Message-ID: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>

I've encountered a problem with retrieving a set of records using  
efetch.

Code snippet:

     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'efetch',
         -db      => 'protein',
         -rettype => 'genbank',
         -id      => \@ginumber_search
     );
     $file = 'temp_hold.gb';

     $gpeptfactory->get_Response( -file => $file );



If the array of gi numbers that I submit is large (482 elements does  
not give the problem but 1517 does) I am getting an error at the  
get_response step:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:144
-----------------------------------------------------------


Am I correct in thinking that the individual array elements are being  
submitted as part of the URI, and therefore a large array is  
exceeding the acceptable size limit for a URI?

If so, is there a workaround?  Breaking the large request into a set  
of smaller requests?
Or is there a way of submitting a file of gi numbers using  
EUtilities, rather than an array?

Warren Gallin


From cjfields at uiuc.edu  Mon Oct 22 14:16:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 13:16:19 -0500
Subject: [Bioperl-l] Problem with EUtilities
In-Reply-To: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
References: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
Message-ID: <DB401D8A-0DC9-46EB-89A9-58093B8FB171@uiuc.edu>


On Oct 22, 2007, at 12:53 PM, Warren Gallin wrote:

> I've encountered a problem with retrieving a set of records using
> efetch.
>
> Code snippet:
>
>      my $gpeptfactory = Bio::DB::EUtilities->new(
>          -eutil   => 'efetch',
>          -db      => 'protein',
>          -rettype => 'genbank',
>          -id      => \@ginumber_search
>      );
>      $file = 'temp_hold.gb';
>
>      $gpeptfactory->get_Response( -file => $file );
>
>
>
> If the array of gi numbers that I submit is large (482 elements does
> not give the problem but 1517 does) I am getting an error at the
> get_response step:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:144
> -----------------------------------------------------------
>
>
> Am I correct in thinking that the individual array elements are being
> submitted as part of the URI, and therefore a large array is
> exceeding the acceptable size limit for a URI?

Yes.

> If so, is there a workaround?  Breaking the large request into a set
> of smaller requests?
> Or is there a way of submitting a file of gi numbers using
> EUtilities, rather than an array?
>
> Warren Gallin

You can use epost and post your IDs first, then retrieve them.   
Alternatively, you can fetch them in small batches.  The following  
two code bits should help:

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_post_a_specific_list_of_UIDs_to_NCBI. 
27s_history_server.3F

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_usi 
ng_a_query.3F

chris


From er at xs4all.nl  Mon Oct 22 12:05:29 2007
From: er at xs4all.nl (Erikjan)
Date: Mon, 22 Oct 2007 18:05:29 +0200 (CEST)
Subject: [Bioperl-l] postgres datatype: VARCHAR to TEXT - patch
Message-ID: <22811.156.83.0.216.1193069129.squirrel@webmail.xs4all.nl>

Hello,

Using load_seqdatabase.pl to load uniprot_sprot.dat into
postgres (8.2.5), biosql gave me:

ERROR:  value too long for type character varying(40)

(all fresh from cvs)

Changing 'VARCHAR(N)' to 'TEXT' fixed those errors.

Generally, VARCHAR[(N)], (=character varying) are probably
better replaced with 'TEXT' as VARCHAR(N) is implemented
as TEXT with a check on length.



Attached is a patch for the table definitions in
biosqldb-pg.sql; I haven't changed the other scripts, as I
don't know if you will agree with this improvement.

(The other table-creating scripts are probably also better
off with a change from VARCHAR (=character varying) to the
text datatype.)

(loading uniprot_sprot.dat took 20 hours to load, but now
without errors, so I won't complain :)


Thanks,

Erik



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From hangsyin at gmail.com  Mon Oct 22 18:30:10 2007
From: hangsyin at gmail.com (Hang)
Date: Mon, 22 Oct 2007 22:30:10 +0000 (UTC)
Subject: [Bioperl-l] Extract features from GFF
Message-ID: <loom.20071022T221835-291@post.gmane.org>

Hello,

I have a list of about 100,000 short genomic regions with paired start and end
coordinations on reference fly genome (R5.3). I also have GFF files from the
same genome release. I wonder how I can extract all overlapping features from
these regions.

For example:

region A is on chromosome 2L between 123,456 bp to 123,489 bp. What code should
I use to extract feature, like gene, CDS etc., that overlaps with this region?

Thank you in advance!

-- Hang



From wgallin at ualberta.ca  Mon Oct 22 20:28:55 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 18:28:55 -0600
Subject: [Bioperl-l] More on EUtilities problem
Message-ID: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>

I seem to be missing something here.

I took the code from the HOWTO as a template and wrote the following  
code snippet (@gisearch_number is an array of gi numbers, prints out  
as expected and can be used to successfully download the relevant  
records using Batch Entrez):
______________________________________________________________

#Create new EUTILS  history object for submitting a large array of gi  
numbers
     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'epost',
         -db      => 'protein',
         -id      => \@ginumber_search,
         -keep_histories => 1
     );

     my $count = @ginumber_search;


     my $history;
     if ($history = $gpeptfactory -> next_History){
    		print "Posted successfully\n";                            
#Prints as expected for successful history
     	print "WebEnv    : ", $history -> get_webenv,"\n";
     	print "Query_key : ",$history->get_query_key,"\n";
     }
     $file = 'temp_hold.gb';

     $gpeptfactory->set_parameters (-eutil => 'efetch',
     							   -rettype => 'genbank',
     							   -history => $history,
     							
	);
	my ($retmax, $retstart) = (300,0);
	my $retry = 0;
RETRIEVE_SEQS: while ($retstart < $count) {
	
     $gpeptfactory->set_parameters(
     						-retmax => $retmax,
                             -retstart => $retstart,
                             );
     eval{
         $gpeptfactory->get_Response(-file => $file);
         print "Output file is $file.\n";
     };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++ && goto RETRIEVE_SEQS;
     }
     else{
     	
     	my $retend = $retstart + $ retmax;
     	print "Loaded entries $retstart through $retend on retry # 
$retry.\n";

     	$retstart += $retmax;
     	$retry = 0;
     }
}

         $retr_seq = Bio::SeqIO->new(
             -file   => $file,
             -format => 'genbank'
         );

________________________________________________
At this point the program fails because there is no file written.

It appears that the get_Response method is not doing its thing.

Also, on each iteration of the loop enclosing the eval the first pass  
fails with the following error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:177
-----------------------------------------------------------
  and then the second pass evaluates as correct - but the output file  
is never opened or written to.

I've tried to pass $file,  "$file" , ">>$file"  and a literal string  
of a file name, with and without the >>, but to no avail.

So I think that I must be missing something basic here, but I am  
unable to see what.

Any advice would be most welcome.

Warren Gallin




From cjfields at uiuc.edu  Mon Oct 22 20:43:31 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 19:43:31 -0500
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>


On Oct 22, 2007, at 5:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang

Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
depend on the GFF version of the data you have.

chris


From cjfields at uiuc.edu  Mon Oct 22 23:50:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 22:50:19 -0500
Subject: [Bioperl-l] More on EUtilities problem
In-Reply-To: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
References: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
Message-ID: <52D724FE-A586-489A-81BE-F9AAA6963435@uiuc.edu>


On Oct 22, 2007, at 7:28 PM, Warren Gallin wrote:

> I seem to be missing something here.
>
> I took the code from the HOWTO as a template and wrote the following
> code snippet (@gisearch_number is an array of gi numbers, prints out
> as expected and can be used to successfully download the relevant
> records using Batch Entrez):
> ...

One problem (but not the main one):

>      $file = 'temp_hold.gb';

You don't indicate the file needs appending (such as when rewriting  
to the same file in the loop below); you should change it to:

$file = '>>temp_hold.gb';

The below section is the main issue:

>      $gpeptfactory->set_parameters (-eutil => 'efetch',
>      							   -rettype => 'genbank',
>      							   -history => $history,
>      							
> 	);

In general, unless you're absolutely sure you want to carry over  
parameters from the previous eutil search (such as when you are  
looping through and changing the retmax/retstart parameters below),  
use reset_parameters():

$gpeptfactory->reset_parameters(
        -eutil => 'efetch',
        -db  => 'protein',
        -rettype => 'genbank',
        -history => $history
);

What's I believe is happening is the id parameter setting from your  
first eutil search is carried over and is reposted in the URL (thus  
getting the error).  reset_parameters() resets all parameters to  
undef unless new parameter args are passed in, in which case those  
are set to the new values, so nothing carries over.

 From that point on everything works fine (though again you'll want  
to specify that you are appending to a file instead of overwriting it  
within the loop).

chris

> 	my ($retmax, $retstart) = (300,0);
> 	my $retry = 0;
> RETRIEVE_SEQS: while ($retstart < $count) {
> 	
>      $gpeptfactory->set_parameters(
>      						-retmax => $retmax,
>                              -retstart => $retstart,
>                              );
>      eval{
>          $gpeptfactory->get_Response(-file => $file);
>          print "Output file is $file.\n";
>      };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++ && goto RETRIEVE_SEQS;
>      }
>      else{
>      	
>      	my $retend = $retstart + $ retmax;
>      	print "Loaded entries $retstart through $retend on retry #
> $retry.\n";
>
>      	$retstart += $retmax;
>      	$retry = 0;
>      }
> }
>
>          $retr_seq = Bio::SeqIO->new(
>              -file   => $file,
>              -format => 'genbank'
>          );
>
> ________________________________________________
> At this point the program fails because there is no file written.
>
> It appears that the get_Response method is not doing its thing.
>
> Also, on each iteration of the loop enclosing the eval the first pass
> fails with the following error message:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:177
> -----------------------------------------------------------
>   and then the second pass evaluates as correct - but the output file
> is never opened or written to.
>
> I've tried to pass $file,  "$file" , ">>$file"  and a literal string
> of a file name, with and without the >>, but to no avail.
>
> So I think that I must be missing something basic here, but I am
> unable to see what.
>
> Any advice would be most welcome.
>
> Warren Gallin
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From barry.moore at genetics.utah.edu  Tue Oct 23 00:09:05 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:09:05 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <7691F0B8-9771-477F-A982-21360F769D4A@genetics.utah.edu>

Hang-

Something like this would work, although for simply querying the  
coordinates on GFF like that you could iterate over the file with  
your own while loop, split the columns and do the same thing with  
about as many lines.  You'll need to do each chromosome as a separate  
GFF file or add some code to the loop to check the chromosome  
($feature->seq_id I think).

     use Bio::Tools::GFF;

     my $coord_start = 12345;
     my $coord_end  = 67890;

     # specify input via -fh or -file
     my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version =>  
2);
     my $feature;
     # loop over the input stream
     while($feature = $gffio->next_feature()) {
	 if ($coord_start <= $feature->start && $coord_end >= $feature->end) {
	 	print $feature->gff_string;
	}
     }
     $gffio->close();

Barry

On Oct 22, 2007, at 4:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From barry.moore at genetics.utah.edu  Tue Oct 23 00:37:07 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:37:07 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <C837CA5E-4E55-4B23-8451-27E74426BB52@genetics.utah.edu>

Oh yeah, much better option if you've got a database running.  Look  
at the docs for the modules Chris suggested.  Something like:

my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                  -dsn     =>  
'dbi:mysql:test',
                                                  -write   => 1 );
# load an entire GFF3 file, using the GFF3 loader...
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    =>  
$db,
							   -verbose  => 1,
							   -fast     => 1);

$loader->load('./my_genome.gff3');

@features = $db->get_features_by_location(-seq_id=>'Chr1',- 
start=>4000,-end=>600000);

Barry

On Oct 22, 2007, at 6:43 PM, Chris Fields wrote:

>
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
>
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files
>> from the
>> same genome release. I wonder how I can extract all overlapping
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
>
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will
> depend on the GFF version of the data you have.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sdavis2 at mail.nih.gov  Tue Oct 23 07:00:12 2007
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 23 Oct 2007 07:00:12 -0400
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <471DD43C.8060203@mail.nih.gov>

Chris Fields wrote:
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
> 
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired  
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files  
>> from the
>> same genome release. I wonder how I can extract all overlapping  
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with  
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
> 
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
> depend on the GFF version of the data you have.
> 
> chris

Not a bioperl solution, but still a very cool application, see:

http://main.g2.bx.psu.edu/

It is web-based and allows for set operations (intersection, union,
etc.) on genomic coordinates.  If you have two sets of regions of
interest, you can then ask (very quickly) for all regions that overlap,
contain, are distinct, etc.

Sean


From forrest_zhang at 163.com  Tue Oct 23 23:27:00 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Wed, 24 Oct 2007 11:27:00 +0800
Subject: [Bioperl-l]
	=?gb2312?B?tPC4tDogW0Jpb3BlcmwtbF0gbG9hZF9zZXFkYXRhYmFzZS5wbCBlcnJvcg==?=
In-Reply-To: <FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
Message-ID: <000101c815ed$bdafb2e0$390f18a0$@com>

Dear Chris:
	What's the result of test? In my computer, the test haven't been
passed.

Forrest Zhang

-----????????-----
??????: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] ???? Chris Fields
????????: 2007??9??29?? 6:03
??????: Forrest Zhang
????: bioperl-l at bioperl.org BioPerl
????: Re: [Bioperl-l] load_seqdatabase.pl error

Okay, fixed the recursion (extra copy of a BasePersistentAdaptor  
module I was working which tripped it, so nothing in CVS).

Forrest, I get all tests passing.  I used a database without taxonomy  
loaded with bioperl-db and bioperl from cvs and it worked w/o  
problems.  I'll try working with your sequence when I have time this  
weekend.

chris

On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:

> I'm actually getting some odd recursion issues again; not sure what's
> causing it, but a reinstall of both bioperl and bioperl-db fixed it
> last time.  It may be related to the rollback, just not sure yet.
>
> I'll try tracking it down if it persists (bad pun).
>
> t/04swiss....ok 3/52
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
> t/04swiss....ok
> All tests successful.
> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
> CPU)
>
> The specific error under verbose running is:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:680
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:658
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:252
> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> PrimarySeqAdaptor.pm:229
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/src/
> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:213
> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
> STACK toplevel t/04swiss.t:37
> ---------------------------------------------------
>
>
> chris
>
> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>
>> Chris let me know if you get stumped. I'm surprised that the special
>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>> assign ranks to them? I thought I filter them out. Needs to be looked
>> into too.), but at any rate I don't understand why they aren't being
>> accepted.
>>
>> Also, maybe we need a more verbose output here - Forrest, can you run
>> this with adding a --printerror argument. (I'm embarrassed to find
>> that this doesn't seem to be documented. Sigh.)
>>
>> 	-hilmar
>>
>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>
>>> If this is occurring using bioperl from CVS then I'll try taking a
>>> look at it.
>>>
>>> chris
>>>
>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>
>>>> Hilmar,
>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I
>>>> was
>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>> | rosids
>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>> Euphyllophyta |
>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>> ---------------------------------------------------
>>>> Could not store Q40784:
>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>> by unique
>>>> key
>>>> STACK: Error::throw
>>>> STACK: Bio::Root::Root::throw
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:206
>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:244
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:169
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:251
>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:271
>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>> -----------------------------------------------------------
>>>> Sigh~~~~~~
>>>>
>>>> Forrest Zhang
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>> Lapp
>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>> To: Forrest
>>>> Cc: bioperl-l at bioperl.org
>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>
>>>> Forrest,
>>>>
>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>> the
>>>> code will try to use it to look up species and their lineage,  
>>>> rather
>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>> sequence record.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>
>>>>> Hi, all
>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>> swissport data.
>>>>> But the programe show some error as below:
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>> mysql
>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>> Could not store Q6DAH5:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>> subsp.
>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>> Pectobacterium |
>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>> Proteobacteria | Bacteria')
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>> STACK: Bio::Species::classification
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:552
>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:1305
>>>>> STACK:  
>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:973
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:852
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:182
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: load_seqdatabase.pl:620
>>>>> -----------------------------------------------------------
>>>>>
>>>>>  at load_seqdatabase.pl line 633
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>
>>>>> How can I solve it, please help me, Thank you.
>>>>>
>>>>> Thanks
>>>>> Forrest zhang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From cjfields at uiuc.edu  Wed Oct 24 00:21:00 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 23 Oct 2007 23:21:00 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000101c815ed$bdafb2e0$390f18a0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
Message-ID: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From martin.burkert at uni-bielefeld.de  Wed Oct 24 08:25:13 2007
From: martin.burkert at uni-bielefeld.de (Martin Burkert)
Date: Wed, 24 Oct 2007 14:25:13 +0200
Subject: [Bioperl-l] Problems parsing Glimmer output
Message-ID: <471F39A9.6050909@uni-bielefeld.de>

Hello,

i can't figure out why my Glimmer files can not be parsed from
Bio::Tools::Glimmer.

---- pbglimmer.pl ----
use strict;
use Bio::Tools::Glimmer;

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
my $predictionCount = 0;

while(my $gene = $parser->next_prediction()) {
	$predictionCount++;
	print $predictionCount.	':' .$gene->display_name().
				', '.$gene->start().
				', '.$gene->stop()."\n";
}
print "Total predictions: ".$predictionCount;

---- pb4.predict ----
>pb4
orf00001     1022     1138  +2     0.90
orf00002     1655     1131  -3     2.77
orf00003     1638     2390  +3     3.59
orf00004     3176     3472  +2     0.30
orf00006     4395     5561  +3     2.96
orf00008     5576     8719  +2     2.98
orf00012     8725    10152  +1     2.96
orf00013    10906    11019  +1     0.21
orf00014    12188    12292  +2     2.41
orf00017    12518    14077  +2     2.97
orf00019    15356    15246  -3     2.21
orf00020    17864    17748  -3     0.23
orf00021    18153    18037  -1     0.32
orf00023    19253    19462  +2     0.48
orf00025    21018    20902  -1     0.23
orf00027    21658    24708  +1     2.92
orf00030    26115    24898  -1     2.96
orf00031    26414    26112  -3     3.21
orf00032    28015    28473  +1     3.54
orf00033    28044    27223  -1     2.85
orf00037    30137    30033  -3     2.80
orf00041    30183    33152  +3     2.98
orf00045    34860    33637  -1     2.96
orf00047    35142    34909  -1     2.54
orf00050    36606    36737  +3     1.44
orf00052    37616    37789  +2     2.23
orf00054    37786    40344  +1     2.98
orf00056    40624    40505  -2     0.79
orf00057    42508    43890  +1     2.96
orf00059    44183    44680  +2     1.49
orf00060    44705    44908  +2     0.05
orf00063    44920    46632  +1     2.97
orf00068    47296    47865  +1     0.39
orf00071    47953    49134  +1     2.90
orf00072    49208    49318  +2     1.15
orf00074    51139    51270  +1     1.16
orf00083    58362    53767  -1     2.99
orf00088    60846    58783  -1     2.98
orf00090    63298    61394  -2     2.97
orf00093    65553    63295  -1     2.98
orf00095    65959    65588  -2     1.13
orf00096    66185    65964  -3     2.98
orf00098    66610    66933  +1     0.11
orf00099    67371    67658  +3     0.27
orf00102    71019    68134  -1     2.98
orf00103    71825    72628  +2     2.71
orf00105    75062    73740  -3     2.96
orf00106    75817    76221  +1     0.73
orf00109    78206    76734  -3     2.92
orf00113      198    79299  -3     4.22


The program always outputs "Total predictions: 0".

I also tried to force the parsing format to be just 'Glimmer'
(prokaryotic) and not 'GlimmerHmm'  with:

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', -format =>
'Glimmer');

The pb4.predict was generated by glimmer3.02. I also tried to parse an
output from glimmer2.X, but without success.

Printing $parser with Data::Dumper outputs:

$VAR1 = bless( {
                 '_file' => 'pb4.predict',
                 '_preds_parsed' => 0,
                 '_analysis_date' => undef,
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_analysis_sbjct' => undef,
                 '_analysis_progVersion' => undef,
                 '_flush_on_write' => 1,
                 '_analysis_prog' => undef,
                 '_filehandle' => \*Symbol::GEN0,
                 '_analysis_query' => undef,
                 '_root_verbose' => 0,
                 '_preds' => []
               }, 'Bio::Tools::Glimmer' );

My installation:

Perl v5.8.8 built for MSWin32-x86-multi-thread
Bioperl 1.4

Thank you.

-- 
Viele Gr??e,

MARTIN BURKERT
mailto:martin.burkert at uni-bielefeld.de


From cjfields at uiuc.edu  Wed Oct 24 09:38:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 08:38:03 -0500
Subject: [Bioperl-l] Problems parsing Glimmer output
In-Reply-To: <471F39A9.6050909@uni-bielefeld.de>
References: <471F39A9.6050909@uni-bielefeld.de>
Message-ID: <37465B90-4A03-4A53-B4EF-BCC8296BAE2C@uiuc.edu>

Update to bioperl-live (from CVS).  The Glimmer parser was recently  
revised by Mark Johnson for Glimmer3 output.  I added a few fixes  
myself to correct start/end issues.

chris

On Oct 24, 2007, at 7:25 AM, Martin Burkert wrote:

> Hello,
>
> i can't figure out why my Glimmer files can not be parsed from
> Bio::Tools::Glimmer.
>
> ---- pbglimmer.pl ----
> use strict;
> use Bio::Tools::Glimmer;
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
> my $predictionCount = 0;
>
> while(my $gene = $parser->next_prediction()) {
> 	$predictionCount++;
> 	print $predictionCount.	':' .$gene->display_name().
> 				', '.$gene->start().
> 				', '.$gene->stop()."\n";
> }
> print "Total predictions: ".$predictionCount;
>
> ---- pb4.predict ----
>> pb4
> orf00001     1022     1138  +2     0.90
> orf00002     1655     1131  -3     2.77
> orf00003     1638     2390  +3     3.59
> orf00004     3176     3472  +2     0.30
> orf00006     4395     5561  +3     2.96
> orf00008     5576     8719  +2     2.98
> orf00012     8725    10152  +1     2.96
> orf00013    10906    11019  +1     0.21
> orf00014    12188    12292  +2     2.41
> orf00017    12518    14077  +2     2.97
> orf00019    15356    15246  -3     2.21
> orf00020    17864    17748  -3     0.23
> orf00021    18153    18037  -1     0.32
> orf00023    19253    19462  +2     0.48
> orf00025    21018    20902  -1     0.23
> orf00027    21658    24708  +1     2.92
> orf00030    26115    24898  -1     2.96
> orf00031    26414    26112  -3     3.21
> orf00032    28015    28473  +1     3.54
> orf00033    28044    27223  -1     2.85
> orf00037    30137    30033  -3     2.80
> orf00041    30183    33152  +3     2.98
> orf00045    34860    33637  -1     2.96
> orf00047    35142    34909  -1     2.54
> orf00050    36606    36737  +3     1.44
> orf00052    37616    37789  +2     2.23
> orf00054    37786    40344  +1     2.98
> orf00056    40624    40505  -2     0.79
> orf00057    42508    43890  +1     2.96
> orf00059    44183    44680  +2     1.49
> orf00060    44705    44908  +2     0.05
> orf00063    44920    46632  +1     2.97
> orf00068    47296    47865  +1     0.39
> orf00071    47953    49134  +1     2.90
> orf00072    49208    49318  +2     1.15
> orf00074    51139    51270  +1     1.16
> orf00083    58362    53767  -1     2.99
> orf00088    60846    58783  -1     2.98
> orf00090    63298    61394  -2     2.97
> orf00093    65553    63295  -1     2.98
> orf00095    65959    65588  -2     1.13
> orf00096    66185    65964  -3     2.98
> orf00098    66610    66933  +1     0.11
> orf00099    67371    67658  +3     0.27
> orf00102    71019    68134  -1     2.98
> orf00103    71825    72628  +2     2.71
> orf00105    75062    73740  -3     2.96
> orf00106    75817    76221  +1     0.73
> orf00109    78206    76734  -3     2.92
> orf00113      198    79299  -3     4.22
>
>
> The program always outputs "Total predictions: 0".
>
> I also tried to force the parsing format to be just 'Glimmer'
> (prokaryotic) and not 'GlimmerHmm'  with:
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', - 
> format =>
> 'Glimmer');
>
> The pb4.predict was generated by glimmer3.02. I also tried to parse an
> output from glimmer2.X, but without success.
>
> Printing $parser with Data::Dumper outputs:
>
> $VAR1 = bless( {
>                  '_file' => 'pb4.predict',
>                  '_preds_parsed' => 0,
>                  '_analysis_date' => undef,
>                  '_root_cleanup_methods' => [
>                                               sub { "DUMMY" }
>                                             ],
>                  '_analysis_sbjct' => undef,
>                  '_analysis_progVersion' => undef,
>                  '_flush_on_write' => 1,
>                  '_analysis_prog' => undef,
>                  '_filehandle' => \*Symbol::GEN0,
>                  '_analysis_query' => undef,
>                  '_root_verbose' => 0,
>                  '_preds' => []
>                }, 'Bio::Tools::Glimmer' );
>
> My installation:
>
> Perl v5.8.8 built for MSWin32-x86-multi-thread
> Bioperl 1.4
>
> Thank you.
>
> -- 
> Viele Gr??e,
>
> MARTIN BURKERT
> mailto:martin.burkert at uni-bielefeld.de
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From forrest_zhang at 163.com  Wed Oct 24 12:00:24 2007
From: forrest_zhang at 163.com (Forrest)
Date: Thu, 25 Oct 2007 00:00:24 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
Message-ID: <000001c81657$0067fd40$0137f7c0$@com>

Dear Chris,
	I was using different swissprot data all of the have some error about the taxon.
Maybe I should re-install bioperl and biosql. Could you give me the install protocol 
what you used.


Forrest Zhang

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Wednesday, October 24, 2007 12:21 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign









From cjfields at uiuc.edu  Wed Oct 24 12:47:45 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 11:47:45 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000001c81657$0067fd40$0137f7c0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
	<000001c81657$0067fd40$0137f7c0$@com>
Message-ID: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Wed Oct 24 14:56:55 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 11:56:55 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
Message-ID: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>

Has anyone else encountered a problem parsing wu-blast output with
Bio::SearchIO ?

The ->next_hit method first returns the "unfiltered+1" sequence; that is,
the plus strand representation of the query sequence that is listed (before
the minus strand) before the summary of hits and e-values.

Then, the next time the next_hit method is called, it returns the second hit
on the list.

The only caveat to my "bug" report here is that I was searching a database
that included the query sequence, so the first hit was identical to the
query (and maybe somehow retained the "unfiltered+1" tag?) ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 15:39:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 12:39:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
Message-ID: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>

I'm relatively new to both objects and bioperl, and I'm having trouble
finding documentation on what values an attribute can have.  For example, in
Bio::Assembly::Contig the example script invokes the 'new' method with an
example filename and assigns the -format attribute (I think that's the
correct terminology) a value of 'phrap' ...

now, I'm wanting to process contig output from the cap3 program, so I'll try
assigning 'cap3' to the -format attribute (haven't tried yet so I don't know
if it will work), but where do I look for a complete list of what possible
values I can use?  I can't find it via either the Pdoc or CPAN documentation
links from the bioperl wiki pages.  Any help would be appreciated ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From David.Messina at sbc.su.se  Wed Oct 24 16:35:48 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:35:48 +0200
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
Message-ID: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>

Hi Joseph,

Could you post the blast report that's giving you trouble? And also could
you tell us what version of WU-BLAST you're running and what version of
BioPerl you're using?

I'd like to try and reproduce your problem.

Thanks,
Dave


From David.Messina at sbc.su.se  Wed Oct 24 16:59:12 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:59:12 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
Message-ID: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>

I couldn't find the formats for Bio::Assembly::Contig in any of the
documentation either.

In situations like these, I poke around in the code for methods that deal
with whatever I'm looking for. In this case, I went to the pdoc for
Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
_guess_format method:

sub _guess_format {

   my $class = shift;
   my $arg   = shift;


return unless defined($arg);
   return 'ace'
 if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap'
 if ($arg =~ /\.phrap\.out$/i);

}

So it looks like 'ace' and 'phrap' are the two assembly formats that are
supported.

The other place where the question of formats often comes up is with
sequence formats. Those are better documented, in the SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats


Dave


From florent.angly at gmail.com  Wed Oct 24 17:25:25 2007
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 24 Oct 2007 14:25:25 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
Message-ID: <471FB845.2080201@gmail.com>

Dave,
Have a look in Bio::Assembly::Contig::IO, that's where all the supported 
assembly input/output formats are located. It's convenient to use the 
BioPerl Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query 
<http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query>
'ace' and 'phrap' are the supported formats. The 'tigr' assembler format 
has been added in the CVS version recently too.
Florent


Dave Messina wrote:
> I couldn't find the formats for Bio::Assembly::Contig in any of the
> documentation either.
>
> In situations like these, I poke around in the code for methods that deal
> with whatever I'm looking for. In this case, I went to the pdoc for
> Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> _guess_format method:
>
> sub _guess_format {
>
>    my $class = shift;
>    my $arg   = shift;
>
>
> return unless defined($arg);
>    return 'ace'
>  if ($arg =~ /\.ace\.\d+$/i);
>    return 'phrap'
>  if ($arg =~ /\.phrap\.out$/i);
>
> }
>
> So it looks like 'ace' and 'phrap' are the two assembly formats that are
> supported.
>
> The other place where the question of formats often comes up is with
> sequence formats. Those are better documented, in the SeqIO HOWTO:
>
> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
>
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From joseph.fass at gmail.com  Wed Oct 24 17:43:08 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:43:08 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
Message-ID: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 17:45:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:45:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <471FB845.2080201@gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
Message-ID: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>

thanks, both of you!

On 10/24/07, Florent Angly <florent.angly at gmail.com> wrote:
>
> Dave,
> Have a look in Bio::Assembly::Contig::IO, that's where all the supported
> assembly input/output formats are located. It's convenient to use the
> BioPerl Deobfuscator:
>
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> <
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> >
> 'ace' and 'phrap' are the supported formats. The 'tigr' assembler format
> has been added in the CVS version recently too.
> Florent
>
>
> Dave Messina wrote:
> > I couldn't find the formats for Bio::Assembly::Contig in any of the
> > documentation either.
> >
> > In situations like these, I poke around in the code for methods that
> deal
> > with whatever I'm looking for. In this case, I went to the pdoc for
> > Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> > Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> > _guess_format method:
> >
> > sub _guess_format {
> >
> >    my $class = shift;
> >    my $arg   = shift;
> >
> >
> > return unless defined($arg);
> >    return 'ace'
> >  if ($arg =~ /\.ace\.\d+$/i);
> >    return 'phrap'
> >  if ($arg =~ /\.phrap\.out$/i);
> >
> > }
> >
> > So it looks like 'ace' and 'phrap' are the two assembly formats that are
> > supported.
> >
> > The other place where the question of formats often comes up is with
> > sequence formats. Those are better documented, in the SeqIO HOWTO:
> >
> > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
> >
> >
> > Dave
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From jason at bioperl.org  Wed Oct 24 18:18:09 2007
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Oct 2007 18:18:09 -0400
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
Message-ID: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>

I'm pretty sure we fixed this problem after 1.4 so current "unstable"  
code a try first and let us know nif that solves the problem.

also - copy+paste of BLAST files on mailing list doesn't work so well  
so either a link to  URL or posting the file in a bugzilla bug  
(bugzilla.open-bio.org) make it easier for someone to try this at home.

-jason
On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:

> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what  
> you find.
>
> Joe
>
[SNIP]
--
Jason Stajich
jason at bioperl.org



From joseph.fass at gmail.com  Wed Oct 24 18:53:41 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 15:53:41 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
Message-ID: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>

I just updated to 1.5.2 via CPAN, and verified that that worked, and re-ran
my code ... same problem: it's still picking up "unfiltered+1" as the first
->next_hit result from wu-blast output.  This is a different issue than the
fixed bug (ID: 1649) I just found on bugzilla; that bug concerned the hit
sequences.  I'll post a report on bugzilla along with some files to try it
with (please let me know if what I upload there is incomplete).

Thanks for the quick attention, all!

~joe




On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I'm pretty sure we fixed this problem after 1.4 so current "unstable" code
> a try first and let us know nif that solves the problem.
>
> also - copy+paste of BLAST files on mailing list doesn't work so well so
> either a link to  URL or posting the file in a bugzilla bug (
> bugzilla.open-bio.org) make it easier for someone to try this at home.
>
> -jason
> On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
>
> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what you find.
>
> Joe
>
> [SNIP]
> --
> Jason Stajich
> jason at bioperl.org
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 19:25:50 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 16:25:50 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
	<195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
Message-ID: <195e25cb0710241625o8b92fe0y65925025fc9144c0@mail.gmail.com>

There's a script and sample input file to demonstrate this in Bugzilla, bug#
2388 <http://bugzilla.open-bio.org/show_bug.cgi?id=2388>

~joe



On 10/24/07, Joseph Fass <joseph.fass at gmail.com> wrote:
>
> I just updated to 1.5.2 via CPAN, and verified that that worked, and
> re-ran my code ... same problem: it's still picking up "unfiltered+1" as the
> first ->next_hit result from wu-blast output.  This is a different issue
> than the fixed bug (ID: 1649) I just found on bugzilla; that bug concerned
> the hit sequences.  I'll post a report on bugzilla along with some files to
> try it with (please let me know if what I upload there is incomplete).
>
> Thanks for the quick attention, all!
>
> ~joe
>
>
>
>
> On 10/24/07, Jason Stajich <jason at bioperl.org > wrote:
> >
> >  I'm pretty sure we fixed this problem after 1.4 so current "unstable"
> > code a try first and let us know nif that solves the problem.
> >
> > also - copy+paste of BLAST files on mailing list doesn't work so well so
> > either a link to  URL or posting the file in a bugzilla bug (
> > bugzilla.open-bio.org) make it easier for someone to try this at home.
> >
> > -jason
> > On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
> >
> > Hi Dave,
> >
> > here's my code, followed by a sample wu-blast report (below).
> > I'm using bioperl version 1.4
> > Thanks for looking into it, and I'd be very curious to know what you
> > find.
> >
> > Joe
> >
> > [SNIP]
> > --
> > Jason Stajich
> > jason at bioperl.org
> >
> >
>
>
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
>



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From simona_bazzocchi at yahoo.it  Wed Oct 24 23:46:53 2007
From: simona_bazzocchi at yahoo.it (simona bazzocchi)
Date: Thu, 25 Oct 2007 05:46:53 +0200 (CEST)
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
Message-ID: <594278.55585.qm@web27710.mail.ukl.yahoo.com>

Hi all, 
I'd like to parse my blast file to outuput in a html file filtering on percent identity, (75% identical or better). So I've just copied and pasted to create my perl file.
I launched this command:
perl searchIO.pl blast_file.txt
But it returned this error: "t
Bareword found where operator expected at searchIO.pl line 26, near "->length E"
        (Missing operator before E?)
syntax error at searchIO.pl line 26, near "->length E"
syntax error at searchIO.pl line 30, near "<gt"
Execution of searchIO.pl aborted due to compilation errors."
Here below you can find searchIO.pl
thanks



#!/usr/bin/perl
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);


# to filter your output
my $MinLength = 100; # need a variable with scope outside the method
sub hsp_filter { 
      my $hsp = shift;
      return 1 if $hsp->length('total') > $MinLength;
  }
sub result_filter { 
      my $result = shift;
      return $hsp->num_hits > 0;
  }

  sub hit_filter { 
      my $hit = shift;
      return $hit->length E<gt> 100; # test if length of the hit sequence
                                     # long enough    
  }
  my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HIT' =E<gt> \&hit_filter }  
      );


my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);

# can also set the filter via the writer object
$writer->filter('RESULT', \&result_filter);


 		
---------------------------------
Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3


From torsten.seemann at infotech.monash.edu.au  Thu Oct 25 00:20:13 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 25 Oct 2007 14:20:13 +1000
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
In-Reply-To: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
References: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
Message-ID: <a79f6a4b0710242120g13e9a55dq710d004745b7e68b@mail.gmail.com>

Simona

> So I've just copied and pasted to create my perl file.
> syntax error at searchIO.pl line 26, near "->length E"
> syntax error at searchIO.pl line 30, near "<gt"
>   sub hit_filter {
>       my $hit = shift;
>       return $hit->length E<gt> 100; # test if length of the hit sequence

You have a Perl syntax error due to cutting and pasting from code in
PerlDoc format. It should read:

  return $hit->length > 100;  # not "E<gt>

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From forrest_zhang at 163.com  Thu Oct 25 02:35:19 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 14:35:19 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>	<000101c815ed$bdafb2e0$390f18a0$@com>	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>	<000001c81657$0067fd40$0137f7c0$@com>
	<D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
Message-ID: <000001c816d1$38d70250$aa8506f0$@com>

Dear Chris,
	I try you protocol, but the taxonomy problem is still existent. And the new problem about " The table 'comment' is full" is coming.
The error example like below:
	
Could not store Q6DA52: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp. atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium | Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria | Proteobacteria | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Species::classification /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("-!- CATALYTIC ACTIVITY: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
-!- PATHWAY: Metabolic intermediate biosynthesis; chorismate
    biosynthesis; chorismate from D-erythrose 4-phosphate and PEP:
    step 3/7.
-!- PATHWAY: Context: Aromatic amino acids biosynthesis.
-!- SUBUNIT: Homodimer (By similarity).
-!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
","1") FKs (12352)
The table 'comment' is full
---------------------------------------------------
Could not store Q723F8: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Comment) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

 at load_seqdatabase.pl line 643
	

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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Bioperl-l at lists.open-bio.org
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From forrest_zhang at 163.com  Thu Oct 25 04:16:34 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:34 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000101c816df$600c5c40$202514c0$@com>



-----Original Message-----
From: Forrest Zhang [mailto:forrest_zhang at 163.com] 
Sent: Thursday, October 25, 2007 4:16 PM
To: 'Chris Fields'
Subject: RE: [Bioperl-l] ??: load_seqdatabase.pl error

Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:16:58 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:58 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000201c816df$6c956fb0$45c04f10$@com>


Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:06:27 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:06:27 +0800
Subject: [Bioperl-l] FW:  problem parsing WU-blast output
Message-ID: <000201c816dd$f5c5e5f0$e151b1d0$@com>

Hi, Joe
	My this script(wublast.pl) maybe is useful for you. You can get the
subsequence by using query range and hit range.
	The script is below, and the file name is wublast.pl.

use strict;
use Bio::SearchIO;

die "Usage:perl wublast <File>\n"
      unless @ARGV==1;
my $inputfile = $ARGV[0];
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => $inputfile);
print "query","\t","hit","\t","total_length","\t",
      "query_lenth","\t","hit_length","\t",
      "percent_identity","\t","score","\t","evalue","\t","rank",
      "\t","query range","\t","hit range","\n";

while( my $result = $in->next_result ) {
    my $image=$result->query_name;

    while( my $hit = $result->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {

	print $image,"\t",$hit->name,"\t",$hsp->length('total'),"\t",
	      $hsp->length('query'),"\t",$hsp->length('hit'),"\t",
	    $hsp->percent_identity,"\t",$hsp->score,"\t",$hsp->evalue,"\t",
 
$hsp->rank,"\t",$hsp->start('query'),",",$hsp->end('query'),"\t",
            $hsp->start('hit'),",",$hsp->end('hit'),"\n";

	}  
    }
}


Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
Sent: Thursday, October 25, 2007 5:43 AM
To: Dave Messina
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] problem parsing WU-blast output

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
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From David.Messina at sbc.su.se  Thu Oct 25 04:52:14 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 25 Oct 2007 10:52:14 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
	<195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
Message-ID: <628aabb70710250152l6218fa1as78b9ab23731f1530@mail.gmail.com>

Ah, wonderful -- thanks Florent! Man, that Deobfuscator sure is useful. :)

Dave


From cjfields at uiuc.edu  Thu Oct 25 09:07:23 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 25 Oct 2007 08:07:23 -0500
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
 =?utf-8?q?=2Epl_error?=
In-Reply-To: <000201c816df$6c956fb0$45c04f10$@com>
References: <000201c816df$6c956fb0$45c04f10$@com>
Message-ID: <F7F03A54-34F1-45A8-8141-7E785F0FB555@uiuc.edu>

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Thu Oct 25 17:50:02 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Thu, 25 Oct 2007 14:50:02 -0700
Subject: [Bioperl-l] what's the optimal way to search a fasta file for
	matching ID's?
Message-ID: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>

I would appreciate any advice, big or small, on this ...

I've got a decent-sized database ... 90,000 sequences or so in a single
fasta-format file.  Then, I've got sequence ID's from that database that
show up in blast reports.  I want to collect those ID's and their sequences
(for the purposes of exploring possible contigs).  Since the blast report
only includes sub-sequences (from alignments) of my sequences, I want to
parse the report, then match each hit ID against an ID in the database, so I
can pull out its full sequence.  Is there a faster way to do this than
opening the database file each time I have a new hit ID, so I can search it
from beginning to end?  If I push each sequence onto a list or hash, it's
liable to chew up a lot of RAM, I'm guessing.  Any suggestions?

Thanks in advance,
~joe

-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From MEC at stowers-institute.org  Thu Oct 25 18:17:04 2007
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Thu, 25 Oct 2007 17:17:04 -0500
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
Message-ID: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>

If you have the fasta database already indexed for blast searching, then
you should use fastacmd, which comes with the blast package, for
extracting (sub)sequences based on ID (and indices).

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
> Sent: Thursday, October 25, 2007 4:50 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] what's the optimal way to search a fasta 
> file formatching ID's?
> 
> I would appreciate any advice, big or small, on this ...
> 
> I've got a decent-sized database ... 90,000 sequences or so 
> in a single fasta-format file.  Then, I've got sequence ID's 
> from that database that show up in blast reports.  I want to 
> collect those ID's and their sequences (for the purposes of 
> exploring possible contigs).  Since the blast report only 
> includes sub-sequences (from alignments) of my sequences, I 
> want to parse the report, then match each hit ID against an 
> ID in the database, so I can pull out its full sequence.  Is 
> there a faster way to do this than opening the database file 
> each time I have a new hit ID, so I can search it from 
> beginning to end?  If I push each sequence onto a list or 
> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any 
> suggestions?
> 
> Thanks in advance,
> ~joe
> 
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From jason at bioperl.org  Fri Oct 26 00:57:52 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 00:57:52 -0400
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
	<CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
Message-ID: <8F627E8A-EE44-4953-9A90-F82BC69C15D9@bioperl.org>

or see Bio::DB::Fasta if you want a bioperl soln.

On Oct 25, 2007, at 6:17 PM, Cook, Malcolm wrote:

> If you have the fasta database already indexed for blast searching,  
> then
> you should use fastacmd, which comes with the blast package, for
> extracting (sub)sequences based on ID (and indices).
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph  
>> Fass
>> Sent: Thursday, October 25, 2007 4:50 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] what's the optimal way to search a fasta
>> file formatching ID's?
>>
>> I would appreciate any advice, big or small, on this ...
>>
>> I've got a decent-sized database ... 90,000 sequences or so
>> in a single fasta-format file.  Then, I've got sequence ID's
>> from that database that show up in blast reports.  I want to
>> collect those ID's and their sequences (for the purposes of
>> exploring possible contigs).  Since the blast report only
>> includes sub-sequences (from alignments) of my sequences, I
>> want to parse the report, then match each hit ID against an
>> ID in the database, so I can pull out its full sequence.  Is
>> there a faster way to do this than opening the database file
>> each time I have a new hit ID, so I can search it from
>> beginning to end?  If I push each sequence onto a list or
>> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any
>> suggestions?
>>
>> Thanks in advance,
>> ~joe
>>
>> --
>> Joseph Fass
>> joseph.fass at gmail.com  ||  joefass at hotmail.com
>> 970.227.5928 (c)  ||  530.754.7978 (w)
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From forrest_zhang at 163.com  Fri Oct 26 04:21:56 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Fri, 26 Oct 2007 16:21:56 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICBGVzogIOetlOWkjTogIGxvYWRfc2VxZGF0?=
	=?utf-8?q?abase=2Epl_error?=
Message-ID: <000701c817a9$4733fb40$d59bf1c0$@com>

Chris,
	I am using --safe to loading sequence. Maybe I would load species data one by one.
It seem be OK now.

	Thanks for your help so much Chris.

Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 9:07 PM
To: Forrest Zhang; BioSQL
Cc: bioperl-l at bioperl.org BioPerl
Subject: Re: [Bioperl-l] FW: ??: load_seqdatabase.pl error

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From avilella at gmail.com  Fri Oct 26 05:33:09 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 10:33:09 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
Message-ID: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>

Hi all,

I was looking at the Gumby runnable, which is pretty cool. But I got an
error
when running the tests (see below). Can other people reproduce this?

It seems to me that the runnable is expecting a tree object, not the
filename for a tree...

avilella at magneto:~/bioperl/vanilla/bioperl-run$ perl t/Gumby.t
1..124
ok 1 - use Bio::Tools::Run::Phylo::Gumby;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::TreeIO;
ok 4 - use Bio::DB::Taxonomy;
ok 5 - use Bio::Tools::GFF;
ok 6 - Found input alignment file
ok 7 - Found input tree file
ok 8 - Found input gff file
ok 9 - The object isa Bio::Tools::Run::Phylo::Gumby
ok 10 - has a created method not in args
ok 11 - quiet was set
ok 12 - program_dir returned correct default
ok 13 - Correct exe default name
Can't call method "value" without a package or object reference at
/home/avilella/bioperl/vanilla/bioperl-live/Bio/Tools/Phylo/Gumby.pm line
136, <GEN2> line 6.
# Looks like you planned 124 tests but only ran 13.
# Looks like your test died just after 13.


From bix at sendu.me.uk  Fri Oct 26 06:10:41 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 11:10:41 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <4721BD21.9060805@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got
> an error when running the tests (see below). Can other people
> reproduce this?
> 
> It seems to me that the runnable is expecting a tree object, not the 
> filename for a tree...

No, most likely this is another thing broken by the SeqFeature changes.
I'm going to go ahead and try out some of my proposals in the
'Bio::SeqFeature::Annotated API change' thread.


From Rohit.Ghai at mikrobio.med.uni-giessen.de  Fri Oct 26 07:30:43 2007
From: Rohit.Ghai at mikrobio.med.uni-giessen.de (Rohit Ghai)
Date: Fri, 26 Oct 2007 13:30:43 +0200
Subject: [Bioperl-l] cannot run emboss from bioperl on windows
Message-ID: <4721CFE3.4060805@mikrobio.med.uni-giessen.de>

Dear all,

I have emboss installed on a windows machine. (Embosswin). I can run
this from the dos command line and the path is present. However, when I 
try to call
an emboss application from bioperl I get a "Application not found error"


   my $f = Bio::Factory::EMBOSS->new();
   # get an EMBOSS application  object from the factory
   my $fuzznuc = $f->program('fuzznuc');
     $fuzznuc->run(
                   { -sequence  => $infile,
                         -pattern   => $motif,
                        -outfile   => $outfile                       
               });
  gives the following error

-------------------- WARNING ---------------------
MSG: Application [fuzznuc] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at searchPatterns.pl line 
102.

Can somebody help me fix this ?

best regards
Rohit

-- 

Dr. Rohit Ghai
Institute of Medical Microbiology
Faculty of Medicine
Justus-Liebig University
Frankfurter Strasse 107
35392 - Giessen
GERMANY

Tel  :	0049 (0)641-9946413
Fax  :	0049 (0)641-9946409
Email:  Rohit.Ghai at mikrobio.med.uni-giessen.de



From cjfields at uiuc.edu  Fri Oct 26 08:51:26 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 07:51:26 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <4721BD21.9060805@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<4721BD21.9060805@sendu.me.uk>
Message-ID: <D2A5B64D-9534-4421-A6B5-6EA607F3D649@uiuc.edu>


On Oct 26, 2007, at 5:10 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I got
>> an error when running the tests (see below). Can other people
>> reproduce this?
>>
>> It seems to me that the runnable is expecting a tree object, not the
>> filename for a tree...
>
> No, most likely this is another thing broken by the SeqFeature  
> changes.
> I'm going to go ahead and try out some of my proposals in the
> 'Bio::SeqFeature::Annotated API change' thread.

I was able to repeat it on my end.  If you have a fix for it  
involving B::SF::A then definitely go ahead.

chris


From bix at sendu.me.uk  Fri Oct 26 10:48:27 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 15:48:27 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
Message-ID: <4721FE3B.2080507@sendu.me.uk>

Hilmar Lapp wrote:
> 
> On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:
> 
>> seq_id()
>>   Usage   : $obj->seq_id($newval)
>>   Function: holds a string corresponding to the unique
>>             seq_id of the sequence underlying the feature
>>             (e.g. database accession or primary key).
>>   Returns : a Bio::Annotation::SimpleValue object representing the
>>             seq_id.
> 
> type() and source() should be ontology-typed in a TypedSeqFeatureI (and 
> therefore be instances of Bio::Annotation::OntologyTerm, not 
> Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't 
> understand what the benefit of typing seq_id() any stronger than a 
> string would be.

Would there be any problem with having source() return a string, but 
still allow access to the OntologyTerm object via 
get_Annotations('source')? (Ditto with type?)

I think that's the way I'm going to go for now.


From bix at sendu.me.uk  Fri Oct 26 12:52:59 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:52:59 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
 problem with Genewise.t
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <47221B6B.5000604@sendu.me.uk>

Sendu Bala wrote:
> Following Chris's changes to SF::Annotated et al., lots of existing user 
> code breaks. Also, at least some Bioperl code breaks, notably 
> Bio::DB::SeqFeature::Store, which in mysql mode calls 
> _get_location_and_bin() which calls $feature->seq_id which ends up 
> storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
> the database, instead of an actual sequence id (which completely breaks 
> searching by seq_id).
> 
> I propose its API be changed to be more consistent with 
> Bio::SeqFeatureI, eg. instead of:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> we have:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> This would apply to seq_id(), name(), type(), source(), phase() and 
> frame(). Internally the implementation could store the string value in a 
> SimpleValue object.

I've now done this except for type() and source(), since these aren't in 
Generic. Instead we have source_tag() and primary_tag() accepting and 
returning strings.

source() and type() return objects as before, but now only accept 
objects when setting for consistency.


One test that pops up with an error is t/Genewise.t
I don't understand what's causing the problem. Can anyone help?


From bix at sendu.me.uk  Fri Oct 26 12:53:43 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:53:43 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <47221B97.10209@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got an
> error

This should now be fixed (update live and run). If you run into any 
other problems please let me know.


From cjfields at uiuc.edu  Fri Oct 26 13:48:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 12:48:55 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <47221B97.10209@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
Message-ID: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>


On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I  
>> got an
>> error
>
> This should now be fixed (update live and run). If you run into any
> other problems please let me know.

Works now!

chris


From jason at bioperl.org  Fri Oct 26 14:22:42 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 14:22:42 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
	problem with Genewise.t
In-Reply-To: <47221B6B.5000604@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk> <47221B6B.5000604@sendu.me.uk>
Message-ID: <053BEEDD-9C6A-4FE8-BCFD-6FD9C70537DB@bioperl.org>

fixed

> One test that pops up with an error is t/Genewise.t
> I don't understand what's causing the problem. Can anyone help?

--
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Fri Oct 26 14:29:37 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:29:37 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
	<34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
Message-ID: <358f4d650710261129v13758f55g2dbc6d788f0e7618@mail.gmail.com>

for me too, thanks Sendu :)

On 10/26/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:
>
> > Albert Vilella wrote:
> >> Hi all,
> >>
> >> I was looking at the Gumby runnable, which is pretty cool. But I
> >> got an
> >> error
> >
> > This should now be fixed (update live and run). If you run into any
> > other problems please let me know.
>
> Works now!
>
> chris
>


From avilella at gmail.com  Fri Oct 26 14:45:29 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:45:29 +0100
Subject: [Bioperl-l] problems to use parsing of rst in
	Bio::Tools::Run::Phylo::PAML::Codeml
In-Reply-To: <41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
References: <471CD625.7090605@rennes.inra.fr>
	<41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
Message-ID: <358f4d650710261145k3e174c5aj94cd69b9ef9a356f@mail.gmail.com>

Hi Claude,

Did you submit the bug in bugzilla?

Or if you want, can you attach me a tar.gz with your script and input file
so I can have a look at this?

Cheers,

    Albert.

On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Claude - Will try and take a look when I have time, but pretty overwhelmed
> with other things for the time being - best bet is to also submit this as a
> bug to bugzilla.open-bio.org
>
> -jason
> On Oct 22, 2007, at 12:56 PM, Claude Rispe wrote:
>
> Dear Dr Stajich
> We have difficulty using this bioperl module to run Paml, when we try to
> parse the reconstruction of ancestral sites (rst). I send a workable extract
> of our program,  and two example fasta files (alignments). The program
> seems to work fine (at least for running codeml) and generates a correct rst
> file (by visual inspection) but we have two problems when we try to parse
> the results.
>
> 1/ we have 36 taxa and 11 internal nodes (see attached .nwk file).
> However, when we use the functions of "get_rst_persite", they do not work
> for node 36 (the last terminal node) and for node 47 (the last internal
> node): they return errors. However, inspecting visually the rst file, there
> are no problemes with these sequences.
>
> 2/ if alignments contain gaps (as eg. the file b1630.fas-GBL), the
> get_rst_persite returns wrong values.It seems the references are not
> correct (gaps being ignored ?) and so we obtain codons which are different
> from those actually expected for most sequences!
>
> May be you will have a bit of time to have a glance at our code and
> example files. We might have not written the code correctly (I am not an
> expert at this task). Thanks a lot in advance for any advice or feedback,
> Claude Rispe
> #!usr/bin/perl -w
>
> use Bio::SeqIO;
> use Bio::AlignIO;
> use Bio::Tools::Phylo::PAML;
> use Bio::Tools::Run::Phylo::PAML::Codeml;
> use Bio::TreeIO;
> use Bio::Tree::TreeI;
>
> use strict;
>
>
> my $treeio=Bio::TreeIO->new(-file =>"entero_topo.nwk", -format=>"newick");
> my $tree=$treeio->next_tree();
>
>
>    # runs PAML and gets encestral sequences (for internal nodes)
> ------------------------------------------------------------
>       my $in=Bio::AlignIO->new(-file => "b3298.fas-GBL",-format  =>
> 'fasta');
>       while ( my $aln=$in->next_aln() ) {
>          my $kaks_factory=new Bio::Tools::Run::Phylo::PAML::Codeml (
> -tree=> $tree, -save_tempfiles=> 'TRUE', -dir=>'/tmp', -params=>
> {'runmode'=>0,'seqtype'=>1,'model'=>0,'RateAncestor'=>1} );
>          $kaks_factory->alignment($aln);
>          my($rc,$parser)= $kaks_factory->run();
>  my $result=$parser->next_result;
>
>
>          # parsing of ancestral states and of mutations along branches
> ------------------------------------------------------------
>  my @trees = $result->get_rst_trees;
>  my $persite = $result->get_rst_persite;
>  my $nbsites=scalar(@$persite)-1;
>  print "$nbsites\n";
>     for my $t ( @trees ) {
>                for my $node ( $t->get_nodes ) {
>                    next unless $node->ancestor; # skip root node
>    printf "node:%s     ancestor: %s  node is leaf?
> %s\n",$node->id,$node->ancestor->id,$node->is_Leaf;
>    if ($node->id=~/^(\d*)/) {
>        for( my $i=1;$i<=$nbsites;$i++) {
>          print " $i ",$persite->[$i]->[$1]->{'codon'}, '
> ',$persite->[$i]->[$1]->{'aa'}," ";
>          unless ($node->is_Leaf) {print "
> ",$persite->[$i]->[$1]->{'prob'}," ";}
>
>
>        }
>    }
>            print "\n";
>                }
>
>
>            }
>
>
>
>
>       }
>
> Eco3
>
> GTCGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Erwca
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCGTTAACG
> TCAATTTTCG GTATCGGTAA AACTCGGTCG CAGGCTATTT GTGCTGCAAC GGAGATTGCC
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG ATAAGCTGCG TGACGAAGTT
> GCCAAGTTTG TTGTAGAAGG TGATCTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTT
> ATGGACCTTG GTACTTATCG TGGTTTGCGT CATCGTCGTG GTCTGCCGGT TCGCGGTCAG
> CGTACCAAGA CTAACGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGTCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Klebs
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCACAAAC ATACCGTTAT CGCTTTAACC
> GCTATTTTCG GTATCGGCAA AACCCGTTCT AAAGCCATCT GCGCTGAAAC GGGCATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATTG ATATTCTGCG TGAAGCAGTA
> GGTAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GTTGCTACCG TGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yent
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCGTTAACT
> GCGATCTACG GCATCGGTAA GACCCGTTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Eco10
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Styphim
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Enterob
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAAAAAC ATGCTGTGAT CGCATTAACT
> TCGATCTATG GCGTCGGCAA GACCCGTTCC AAAGCCATTT TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAGTTA GCATGAGCAT CAAGCGCCTT
> ATGGACCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGCCAG
> CGCACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Eco5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco7
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Serrp
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTAAT CGCCTTAACG
> TCGATCTTCG GAATCGGTAA AACCCGCTCA CAGTCTATCT GTGCGTCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATTG AACAGCTGCG TGAAGCAGTC
> GCCAAATTCA CTGTAGAAGG TGATTTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTG
> ATGGATCTTG GTACTTACCG TGGTTTGCGT CATCGTCGTG GTCTGCCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCAATCAA GAAA
>
> Sodalis
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCCCTAACG
> TCAATCTACG GTATCGGCAA AACCCGCTCG CAGCACATCT GCGCGGCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAGATTG ACACGCTGCG TGAAGCAGTT
> ACCAAGTTTG TTGTCGAAGG CGATCTGCGC CGTGAAGTCA CCCTGAGTAT CAAGCGTCTG
> ATGGACCTTG GTACCTATCG TGGTTTGCGT CATCGTCGTG GTCTTCCGGT TCGCGGTCAG
> CGTACCAAGA CCAATGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGCCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Pholu
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAGC ATACCGTGAT CGCTTTAACA
> TCGATCTACG GAATTGGCAA AACTCGCTCC CAAGCCATTT GTGCTGCGGC GGGTATTGCT
> GAGCATGTTA AGATCAGCGA GCTGTCTGAA GAGCAAATTG ATAAGCTGCG TGACGAAGTT
> GCCAAATACG TTGTAGAAGG CGATTTGCGT CGTGAAGTAA CCCTGAGCAT CAAACGTCTG
> ATGGATCTTG GTACTTATCG TGGTTTACGT CACCGTCGTG GTCTACCTGT TCGCGGCCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCACGTA AGCCGATCAA GAAA
>
> Eco9
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco8
>
> GTAGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTAT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TTCTGGCCGA AGCTCTCGTC
> CTCAAACTAC GCAAGCAGTC GGTAGCTGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGT
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGT TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TGTGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTGGCGGG CTTATTAGTC TGGATGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTTG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig6
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig4
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig5
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig2
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGCT GATATGAACA CACTACACTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Erwca
>
> ATGGCTTTTA TTGCGAGTTC ACCGTTCACA CATAACCAGC AGCGCACGCA GCGCATCATG
> CTGTGGGTTA TTCTGGCCTG CCTGCCGGGC ATGTTGGCGC AGGTCTATTT CTTTGGCTAC
> GGCAACCTGA TTCAGGTCGG GCTGGCGTCT GCCACCGCAC TCATTGCGGA AGGCGTGACG
> CTGTCACTGA GGAAATTTGC GGTTCGTACC ACCCTGGCTG ATAATTCCGC GTTACTGACC
> GCCGTGCTGC TCGGAATCAG TCTACCGCCA TTAGCGCCCT GGTGGATGGT GGTCATGGCA
> ACCGTCTTCG CTATCATTAT CGCTAAACAG CTGTATGGCG GATTAGGGCA AAATCCCTTT
> AACCCCGCGA TGATTGGTTA TGTGGTGTTG CTGATCTCTT TCCCTGTCCA GATGACGAGC
> TGGCTGCCAC CCGAGCCGCT GCAAACCATC TCGCTTAGTT TCCATGACTC GCTAGTCATC
> ATTTTTACCG GACACACGCC TGACGGGCAT ACCATGCAGC AGCTGATGCA CAATGTTGAT
> GGCGTGAGTC AGGCCACCCC GCTGGATACG TTTAAAACCA GCTTACGTTC CGGCCAAACG
> CCACAGAACA TCCTGCAACA GCCGATGTTT GCACAATCAC TGTCTGGTAT TGGCTGGCAG
> TGGGTTAATA TCGGTTTTCT CATCGGCGGG CTGTTCTTGC TGATGCGCGG CACGATTCGC
> TGGCATATTC CAGTCAGTTT CCTGCTGTCG CTGATGTTCT GCGCCCTGCT AAGCTGGATC
> ATCGCGCCGG ATAAATTTGC CCAACCGATG TTACATCTGT TGTCCGGTGC GACCATGCTC
> GGCGCATTTT TCATCGCCAC AGATCCCGTT ACAGCATCAA CCACGAACCG GGGCCGTCTG
> ATTTTCGGTG CGTTGATTGG GTTACTGGTG TGGCTGATTC GCACCTATGG CGGCTACCCA
> GACGGCGTTG CCTTTGCCGT TCTACTGGCG AACATCACCG TCCCGCTGAT CGACTATTAC
> ACCAAGCCAC GTGCTTACGG CCACCATCGC
>
> Shig3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGGT GATATGAACA CACTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig1
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAACAGTC GGTAGCCGCC ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTATATGGCG GTCTGGGACA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCTTGGTT TTATCGACGC CATCCAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Yep2
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep3
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Klebs
>
> ATGGTTTTCA TCGCAAGCTC CCCCTATACC CATAACCAGC GGCAGACCTC GCGTATTATG
> CTGCTGGTGC TGCTCGCCGC TGTGCCTGGC ATTGTGGTCC AGACCTGGTT TTTCGGCTGG
> GGCACCGTAC TGCAGATTGT CCTCGCCGCC CTGACGGCCT GGGCGACCGA AGCCGCTATT
> CTCAAACTGC GTAAACAGCC TGTTGCTGCC ACGCTGAAAG ATAATTCCGC CCTGCTCACC
> GGCCTGCTGC TGGCGGTGAG TATTCCGCCA CTGGCCCCGT GGTGGATGGT GGTGCTCGGC
> ACTGCCTTTG CCGTAGTCAT TGCCAAGCAG TTGTACGGAG GCCTGGGCCA TAACCCCTTC
> AACCCGGCAA TGATCGGCTA TGTCGTGCTG CTGATTTCGT TCCCGGTGCA GATGACCTCC
> TGGCTGCCTT CCTATGAGAT AGCCGCCCAT ATCCCGGCAT TCAGCGACGC GCTGCAGATG
> ATCTTCACCG GTCATACCGC CGCCGGAGGC GACATGGCCA GTCTGCGGCT GGGTATCGAC
> GGCGTCAGCC AGGCCACCCC GCTGGATACC TTTAAAACCT CCCTGCATGC CGGACATAGC
> GTTCAGCAGG TGCTGCAATT GCCGGTCTAC GGCGGCGTGC TGGCAGGTCT GGGCTGGCAG
> TGGGTGAATA TCGCCTGGCT GGCAGGCGGC CTTTTCCTGC TGTGGCAGAA GGCGATCCGC
> TGGCATATCC CGGTCAGCTT CCTTGTTAGC CTCGGCCTGT GCGCCACCCT CGGCTGGATT
> TTTTCGCCGC AGAGCCTGGC CTCACCGCAG ATGCATTTGC TCTCCGGGGC GACCATGCTT
> GGCGCCTTCT TTATCCTGAC CGATCCGGTG ACGGCCTCAA CAACCAACCG CGGCCGTCTG
> ATCTTTGGCG CCCTCGCTGG CCTGCTGGTC TGGCTCATCC GCAGCTTCGG TGGTTATCCG
> GACGGCGTGG CGTTTGCCGT TCTGCTGGCG AATATTACCG TGCCGCTGAT CGATTACTAC
> ACGCGCCCGC GCGTATATGG CCACCGT---
>
> Yep1
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yent
>
> ---------A TAGCCAGTTC CCCTTTTACG CATAATCAAC GTAGCACCCG CAGTATTATG
> CTGCTGGTTA TTTTAGCCTG CATTCCGGGG ATTATCGCCC AGACTTACTT CTTTGGTTAT
> GGCAGCCTAA TCCAAGTTGC ACTGGCTATA ATGACCGCCG TGCTGGCCGA AGGCGCTGTC
> TTGCATTTAC GTAAACAGCC GGTACTGACA CGATTACAGG ATAACTCTGC CCTGCTCACT
> GGCTTATTGT TAGGTATCAG TCTGCCGCCA CTTGCCCCTT GGTGGATGAT TGTTCTGGGT
> ACGGCATTTG CCATTATTAT TGCCAAACAA CTTTACGGCG GTTTAGGTCA GAATCCGTTT
> AATCCTGCCA TGGTCGGCTA TGTTGTACTA CTGATTTCAT TCCCAGTACA AATGACCAGT
> TGGCTTCCTC CTCTGCCATT ACAGGGAACG CCGGTTGGAT TCTATGACAG CTTATTAACT
> ATTTTCACCG GATTCACCCA AAATGGTGCC GATATTCACC AACTGCAGAT TGGCTATGAT
> GGGATAAGTC AGGCCACGCC TCTCGATAAC TTTAAAACCT CACTGCGCTC C---CAACCC
> GTGGAACAGA TTCTGCAACA ACCGATTTTT ACCGCGGGGC TGGCGGGTAT TGGTTGGCAA
> TGGATTAACC TCGGTTTTCT GGCGGGCGGT CTGTTGCTGC TATGGCGTAA AGCCATCCAC
> TGGCATATTC CGGTGAGTTT CCTATTGGCT TTGGCAGGTT GTGCTGCTAT CAGTTGGATG
> ATTGCGCCAC ACAGCTTCGC CCCCCCTATG TTGCATCTGT TTTCCGGTGC CACCATGTTG
> GGTGCTTTCT TTATTGCCAC CGATCCGGTC AGCGCCTCGA CAACACCTCG TGGTCGGCTG
> ATTTTCGGCG CATTGATTGG TATTTTGGTG TGGCTGATTC GCGTTTACGG CGGTTATCCC
> GATGGGGTAG CATTTGCGGT GCTGCTGGCC AACATCTGTG TTCCACTGAT TGATCACTAC
> ACTCAACCAC GCGTTTATGG TCATCAGCGC
>
> Yep4
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep5
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yeps2
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTGCTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATC TCGGCTTTCT GGTTGGCGGT TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
>
> ...
>
> [Message clipped]


From hlapp at gmx.net  Fri Oct 26 19:32:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 26 Oct 2007 19:32:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4721FE3B.2080507@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
Message-ID: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>


On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:

> Would there be any problem with having source() return a string,  
> but still allow access to the OntologyTerm object via  
> get_Annotations('source')? (Ditto with type?)

Do I interpret your second email that you abandoned this plan? I.e.,  
source() and type() return objects? I think that's the right way.  
(Otherwise source() is redundant with source_tag().)

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From bix at sendu.me.uk  Fri Oct 26 19:47:11 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 00:47:11 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
Message-ID: <47227C7F.9010709@sendu.me.uk>

Hilmar Lapp wrote:
> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
> 
>> Would there be any problem with having source() return a string,  
>> but still allow access to the OntologyTerm object via  
>> get_Annotations('source')? (Ditto with type?)
> 
> Do I interpret your second email that you abandoned this plan? I.e.,  
> source() and type() return objects? I think that's the right way.  
> (Otherwise source() is redundant with source_tag().)

Yes, I abandoned the above plan. I've left source() as a SimpleValue, at 
least until issues with DB::Store are resolved wrt ontologies (it stores 
the entire ontology for each feature in the database, increasing storage 
requirments > 800x).


From cjfields at uiuc.edu  Fri Oct 26 23:39:09 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 22:39:09 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <47227C7F.9010709@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
Message-ID: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>


On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
>>
>>> Would there be any problem with having source() return a string,
>>> but still allow access to the OntologyTerm object via
>>> get_Annotations('source')? (Ditto with type?)
>>
>> Do I interpret your second email that you abandoned this plan? I.e.,
>> source() and type() return objects? I think that's the right way.
>> (Otherwise source() is redundant with source_tag().)
>
> Yes, I abandoned the above plan. I've left source() as a  
> SimpleValue, at
> least until issues with DB::Store are resolved wrt ontologies (it  
> stores
> the entire ontology for each feature in the database, increasing  
> storage
> requirments > 800x).

Do you mean SeqFeature::Store or OntologyStore (I'm guessing the  
latter)?

chris


From bix at sendu.me.uk  Sat Oct 27 03:03:12 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 08:03:12 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
Message-ID: <4722E2B0.3050503@sendu.me.uk>

Chris Fields wrote:
> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>> I've left source() as a SimpleValue, at least until issues with
>> DB::Store are resolved wrt ontologies (it stores the entire
>> ontology for each feature in the database, increasing storage 
>> requirments > 800x).
> 
> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the 
> latter)?

Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you 
set the type() as well of course; the only reason I don't suffer from 
that is that I deliberately avoid setting the type on my features.


From cjfields at uiuc.edu  Sat Oct 27 10:53:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sat, 27 Oct 2007 09:53:59 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4722E2B0.3050503@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
	<4722E2B0.3050503@sendu.me.uk>
Message-ID: <C69BF9A1-1B61-4CE6-80F2-0941D6DB31AB@uiuc.edu>


On Oct 27, 2007, at 2:03 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>>> I've left source() as a SimpleValue, at least until issues with
>>> DB::Store are resolved wrt ontologies (it stores the entire
>>> ontology for each feature in the database, increasing storage
>>> requirments > 800x).
>>
>> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the
>> latter)?
>
> Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you
> set the type() as well of course; the only reason I don't suffer from
> that is that I deliberately avoid setting the type on my features.

Makes sense if you're using $store->add_SeqFeatures (it stores a  
serializized SF along with the data via Storable, so the  
OntologyStore probably goes along for the ride).  If we make type  
checking optional and lazily create the OntologyStore singleton it  
would probably reduce the space, as you wouldn't create it unless  
needed.  Or you could map it over to a DB::SeqFeature after  
validating the type.

Just noticed something: DB::SeqFeature uses type() and source() as  
synonyms of primary_tag() and source_tag(); both use strings instead  
of SimpleValues.

chris


From snaphit at planet.nl  Thu Oct 25 04:07:00 2007
From: snaphit at planet.nl (Jelle86)
Date: Thu, 25 Oct 2007 01:07:00 -0700 (PDT)
Subject: [Bioperl-l]  get_Stream_by_gi: Memory going up every call.
Message-ID: <13401838.post@talk.nabble.com>


Hi, 
I have a problem when using Bio::DB::GenBank->get_Stream_by_gi . My usage
memory for the perl script keeps going up each time a piece of the list is
downloaded. 
I have a gilist, that consist of about 1300 gi's, and i split it in pieces
of 100gi's since get_stream_by_gi doesn't work on more than 300 or so (don't
know why..). 
But either way, using this constructing makes the script take more and more
memory each time 100entries are downloaded. For 1300 gi's not a problem, but
i'm planning on doing it for at least 200.000 gi's.
How can i solve it. At the end of the end of the loops and end of the usage
of the package genbankQuery I empty all the used objects with undef. 
Below are some snippets of my code. Is there a way to find out what actually
causes the problem and more how to solve it?


I use:
perl 5.8.8.822
bioper1.5.2
winxp
behind a proxy


=========
ESTdownload;
makeChunks(){
  while (@small_list = splice(@{$gilist_ref->{gilist}}, 0, 100)) {
        $self->callStream(\@small_list);
 }
}
callStream(){
  $smallref=shift;#contains @small_list ref.
  my $query = genbankQuery->new(ids=>$smallref);
  my $part_result = $query->streamQuery();
}
=========
genbankQuery;
new{
  
  my $self = {
			ids => '',			
			@_,					
		    };
  $self->{gb}=Bio::DB::GenBank->new();
}
streamQuery(){
  my $stream_obj = $self->{gb}->get_Stream_by_gi(\@ids);
  my $seq_obj;       
  #Step through the results 
  while ($seq_obj = $stream_obj->next_seq) {
    #make lines from features and return them in an array ref
  }
}
_____________
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13401838
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From snaphit at planet.nl  Fri Oct 26 08:42:13 2007
From: snaphit at planet.nl (Jelle86)
Date: Fri, 26 Oct 2007 05:42:13 -0700 (PDT)
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13401838.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com>
Message-ID: <13426480.post@talk.nabble.com>


Ok I stripped a lot. And this is causing the problem:

use Bio::DB::Genbank;
sub new(){
  my $invocant = shift;
  my $class = ref($invocant) || $invocant;
  my $self = {@_};
  $self->{gb} = Bio::DB::GenBank->new();
  bless $self, $class;
  return $self;
}

sub streamQuery(){
	my $self = shift;        
	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
        while (my $seq_obj = $stream_obj->next_seq) {
                
        }
}

Both subs (new and streamQuery) are called several times with a new
accessionlist. 
Removing the while loop, will use a bit less memory. But the memory usage is
still going up.
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13426480
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From wgallin at ualberta.ca  Mon Oct 29 00:03:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Sun, 28 Oct 2007 22:03:24 -0600
Subject: [Bioperl-l] Not catching an error in EUtilities
Message-ID: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>

I've been having an intermittent problem, when the NCBI service that  
is accessed by EUtilities (in particular efetch) is not available.

I have the calls enclosed in eval statements, but an exception is not  
thrown.  Instead I find that the  file that should contain the  
results of the efetch only has the following text:

Error: The resource is temporarily unavailable

So it appears that this is not generating an exception (maybe that is  
not desireable in general, but it would be useful in my case).

The result is that my script tries to access the file using  
Bio::Seq::IO, and the expected text is not there.

The relevant snippet of code and the output are copied below.

The only way that I can think of to catch this outcome is to open the  
file and check the firt three lines for this text, and then go back  
and redo the efetch if this particular text is found.

Is this behaviour considered a bug, or just an outcome that needs to  
be checked for when code is written using efetch?

If so, is there a standard way of checking for this?

Thanks,

Warren Gallin

[Code that successfully executes an epost and retrieves the history]

   RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
         -eutil   => 'efetch',
         -rettype => 'genbank',
         -db      => 'protein',
         -history => $history
     );};
     if ($@){
     	print "efetch error trapped\n$@\n";
     	goto RETRIEVE_LIST;

     }

     $file1 = ">" . $file1;
     $retry = 0;
     eval { $prot_eutil->get_Response( -file => $file1 ); };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++;
         sleep(5);
         goto RETRIEVE_LIST;
     }
     else {
         print "efetch ran on $loop_bottom through $loop_top.\n";
     }

The output to the terminal from this part of the code is:

efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 11:42:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 10:42:43 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <5AEAE8C4-2E18-4BBE-A470-8CB398949BEA@uiuc.edu>


On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
>
> Error: The resource is temporarily unavailable
>
> So it appears that this is not generating an exception (maybe that is
> not desireable in general, but it would be useful in my case).
>
> The result is that my script tries to access the file using
> Bio::Seq::IO, and the expected text is not there.
>
> The relevant snippet of code and the output are copied below.
>
> The only way that I can think of to catch this outcome is to open the
> file and check the firt three lines for this text, and then go back
> and redo the efetch if this particular text is found.
>
> Is this behaviour considered a bug, or just an outcome that needs to
> be checked for when code is written using efetch?
...
> If so, is there a standard way of checking for this?

I may have already mentioned this (it is mentioned in the POD), but  
it's worth repeating: if you running a script to post more than 100  
requests you should be running it btwn 9pm and 5am ET per NCBI's rules:

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

I have built in a way to pass in an LWP::UserAgent-related callback  
to get_Response() using the -cb parameter, primarily to allow piping  
data to a child process for instance.  This could also be used for  
checking the initial data retrieved and throwing if an error is  
returned.  I haven't extensively tested this yet; I can try running a  
stress test to see if I can trigger an efetch error and catch it in  
the callback.  If I can get something working I'll post it later  
today and may incorporate it into EUtilities in CVS.

A bit of background: efetch is the only eutil that doesn't have a  
specific parser (Bio::Tools::EUtilities) attached to it, primarily b/ 
c the data retrieved is very diverse (seq/pubmed/snp/etc data in XML,  
asn.1, text, HTML).  All other eutils besides efetch generate error  
codes via the HTTP::Response header (the norm) or in the XML  
returned; both of the previous types are errors that EUtilities  
catches and throws, so an eval{} works.  efetch errors seen to be  
atypical and may be related to the server load or specific database  
availability.

chris

> Thanks,
>
> Warren Gallin
>
> [Code that successfully executes an epost and retrieves the history]
>
>    RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
>          -eutil   => 'efetch',
>          -rettype => 'genbank',
>          -db      => 'protein',
>          -history => $history
>      );};
>      if ($@){
>      	print "efetch error trapped\n$@\n";
>      	goto RETRIEVE_LIST;
>
>      }
>
>      $file1 = ">" . $file1;
>      $retry = 0;
>      eval { $prot_eutil->get_Response( -file => $file1 ); };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++;
>          sleep(5);
>          goto RETRIEVE_LIST;
>      }
>      else {
>          print "efetch ran on $loop_bottom through $loop_top.\n";
>      }
>
> The output to the terminal from this part of the code is:
>
> efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 12:06:24 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 11:06:24 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13426480.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
Message-ID: <8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>

It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Oct 29 16:45:53 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 15:45:53 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <A5708C31-CA39-43D8-ADE2-E1791D3332C7@uiuc.edu>

Warren,

For efetch the following works for me; it include a simple callback  
to check the initial data chunk (note the die in the callback and the  
extra call to check the header) and prints to the file if no error is  
detected, otherwise it retries.  I'll see if there is an easy way to  
integrate this into EUtilities.


# after eutil calls

open (my $SEQFILE, '>', $file) || die "Can't write to file:$!";
my $expected;
my $bytes = 0;

RETRIEVE_SEQS:
while ($retstart < $count) {
      $gpeptfactory->set_parameters(
		-retmax => $retmax,
                 -retstart => $retstart,
                              );
      my $response;
      eval{
         $response= $gpeptfactory->get_Response(-cb => sub {
            my ($chunk, $res) = @_;
             if ($bytes == 0 && $chunk =~ m{^Error:(.*)}i) {
                 die "$1\n";
             }
             $bytes += length($chunk);
             print $SEQFILE $chunk;
         });
      };
      if ($@ || $response->header('x-died')) {
          my $error = $@ || $response->header('x-died');
          die "Server error: $error.  Try again later" if $retry == 5;
          print STDERR "$error\n";
          print STDERR "Server error, redo #$retry\n";
          $retry++ && redo RETRIEVE_SEQS;
      } else  {
      	my $retend = $retstart + $retmax;
      	print "Loaded entries ",$retstart+1," through $retend on retry  
# $retry.\n";
      	$retstart += $retmax;
      	$retry = 0;
         $bytes = 0; # important!
         undef $expected ;
      }
}

close $SEQFILE;

chris

On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
> ...
> If so, is there a standard way of checking for this?
>
> Thanks,
>
> Warren Gallin
...


From wenbinye at gmail.com  Tue Oct 30 07:46:55 2007
From: wenbinye at gmail.com (Ye Wenbin)
Date: Tue, 30 Oct 2007 19:46:55 +0800
Subject: [Bioperl-l] console version of Deobfuscator
Message-ID: <op.t00dohrc52p72k@tsinghua-64dc66>

Hi, all.
I wrote a console version of Deobfuscator. I think it is easy to
use and more efficient to query and search.
Hope it is helpful!
You can download it from:
http://search.cpan.org/CPAN/authors/id/Y/YE/YEWENBIN/deob-0.02.tar.gz

-- 
Best regards.
Ye Wenbin


From cjfields at uiuc.edu  Tue Oct 30 08:10:41 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 07:10:41 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
Message-ID: <2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>

What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From snaphit at planet.nl  Tue Oct 30 04:51:40 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 09:51:40 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>

This doesn't seem to work. It still keeps using more memory. I already tried it once and didn't seem to make a difference. But gave it another try. But as I said, it doesn't solve the problem.


-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Mon 10/29/2007 5:06 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From jason at bioperl.org  Tue Oct 30 11:16:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Oct 2007 11:16:59 -0400
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>

Denis -
Not sure - the list members will know more.

-jason
Begin forwarded message:

> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
> Date: October 30, 2007 7:41:29 AM EDT
> To: <jason at bioperl.org>
> Subject: Pairwaise_kaks.pl
>
> Good morning,
>
> I'm attempting to set up the pairwise_kaks script here.
>
> I have successfully used an older version in a previous position so  
> I am
> somewhat familiar with it.
>
> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
> And have bioperl             in /usr/local/bioperl-1.5.2_100
>
>
> When I try to run the script I get the following
>
> Can't locate object method "_set_from_args" via package
> "Bio::Tools::Run::Alignment::Clustalw" at
> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>
> I'm not sure how to resolve this so I refer to a higher authority
>
> Merci
>
> Dennis Prickett
>
> Institute for Animal Health
> Compton nr Newbury
> Berkshire
> RG20 7NN
>
> Switchboard: +44  (0)1635 578411
> Central Fax: +44  (0)1635 57723
>

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct 30 11:33:34 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 10:33:34 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
Message-ID: <2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>

It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From bix at sendu.me.uk  Tue Oct 30 12:10:42 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Tue, 30 Oct 2007 16:10:42 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
Message-ID: <47275782.2010200@sendu.me.uk>

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably 
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the 
same place. Ie. 1.5.2 release packages or CVS, not both.


From bix at sendu.me.uk  Wed Oct 31 07:36:09 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 31 Oct 2007 11:36:09 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
	<8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <472868A9.2090706@sendu.me.uk>

dennis prickett (IAH-C) wrote:
> Sendu
> 
> Thanks for the quick response.  
> 
> Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
> the bioperl core package.
> 
> But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

No, that's still 1.5.2 with minor installation-related patches ( 
http://www.bioperl.org/wiki/Release_1.5.2#Updates ). You'll need to 
install bioperl-live from CVS, or bioperl-run-1.5.2_100.


From dennis.prickett at bbsrc.ac.uk  Wed Oct 31 07:32:35 2007
From: dennis.prickett at bbsrc.ac.uk (dennis prickett (IAH-C))
Date: Wed, 31 Oct 2007 11:32:35 -0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <47275782.2010200@sendu.me.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>

Sendu

Thanks for the quick response.  

Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
the bioperl core package.

But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

Thanks 

Dennis Prickett

-----Original Message-----
From: Sendu Bala [mailto:bix at sendu.me.uk] 
Sent: 30 October 2007 16:11
To: Jason Stajich
Cc: bioperl-l list; dennis prickett (IAH-C)
Subject: Re: [Bioperl-l] Fwd: Pairwaise_kaks.pl

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package 
>> "Bio::Tools::Run::Alignment::Clustalw" at 
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the
same place. Ie. 1.5.2 release packages or CVS, not both.



From snaphit at planet.nl  Tue Oct 30 10:56:10 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 15:56:10 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>

I just made a test script which shows the problem.
The second while loop will cause the program to use more and more memory without releasing it.

I will post the bug later today.

Jelle

code:
use Bio::DB::GenBank;
use strict;
use warnings;
my @arraylist = (157043286,157043285,157043189); #use couple of hundreds gi's to see the issue
while (my @small_list = splice(@arraylist, 0, 100)) {
        my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
        my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);        
        while (my $seq_obj = $stream_obj->next_seq) {
            #this is what causes the problem...
        }        
}

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 1:10 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From snaphit at planet.nl  Wed Oct 31 06:07:38 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Wed, 31 Oct 2007 11:07:38 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
	<2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F1A@CPEXBE-EML18.kpnsp.local>

I installed S/SE/SENDU/bioperl-1.5.2_102.tar.gz using cpan -force -notest.
And now running the script doesn't use that much memory. Although it keeps going up, but just a little bit every call. For 14000 +/-20mb (starts at 16mb).

Before I used this bioperl version (only one I was able to install using PPM):
Bioinformatics Toolkit 1.5.2 RC2
Version:	1.5.1.9992
Released:	2006-10-02

I first replaced the modules you mentioned, but it didn't help. So I thought before I report the bug, I will try to install the package with cpan. It gave some errors at first, so I used force and notest. And now it seems to work. I get the output I expect and a lot less memory usage. 

So if you don't see anything on your windows machine, I won't report the bug.

Thanks,
Jelle



-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 4:33 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From swapnatbhat at gmail.com  Wed Oct 31 17:34:38 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 14:34:38 -0700 (PDT)
Subject: [Bioperl-l]  BLAST output parsing
Message-ID: <13519112.post@talk.nabble.com>


Hi all,

I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
it.  I did use -m 9 option to get a tabular information of the blast data. 
But it does not include the gene names or the names of the organisms of each
hit.  Are there any parsers that can do this job ??

I would really appreciate if anybody can help me with this.

Swapna
-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13519112
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From torsten.seemann at infotech.monash.edu.au  Wed Oct 31 21:27:29 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 1 Nov 2007 12:27:29 +1100
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <13519112.post@talk.nabble.com>
References: <13519112.post@talk.nabble.com>
Message-ID: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>

Swapna,

> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
> it.  I did use -m 9 option to get a tabular information of the blast data.
> But it does not include the gene names or the names of the organisms of each
> hit.  Are there any parsers that can do this job ??

The -m 9 tabular output does not include gene descriptions and
organisms. It only includes the "gene id" that was present immediately
after the ">" sign in the FASTA file that was used to create the BLAST
database you specified with the -d option when you ran BLAST.

Hence, no parser will help you. You either have to re-do the BLAST
with a different -m value that includes the information you desire, or
write code to convert your gene IDs into what you want.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University


From swapnatbhat at gmail.com  Wed Oct 31 23:49:45 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 20:49:45 -0700 (PDT)
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
References: <13519112.post@talk.nabble.com>
	<a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
Message-ID: <13523150.post@talk.nabble.com>


which -m option do you think will be helpful.  

swapna

Torsten Seemann wrote:
> 
> Swapna,
> 
>> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to
>> parse
>> it.  I did use -m 9 option to get a tabular information of the blast
>> data.
>> But it does not include the gene names or the names of the organisms of
>> each
>> hit.  Are there any parsers that can do this job ??
> 
> The -m 9 tabular output does not include gene descriptions and
> organisms. It only includes the "gene id" that was present immediately
> after the ">" sign in the FASTA file that was used to create the BLAST
> database you specified with the -d option when you ran BLAST.
> 
> Hence, no parser will help you. You either have to re-do the BLAST
> with a different -m value that includes the information you desire, or
> write code to convert your gene IDs into what you want.
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Monash University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13523150
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From outaleb at web.de  Mon Oct  1 07:46:08 2007
From: outaleb at web.de (issam outaleb)
Date: Mon, 01 Oct 2007 13:46:08 +0200
Subject: [Bioperl-l] help about Fasta file???
Message-ID: <2005673060@web.de>



hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;

all 



#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht m?glich zum ?ffnen!!" ;open (OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;        if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {        #print OUT $1."\n"; #print this IPIs in this file.


 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new file with the description


#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    


		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){


$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien  geschlossen, Kopiervorgang 


. 


	
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From shameer at ncbs.res.in  Mon Oct  1 12:57:15 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Mon, 1 Oct 2007 22:27:15 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>

Dear All,

Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
 My input file are in phylip  treefile format. Any Modules / codes in
Bio::Graphics / Phylogeny sections ?

Input file :
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);

-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 14:03:00 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:03:00 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
Message-ID: <1191261780.47013654cb81b@webmail.sas.upenn.edu>

I think you'll have better luck using some of already available programs to do
that, you'll get better looking trees. If you just have one tree to draw I
recommend you use:
http://itol.embl.de/

Lucia


Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear All,
>
> Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
>  My input file are in phylip  treefile format. Any Modules / codes in
> Bio::Graphics / Phylogeny sections ?
>
> Input file :
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
> 
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
> 
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From shameer at ncbs.res.in  Mon Oct  1 14:39:05 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Tue, 2 Oct 2007 00:09:05 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191263834.47013e5a6af93@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
Message-ID: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>

Dear Lucia,

Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
methods. Some how missed this excellent HOWTO :
http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
tried that and it worked very nicely. I have to work around to beautify
the tree and I am just going to do that.

Thanks & Cheers,
Shameer

> OK
>
> you can use the implementations in Bio::TreeIO
>
> you can basically read the tree in newick format and out as an svg graph
> something like this:
>
> my $in = new Bio::TreeIO(-file => 'input',
>                          -format => 'newick');
> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>                           -format => 'svggraph');
> while( my $tree = $in->next_tree ) {
>     $out->write_tree($tree);
> }
>
> you can also use Bio::Tree::Draw
>
> hope that helps
>
> Lucia
>
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Hi,
>>
>> Thanks for your mail. I have to create these trees as a part of a
>> webserver. i need to generate them dynamically using users input
>> sequence.
>> I think ITOL is not the stuff best suited for my purpose.
>>
>> > I think you'll have better luck using some of already available
>> programs
>> > to do
>> > that, you'll get better looking trees. If you just have one tree to
>> draw I
>> > recommend you use:
>> > http://itol.embl.de/
>> >
>> > Lucia
>> >
>> >
>> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
>> >
>> >> Dear All,
>> >>
>> >> Is it possible to draw a phylogeny tree file in PNG format using
>> Bioperl
>> >> ?
>> >>  My input file are in phylip  treefile format. Any Modules / codes in
>> >> Bio::Graphics / Phylogeny sections ?
>> >>
>> >> Input file :
>> >>
>> >
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
>>  3.
>> >>
>> >
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>  5
>> >>
>> >
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>> >>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
>


-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 14:48:51 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:48:51 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
Message-ID: <1191264531.47014113f2b54@webmail.sas.upenn.edu>

Yes,
that's the issue about those commands, trees are not pretty at all
that's why for a one tree only kind of thing I rather use ITOL
other thing to try is the tree drawer of the Mesquite package
glad I could help

Lucia

Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear Lucia,
>
> Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
> methods. Some how missed this excellent HOWTO :
> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
> tried that and it worked very nicely. I have to work around to beautify
> the tree and I am just going to do that.
>
> Thanks & Cheers,
> Shameer
>
> > OK
> >
> > you can use the implementations in Bio::TreeIO
> >
> > you can basically read the tree in newick format and out as an svg graph
> > something like this:
> >
> > my $in = new Bio::TreeIO(-file => 'input',
> >                          -format => 'newick');
> > my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >                           -format => 'svggraph');
> > while( my $tree = $in->next_tree ) {
> >     $out->write_tree($tree);
> > }
> >
> > you can also use Bio::Tree::Draw
> >
> > hope that helps
> >
> > Lucia
> >
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Hi,
> >>
> >> Thanks for your mail. I have to create these trees as a part of a
> >> webserver. i need to generate them dynamically using users input
> >> sequence.
> >> I think ITOL is not the stuff best suited for my purpose.
> >>
> >> > I think you'll have better luck using some of already available
> >> programs
> >> > to do
> >> > that, you'll get better looking trees. If you just have one tree to
> >> draw I
> >> > recommend you use:
> >> > http://itol.embl.de/
> >> >
> >> > Lucia
> >> >
> >> >
> >> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >> >
> >> >> Dear All,
> >> >>
> >> >> Is it possible to draw a phylogeny tree file in PNG format using
> >> Bioperl
> >> >> ?
> >> >>  My input file are in phylip  treefile format. Any Modules / codes in
> >> >> Bio::Graphics / Phylogeny sections ?
> >> >>
> >> >> Input file :
> >> >>
> >> >
> >>
> >
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
> >>  3.
> >> >>
> >> >
> >>
> >
>
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>  5
> >> >>
> >> >
> >>
> >
>
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
> >> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> >
>
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From jason at bioperl.org  Mon Oct  1 15:32:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 1 Oct 2007 12:32:38 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191264531.47014113f2b54@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
	<1191264531.47014113f2b54@webmail.sas.upenn.edu>
Message-ID: <F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>

I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
for prettier trees - you get postscript out but you can render this  
to png or jpg with unix tools.  If there is a better stand alone tree  
drawing engine we're happy to try and integrate it into bioperl - the  
modules here are native Perl only and you can use the bioperl-run  
modules that wrap DrawTree and DrawGram from EMBOSS to get other PS  
rendering output.

Mesquite, TreeView or other tools are usually much better but not  
always an option if you want to auto-render these images for a  
website, etc.

-jason


On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:

> Yes,
> that's the issue about those commands, trees are not pretty at all
> that's why for a one tree only kind of thing I rather use ITOL
> other thing to try is the tree drawer of the Mesquite package
> glad I could help
>
> Lucia
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Dear Lucia,
>>
>> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
>> Tree::Draw
>> methods. Some how missed this excellent HOWTO :
>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as  
>> well. I
>> tried that and it worked very nicely. I have to work around to  
>> beautify
>> the tree and I am just going to do that.
>>
>> Thanks & Cheers,
>> Shameer
>>
>>> OK
>>>
>>> you can use the implementations in Bio::TreeIO
>>>
>>> you can basically read the tree in newick format and out as an  
>>> svg graph
>>> something like this:
>>>
>>> my $in = new Bio::TreeIO(-file => 'input',
>>>                          -format => 'newick');
>>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>>>                           -format => 'svggraph');
>>> while( my $tree = $in->next_tree ) {
>>>     $out->write_tree($tree);
>>> }
>>>
>>> you can also use Bio::Tree::Draw
>>>
>>> hope that helps
>>>
>>> Lucia
>>>
>>>
>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>
>>>> Hi,
>>>>
>>>> Thanks for your mail. I have to create these trees as a part of a
>>>> webserver. i need to generate them dynamically using users input
>>>> sequence.
>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>
>>>>> I think you'll have better luck using some of already available
>>>> programs
>>>>> to do
>>>>> that, you'll get better looking trees. If you just have one  
>>>>> tree to
>>>> draw I
>>>>> recommend you use:
>>>>> http://itol.embl.de/
>>>>>
>>>>> Lucia
>>>>>
>>>>>
>>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>> Bioperl
>>>>>> ?
>>>>>>  My input file are in phylip  treefile format. Any Modules /  
>>>>>> codes in
>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>
>>>>>> Input file :
>>>>>>
>>>>>
>>>>
>>>
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> 1.51514,_H_255_263:6.20895):0.83877, 
> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> 0.92645,_H_520_534:7.97418):0.15279, 
> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> 1.52226,_H_463_464:5.42226):0.94093, 
> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> 1.64489,_L_336_343:8.00808):0.88402, 
> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> (((((_E_470_474:3.85000,_E_344_348:
>>>>  3.
>>>>>>
>>>>>
>>>>
>>>
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107, 
> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> 0.71112,_L_513_519:6.65273):0.67204, 
> ((_L_296_304:5.00000,_H_292_295:5.00000): 
> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> 1.08193,_H_229_243:7.93459):0.18730, 
> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> 0.07448,_L_120_122:7.07448):1.59389, 
> ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>>>  5
>>>>>>
>>>>>
>>>>
>>>
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> 0.88488,_E__40__48:5.79344):0.60814, 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> 1.25080):0.17461):6.94325);
>>>>>>
>>>>
>>>> --
>>>> Shameer Khadar
>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>> National Centre for Biological Sciences (TIFR)
>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>> T - 91-080-23666001 EXT - 6251
>>>> W - http://www.ncbs.res.in
>>>>
>>>
>>>
>>> Lucia Peixoto
>>> Department of Biology,SAS
>>> University of Pennsylvania
>>>
>>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From outaleb at web.de  Mon Oct  1 22:37:26 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 04:37:26 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
Message-ID: <4701AEE6.6070506@web.de>

Hi every body,
i have some AccNum in a file-> IPI67675
                                                 IPI98976.
                                                 ...

what i want is how can i look in the fasta file (db fasta) if there is 
some match
if yes then copy the entire entry into a new fasta file.
i tried with bioperl but cause i m noob:-(( i don t get it.
thx all



From ULNJUJERYDIX at spammotel.com  Tue Oct  2 02:21:31 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Tue, 2 Oct 2007 14:21:31 +0800
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
Message-ID: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>

Hi!
I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
sequence)
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in
bioperl.

I found similar solutions like
http://www.bio.davidson.edu/projects/DAB/DAB.html
divide and blast (but I need to specify coords)

there also this from the bioperl archives
http://bioinformatics.org/pipermail/bioclusters/2002-August/000375.html

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?


From n.haigh at sheffield.ac.uk  Tue Oct  2 03:56:57 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 08:56:57 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701AEE6.6070506@web.de>
References: <4701AEE6.6070506@web.de>
Message-ID: <4701F9C9.4050808@sheffield.ac.uk>

outaleb Issame wrote:
> Hi every body,
> i have some AccNum in a file-> IPI67675
>                                                  IPI98976.
>                                                  ...
>
> what i want is how can i look in the fasta file (db fasta) if there is 
> some match
> if yes then copy the entire entry into a new fasta file.
> i tried with bioperl but cause i m noob:-(( i don t get it.
> thx all
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   

Can you state clearly, what is in the "AccNum" file exactly, some sample
text from the actual file would be good. Is the FASTA file containing
the sequences in raw FASTA format or has it been processed using
somthing like formatdb from the BLAST software?

A few more details will help people understand and in turn help you with
a swift solution.

Cheers
Nath


From outaleb at web.de  Tue Oct  2 05:22:17 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 11:22:17 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701F9C9.4050808@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
Message-ID: <47020DC9.8040401@web.de>

hi,
with this file i mean, i picked out this Accession Number from IPI-Human 
Dbase,they come from a fasta file,
so they re under eachother like a i a table in separate file now.
what i want is how how can i check it in the fasta File (so in the 
IPI-Human FAsta File), i they re really there;
if yes please copy the entire entry of this Number (>....the sequence 
also)in new fasta file.so that i get at the end a new
FASTA file with jus this IPI Accession Number.
thx and hope was clearly.

Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>Hi every body,
>>i have some AccNum in a file-> IPI67675
>>                                                 IPI98976.
>>                                                 ...
>>
>>what i want is how can i look in the fasta file (db fasta) if there is 
>>some match
>>if yes then copy the entire entry into a new fasta file.
>>i tried with bioperl but cause i m noob:-(( i don t get it.
>>thx all
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>  
>>    
>>
>
>Can you state clearly, what is in the "AccNum" file exactly, some sample
>text from the actual file would be good. Is the FASTA file containing
>the sequences in raw FASTA format or has it been processed using
>somthing like formatdb from the BLAST software?
>
>A few more details will help people understand and in turn help you with
>a swift solution.
>
>Cheers
>Nath
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From n.haigh at sheffield.ac.uk  Tue Oct  2 05:56:49 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 10:56:49 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47020DC9.8040401@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de>
Message-ID: <470215E1.4080901@sheffield.ac.uk>

outaleb Issame wrote:
> hi,
> with this file i mean, i picked out this Accession Number from
> IPI-Human Dbase,they come from a fasta file,
> so they re under eachother like a i a table in separate file now.
> what i want is how how can i check it in the fasta File (so in the
> IPI-Human FAsta File), i they re really there;
> if yes please copy the entire entry of this Number (>....the sequence
> also)in new fasta file.so that i get at the end a new
> FASTA file with jus this IPI Accession Number.
> thx and hope was clearly.

Ok, first of all, I'd read the contents of your Accession numbers into a
hash, something like the following (this could be written in a shorter
form, but since you're a newbie I'll leave it in a longer form so you
can follow easier).

-- start script --
use strict;
use Bio::SeqIO;

# change the following three lines to point to the relevant paths
# of your list of accessions file, your fasta file and your output
# fasta file
my $acc_file = "/path/to/your/file";
my $fasta_file_in = "/path/to/your/fasta/file";
my $fasta_file_out = "/path/to/your/fasta/output/file";

# Use a hash to keep a record of accessions we want to find
my %hash_of_req_acc;

# read all the required accessions from the file into the hash as keys
open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
while (<ACC_FILE>) {
  my $line = $_;
  chomp $line;
  $hash_of_req_acc{$_} = 1;
}
close ACC_FILE;

my $seqio_object_in = Bio::SeqIO->new(
  -file => $fasta_file_in,
  -format => 'fasta'
);
my $seqio_object_out = Bio::SeqIO->new(
  -file => $fasta_file_out,
  -format => 'fasta'
);

# loop through all the sequences in the fasta file
while (my $seq_object = $seqio_object_in->next_seq) {
  # get the sequence accession for easy matching
  my $seq_acc = $seq_object->accession_number;

  # write the sequence object to the output fasta file if we have a
matching accession
  $seqio_object_out->write_seq($seq_object) if exists
$hash_of_req_acc{$seq_acc};
}
-- end script --

I haven't tested this, but it should at least get you started. Also, the
fasta description line in the output file may not be exactly as it was
in the input fasta file - if this really matters, you may need to get
back to us. Also, if the input fasta file is huge (many thousands of
sequences) it may be wise to create an index of the fasta file in order
to speed up retrieval.

You may find this page helpful:
http://www.bioperl.org/wiki/HOWTO:SeqIO

Anyway, hope this helps to get you started.
Nath




From outaleb at web.de  Tue Oct  2 06:50:32 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 12:50:32 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <470215E1.4080901@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk>
Message-ID: <47022278.7010700@web.de>

thx for the help, but i got a empty output file,
i think its problem with matching the acc number, my fasta file look like:

*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU...
 >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU..
 >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
MMMMM..*

and my i Accnum File look like:
*IPI00177321
IPI00453473

*i hopt it helps to understand.*
*.


Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>hi,
>>with this file i mean, i picked out this Accession Number from
>>IPI-Human Dbase,they come from a fasta file,
>>so they re under eachother like a i a table in separate file now.
>>what i want is how how can i check it in the fasta File (so in the
>>IPI-Human FAsta File), i they re really there;
>>if yes please copy the entire entry of this Number (>....the sequence
>>also)in new fasta file.so that i get at the end a new
>>FASTA file with jus this IPI Accession Number.
>>thx and hope was clearly.
>>    
>>
>
>Ok, first of all, I'd read the contents of your Accession numbers into a
>hash, something like the following (this could be written in a shorter
>form, but since you're a newbie I'll leave it in a longer form so you
>can follow easier).
>
>-- start script --
>use strict;
>use Bio::SeqIO;
>
># change the following three lines to point to the relevant paths
># of your list of accessions file, your fasta file and your output
># fasta file
>my $acc_file = "/path/to/your/file";
>my $fasta_file_in = "/path/to/your/fasta/file";
>my $fasta_file_out = "/path/to/your/fasta/output/file";
>
># Use a hash to keep a record of accessions we want to find
>my %hash_of_req_acc;
>
># read all the required accessions from the file into the hash as keys
>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>while (<ACC_FILE>) {
>  my $line = $_;
>  chomp $line;
>  $hash_of_req_acc{$_} = 1;
>}
>close ACC_FILE;
>
>my $seqio_object_in = Bio::SeqIO->new(
>  -file => $fasta_file_in,
>  -format => 'fasta'
>);
>my $seqio_object_out = Bio::SeqIO->new(
>  -file => $fasta_file_out,
>  -format => 'fasta'
>);
>
># loop through all the sequences in the fasta file
>while (my $seq_object = $seqio_object_in->next_seq) {
>  # get the sequence accession for easy matching
>  my $seq_acc = $seq_object->accession_number;
>
>  # write the sequence object to the output fasta file if we have a
>matching accession
>  $seqio_object_out->write_seq($seq_object) if exists
>$hash_of_req_acc{$seq_acc};
>}
>-- end script --
>
>I haven't tested this, but it should at least get you started. Also, the
>fasta description line in the output file may not be exactly as it was
>in the input fasta file - if this really matters, you may need to get
>back to us. Also, if the input fasta file is huge (many thousands of
>sequences) it may be wise to create an index of the fasta file in order
>to speed up retrieval.
>
>You may find this page helpful:
>http://www.bioperl.org/wiki/HOWTO:SeqIO
>
>Anyway, hope this helps to get you started.
>Nath
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From cjfields at uiuc.edu  Tue Oct  2 09:00:57 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 08:00:57 -0500
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
Message-ID: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>

There is a script that comes with the bioperl core distribution,  
bp_split_seq.pl, which does this.  Here's the CVS location:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
scripts/seq/?cvsroot=bioperl

chris

On Oct 2, 2007, at 1:21 AM, Kevin Lam wrote:

> Hi!
> I am trying to annotate a 200kb sequence by doing blastx to find  
> the protein
> seq location
> I need to split the sequence up so that I get the best hits for  
> each region
> (the top blast hits will mask the smaller proteins if i do it as a  
> whole
> sequence)
> if i were to do it manually i can set the subsequence in the web  
> gui for
> ncbi's blast.
> this way, the blast hits coords are based on the whole 200kb.
>
> but I can't find this option in blast or a straightforward way to  
> do it in
> bioperl.
>
> I found similar solutions like
> http://www.bio.davidson.edu/projects/DAB/DAB.html
> divide and blast (but I need to specify coords)
>
> there also this from the bioperl archives
> http://bioinformatics.org/pipermail/bioclusters/2002-August/ 
> 000375.html
>
> but isn't there an easier way like i can specify blast subsequence  
> 200-900
> of fasta file and it will return the blastx hits in coords in terms  
> of the
> whole 200kb?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From rrc22 at cam.ac.uk  Tue Oct  2 09:38:45 2007
From: rrc22 at cam.ac.uk (Roy Chaudhuri)
Date: Tue, 02 Oct 2007 14:38:45 +0100
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <470249E5.6050206@cam.ac.uk>

> but isn't there an easier way like i can specify blast subsequence 200-900
> of fasta file and it will return the blastx hits in coords in terms of the
> whole 200kb?

Once you have split up your sequence (as Chris suggested), and run your 
BLAST, then you can add the hits to each subsequence as features. The 
subsequences can then be re-assembled using the cat method from 
Bio::SeqUtils, which will adjust the coordinates of the features 
appropriately.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.


From cjfields at uiuc.edu  Tue Oct  2 11:03:29 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 10:03:29 -0500
Subject: [Bioperl-l] exonerate
In-Reply-To: <29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
Message-ID: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>

One option is to try running $run->cleanup() after you finish  
parsing, which gets rid of the tempfiles on each run.

chris

On Sep 30, 2007, at 8:53 PM, alan wrote:

> Hi,
>
>
>>> I am calling exonerate.pm within my script while attempting to
>>> align cDNA  to multiple genomic fragments. After processing about
>>> 120+ genomic fragments my code crashes with the following error:
>>>
>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>> aborting...
>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>
>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>> routine yet I get the error message about "too many open files".
>>> Any suggestions on how I should be closing these files?
>>>
>>>
>>> Extract from my code that runs exonerate is listed below.
>>>
>>> foreach my $f(@files) {
>>>   next unless (-f  "$dir/$f");
>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>   my $query_obj = $q_in->next_seq();
>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>> format=>"Fasta");
>>>   my $target_obj = $target_in->next_seq();
>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>
>>>   [code for parsing the data.......]
>>>
>>>   $exonerate_io->close; #tried this line out of desperation but it
>>> did not help :-)
>>> }
>>>
>>> thanks
>>> alan




From outaleb at web.de  Tue Oct  2 10:51:05 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 16:51:05 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47022278.7010700@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de>
Message-ID: <47025AD9.1090105@web.de>

hi again,
i think i can resolve this problem with the method : id_parser();
how can i do that?
any suggestion .or experience??
ehx again



outaleb Issame wrote:

>thx for the help, but i got a empty output file,
>i think its problem with matching the acc number, my fasta file look like:
>
>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU...
> >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU..
> >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>MMMMM..*
>
>and my i Accnum File look like:
>*IPI00177321
>IPI00453473
>
>*i hopt it helps to understand.*
>*.
>
>
>Nathan S. Haigh wrote:
>
>  
>
>>outaleb Issame wrote:
>> 
>>
>>    
>>
>>>hi,
>>>with this file i mean, i picked out this Accession Number from
>>>IPI-Human Dbase,they come from a fasta file,
>>>so they re under eachother like a i a table in separate file now.
>>>what i want is how how can i check it in the fasta File (so in the
>>>IPI-Human FAsta File), i they re really there;
>>>if yes please copy the entire entry of this Number (>....the sequence
>>>also)in new fasta file.so that i get at the end a new
>>>FASTA file with jus this IPI Accession Number.
>>>thx and hope was clearly.
>>>   
>>>
>>>      
>>>
>>Ok, first of all, I'd read the contents of your Accession numbers into a
>>hash, something like the following (this could be written in a shorter
>>form, but since you're a newbie I'll leave it in a longer form so you
>>can follow easier).
>>
>>-- start script --
>>use strict;
>>use Bio::SeqIO;
>>
>># change the following three lines to point to the relevant paths
>># of your list of accessions file, your fasta file and your output
>># fasta file
>>my $acc_file = "/path/to/your/file";
>>my $fasta_file_in = "/path/to/your/fasta/file";
>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>
>># Use a hash to keep a record of accessions we want to find
>>my %hash_of_req_acc;
>>
>># read all the required accessions from the file into the hash as keys
>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>while (<ACC_FILE>) {
>> my $line = $_;
>> chomp $line;
>> $hash_of_req_acc{$_} = 1;
>>}
>>close ACC_FILE;
>>
>>my $seqio_object_in = Bio::SeqIO->new(
>> -file => $fasta_file_in,
>> -format => 'fasta'
>>);
>>my $seqio_object_out = Bio::SeqIO->new(
>> -file => $fasta_file_out,
>> -format => 'fasta'
>>);
>>
>># loop through all the sequences in the fasta file
>>while (my $seq_object = $seqio_object_in->next_seq) {
>> # get the sequence accession for easy matching
>> my $seq_acc = $seq_object->accession_number;
>>
>> # write the sequence object to the output fasta file if we have a
>>matching accession
>> $seqio_object_out->write_seq($seq_object) if exists
>>$hash_of_req_acc{$seq_acc};
>>}
>>-- end script --
>>
>>I haven't tested this, but it should at least get you started. Also, the
>>fasta description line in the output file may not be exactly as it was
>>in the input fasta file - if this really matters, you may need to get
>>back to us. Also, if the input fasta file is huge (many thousands of
>>sequences) it may be wise to create an index of the fasta file in order
>>to speed up retrieval.
>>
>>You may find this page helpful:
>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>
>>Anyway, hope this helps to get you started.
>>Nath
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> 
>>
>>    
>>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From rvos at interchange.ubc.ca  Tue Oct  2 13:00:36 2007
From: rvos at interchange.ubc.ca (rvos at interchange.ubc.ca)
Date: Tue, 02 Oct 2007 10:00:36 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <405453b66e.3b66e40545@interchange.ubc.ca>

An alternative is to explore the Bio::Phylo treedrawer:

http://search.cpan.org/~rvosa/Bio-Phylo-0.17_RC6/lib/Bio/Phylo/Treedrawer.pm

This is a separate install (in the interest of full disclosure: I'm the author).

Rutger

----- Original Message -----
From: Jason Stajich <jason at bioperl.org>
Date: Monday, October 1, 2007 12:32 pm
Subject: Re: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?

> I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
> for prettier trees - you get postscript out but you can render this 
> 
> to png or jpg with unix tools.  If there is a better stand alone 
> tree  
> drawing engine we're happy to try and integrate it into bioperl - 
> the  
> modules here are native Perl only and you can use the bioperl-run  
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS 
> 
> rendering output.
> 
> Mesquite, TreeView or other tools are usually much better but not  
> always an option if you want to auto-render these images for a  
> website, etc.
> 
> -jason
> 
> 
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
> 
> > Yes,
> > that's the issue about those commands, trees are not pretty at all
> > that's why for a one tree only kind of thing I rather use ITOL
> > other thing to try is the tree drawer of the Mesquite package
> > glad I could help
> >
> > Lucia
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Dear Lucia,
> >>
> >> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
> >> Tree::Draw
> >> methods. Some how missed this excellent HOWTO :
> >> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as 
> 
> >> well. I
> >> tried that and it worked very nicely. I have to work around to  
> >> beautify
> >> the tree and I am just going to do that.
> >>
> >> Thanks & Cheers,
> >> Shameer
> >>
> >>> OK
> >>>
> >>> you can use the implementations in Bio::TreeIO
> >>>
> >>> you can basically read the tree in newick format and out as an  
> >>> svg graph
> >>> something like this:
> >>>
> >>> my $in = new Bio::TreeIO(-file => 'input',
> >>>                          -format => 'newick');
> >>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >>>                           -format => 'svggraph');
> >>> while( my $tree = $in->next_tree ) {
> >>>     $out->write_tree($tree);
> >>> }
> >>>
> >>> you can also use Bio::Tree::Draw
> >>>
> >>> hope that helps
> >>>
> >>> Lucia
> >>>
> >>>
> >>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>
> >>>> Hi,
> >>>>
> >>>> Thanks for your mail. I have to create these trees as a part 
> of a
> >>>> webserver. i need to generate them dynamically using users input
> >>>> sequence.
> >>>> I think ITOL is not the stuff best suited for my purpose.
> >>>>
> >>>>> I think you'll have better luck using some of already available
> >>>> programs
> >>>>> to do
> >>>>> that, you'll get better looking trees. If you just have one  
> >>>>> tree to
> >>>> draw I
> >>>>> recommend you use:
> >>>>> http://itol.embl.de/
> >>>>>
> >>>>> Lucia
> >>>>>
> >>>>>
> >>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>>>
> >>>>>> Dear All,
> >>>>>>
> >>>>>> Is it possible to draw a phylogeny tree file in PNG format 
> using>>>> Bioperl
> >>>>>> ?
> >>>>>>  My input file are in phylip  treefile format. Any Modules / 
> 
> >>>>>> codes in
> >>>>>> Bio::Graphics / Phylogeny sections ?
> >>>>>>
> >>>>>> Input file :
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> > (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> > 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> > 1.51514,_H_255_263:6.20895):0.83877, 
> > (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> > 0.92645,_H_520_534:7.97418):0.15279, 
> > (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> > 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> > ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> > 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> > (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> > 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> > 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> > 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> > 1.52226,_H_463_464:5.42226):0.94093, 
> > (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> > 1.64489,_L_336_343:8.00808):0.88402, 
> > (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> > (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> > (((((_E_470_474:3.85000,_E_344_348:
> >>>>  3.
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 85000):0.89054,_L_475_478:4.74054):1.20107, 
> > (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> > 0.71112,_L_513_519:6.65273):0.67204, 
> > ((_L_296_304:5.00000,_H_292_295:5.00000): 
> > 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> > 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> > 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> > 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> > 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> > 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> > 1.08193,_H_229_243:7.93459):0.18730, 
> > (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> > ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> > 0.07448,_L_120_122:7.07448):1.59389, 
> > ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> > 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> > 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> > ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> > (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> > 0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>>>  5
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> > (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> > ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> > 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> > 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> > ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> > (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> > 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> > 0.88488,_E__40__48:5.79344):0.60814, 
> > 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> > 1.25080):0.17461):6.94325);
> >>>>>>
> >>>>
> >>>> --
> >>>> Shameer Khadar
> >>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >>>> National Centre for Biological Sciences (TIFR)
> >>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >>>> T - 91-080-23666001 EXT - 6251
> >>>> W - http://www.ncbs.res.in
> >>>>
> >>>
> >>>
> >>> Lucia Peixoto
> >>> Department of Biology,SAS
> >>> University of Pennsylvania
> >>>
> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From Russell.Smithies at agresearch.co.nz  Tue Oct  2 17:34:20 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 10:34:20 +1300
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>

I know this is the Bioperl list but how about just doing it with grep?

	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of outaleb Issame
> Sent: Wednesday, 3 October 2007 3:51 a.m.
> To: outaleb Issame
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> 
> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
> 
> 
> 
> outaleb Issame wrote:
> 
> >thx for the help, but i got a empty output file,
> >i think its problem with matching the acc number, my fasta file look
like:
> >
> >*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU...
> > >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU..
> > >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >MMMMM..*
> >
> >and my i Accnum File look like:
> >*IPI00177321
> >IPI00453473
> >
> >*i hopt it helps to understand.*
> >*.
> >
> >
> >Nathan S. Haigh wrote:
> >
> >
> >
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>
> >>>hi,
> >>>with this file i mean, i picked out this Accession Number from
> >>>IPI-Human Dbase,they come from a fasta file,
> >>>so they re under eachother like a i a table in separate file now.
> >>>what i want is how how can i check it in the fasta File (so in the
> >>>IPI-Human FAsta File), i they re really there;
> >>>if yes please copy the entire entry of this Number (>....the
sequence
> >>>also)in new fasta file.so that i get at the end a new
> >>>FASTA file with jus this IPI Accession Number.
> >>>thx and hope was clearly.
> >>>
> >>>
> >>>
> >>>
> >>Ok, first of all, I'd read the contents of your Accession numbers
into a
> >>hash, something like the following (this could be written in a
shorter
> >>form, but since you're a newbie I'll leave it in a longer form so
you
> >>can follow easier).
> >>
> >>-- start script --
> >>use strict;
> >>use Bio::SeqIO;
> >>
> >># change the following three lines to point to the relevant paths
> >># of your list of accessions file, your fasta file and your output
> >># fasta file
> >>my $acc_file = "/path/to/your/file";
> >>my $fasta_file_in = "/path/to/your/fasta/file";
> >>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>
> >># Use a hash to keep a record of accessions we want to find
> >>my %hash_of_req_acc;
> >>
> >># read all the required accessions from the file into the hash as
keys
> >>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>while (<ACC_FILE>) {
> >> my $line = $_;
> >> chomp $line;
> >> $hash_of_req_acc{$_} = 1;
> >>}
> >>close ACC_FILE;
> >>
> >>my $seqio_object_in = Bio::SeqIO->new(
> >> -file => $fasta_file_in,
> >> -format => 'fasta'
> >>);
> >>my $seqio_object_out = Bio::SeqIO->new(
> >> -file => $fasta_file_out,
> >> -format => 'fasta'
> >>);
> >>
> >># loop through all the sequences in the fasta file
> >>while (my $seq_object = $seqio_object_in->next_seq) {
> >> # get the sequence accession for easy matching
> >> my $seq_acc = $seq_object->accession_number;
> >>
> >> # write the sequence object to the output fasta file if we have a
> >>matching accession
> >> $seqio_object_out->write_seq($seq_object) if exists
> >>$hash_of_req_acc{$seq_acc};
> >>}
> >>-- end script --
> >>
> >>I haven't tested this, but it should at least get you started. Also,
the
> >>fasta description line in the output file may not be exactly as it
was
> >>in the input fasta file - if this really matters, you may need to
get
> >>back to us. Also, if the input fasta file is huge (many thousands of
> >>sequences) it may be wise to create an index of the fasta file in
order
> >>to speed up retrieval.
> >>
> >>You may find this page helpful:
> >>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>Anyway, hope this helps to get you started.
> >>Nath
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >>
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From thiago.venancio at gmail.com  Tue Oct  2 17:41:06 2007
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Tue, 2 Oct 2007 18:41:06 -0300
Subject: [Bioperl-l] frac_* methods
Message-ID: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>

Hi all,

This topic was discussed before, but I would like to put it on the list
again, maybe someone has an update.

The methods frac_identical, frac_conserved, frac_aligned_query and
frac_aligned_hit can also be used in the hit context, after HSP tilling. In
my point of view, it is better to use it just in HSPs individually, because
there are some rare/strange kinds of alignments. However, we frequently need
to get one measure of the whole alignment.

Any of the BioPerl masters has an update on this topic ? What is the best
current usage ?

Best.

Thiago

-- 
"Innovation distinguishes between a leader and a follower."
    Steve Jobs

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================


From outaleb at web.de  Tue Oct  2 17:47:07 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 23:47:07 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
Message-ID: <4702BC5B.7040407@web.de>

thx for this, but i want just create new fasta file with my accNumbers 
which i search in the FASTA file(localdbase).
so --> just search this Numbers in the FASTA file, if yes then copy the 
Header and Sequence to other new fasta file .
i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
i get crazy guys.
common some expert in this area??
 


Smithies, Russell wrote:

>I know this is the Bioperl list but how about just doing it with grep?
>
>	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
>
>
>
>  
>
>>-----Original Message-----
>>From: bioperl-l-bounces at lists.open-bio.org
>>    
>>
>[mailto:bioperl-l-bounces at lists.open-
>  
>
>>bio.org] On Behalf Of outaleb Issame
>>Sent: Wednesday, 3 October 2007 3:51 a.m.
>>To: outaleb Issame
>>Cc: bioperl-l at lists.open-bio.org
>>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
>>
>>hi again,
>>i think i can resolve this problem with the method : id_parser();
>>how can i do that?
>>any suggestion .or experience??
>>ehx again
>>
>>
>>
>>outaleb Issame wrote:
>>
>>    
>>
>>>thx for the help, but i got a empty output file,
>>>i think its problem with matching the acc number, my fasta file look
>>>      
>>>
>like:
>  
>
>>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>      
>>>
>>protein
>>    
>>
>>>DDHHHU...
>>>      
>>>
>>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>DDHHHU..
>>>      
>>>
>>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>MMMMM..*
>>>
>>>and my i Accnum File look like:
>>>*IPI00177321
>>>IPI00453473
>>>
>>>*i hopt it helps to understand.*
>>>*.
>>>
>>>
>>>Nathan S. Haigh wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>outaleb Issame wrote:
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>hi,
>>>>>with this file i mean, i picked out this Accession Number from
>>>>>IPI-Human Dbase,they come from a fasta file,
>>>>>so they re under eachother like a i a table in separate file now.
>>>>>what i want is how how can i check it in the fasta File (so in the
>>>>>IPI-Human FAsta File), i they re really there;
>>>>>if yes please copy the entire entry of this Number (>....the
>>>>>          
>>>>>
>sequence
>  
>
>>>>>also)in new fasta file.so that i get at the end a new
>>>>>FASTA file with jus this IPI Accession Number.
>>>>>thx and hope was clearly.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Ok, first of all, I'd read the contents of your Accession numbers
>>>>        
>>>>
>into a
>  
>
>>>>hash, something like the following (this could be written in a
>>>>        
>>>>
>shorter
>  
>
>>>>form, but since you're a newbie I'll leave it in a longer form so
>>>>        
>>>>
>you
>  
>
>>>>can follow easier).
>>>>
>>>>-- start script --
>>>>use strict;
>>>>use Bio::SeqIO;
>>>>
>>>># change the following three lines to point to the relevant paths
>>>># of your list of accessions file, your fasta file and your output
>>>># fasta file
>>>>my $acc_file = "/path/to/your/file";
>>>>my $fasta_file_in = "/path/to/your/fasta/file";
>>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>>
>>>># Use a hash to keep a record of accessions we want to find
>>>>my %hash_of_req_acc;
>>>>
>>>># read all the required accessions from the file into the hash as
>>>>        
>>>>
>keys
>  
>
>>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>>>while (<ACC_FILE>) {
>>>>my $line = $_;
>>>>chomp $line;
>>>>$hash_of_req_acc{$_} = 1;
>>>>}
>>>>close ACC_FILE;
>>>>
>>>>my $seqio_object_in = Bio::SeqIO->new(
>>>>-file => $fasta_file_in,
>>>>-format => 'fasta'
>>>>);
>>>>my $seqio_object_out = Bio::SeqIO->new(
>>>>-file => $fasta_file_out,
>>>>-format => 'fasta'
>>>>);
>>>>
>>>># loop through all the sequences in the fasta file
>>>>while (my $seq_object = $seqio_object_in->next_seq) {
>>>># get the sequence accession for easy matching
>>>>my $seq_acc = $seq_object->accession_number;
>>>>
>>>># write the sequence object to the output fasta file if we have a
>>>>matching accession
>>>>$seqio_object_out->write_seq($seq_object) if exists
>>>>$hash_of_req_acc{$seq_acc};
>>>>}
>>>>-- end script --
>>>>
>>>>I haven't tested this, but it should at least get you started. Also,
>>>>        
>>>>
>the
>  
>
>>>>fasta description line in the output file may not be exactly as it
>>>>        
>>>>
>was
>  
>
>>>>in the input fasta file - if this really matters, you may need to
>>>>        
>>>>
>get
>  
>
>>>>back to us. Also, if the input fasta file is huge (many thousands of
>>>>sequences) it may be wise to create an index of the fasta file in
>>>>        
>>>>
>order
>  
>
>>>>to speed up retrieval.
>>>>
>>>>You may find this page helpful:
>>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>>
>>>>Anyway, hope this helps to get you started.
>>>>Nath
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>
>=======================================================================
>Attention: The information contained in this message and/or attachments
>from AgResearch Limited is intended only for the persons or entities
>to which it is addressed and may contain confidential and/or privileged
>material. Any review, retransmission, dissemination or other use of, or
>taking of any action in reliance upon, this information by persons or
>entities other than the intended recipients is prohibited by AgResearch
>Limited. If you have received this message in error, please notify the
>sender immediately.
>=======================================================================
>
>  
>



From jason at bioperl.org  Tue Oct  2 18:22:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 15:22:59 -0700
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>

I think my answer before was something to the tune of:

Use an alignment algorithm that finds a single best alignment like  
FASTA or Smith-Waterman (SW) if what you want is a single number that  
represents the alignment.  BLAST is great for fast searching but  
FASTA or SW/SSEARCH are going to be better at creating an alignment.   
Consider the -postsw option in WUBLAST as well as it will realign the  
HSPs with SW.

I personally never use the frac alignment summary stats for the Hit  
object for this reason unless I know I am going to have a single HSP.

-jason

On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago
>
> -- 
> "Innovation distinguishes between a leader and a follower."
>     Steve Jobs
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct  2 18:32:30 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 17:32:30 -0500
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <B9E32251-2A8E-4079-B256-9665D9987B02@uiuc.edu>

I think their use is based on what you are trying to accomplish.  For  
instance I am currently running a lot of small BLASTN queries  
(limiting by normalized bit score), so I tend to look at the HSP data  
more.  However, in other circumstances I might want the overall  
frac_identical for all HSPs ($hit->frac_identical).  YMMV.

chris

On Oct 2, 2007, at 4:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago




From razi.khaja at gmail.com  Tue Oct  2 19:46:12 2007
From: razi.khaja at gmail.com (Razi Khaja)
Date: Tue, 2 Oct 2007 19:46:12 -0400
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4702BC5B.7040407@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de> <470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
	<4702BC5B.7040407@web.de>
Message-ID: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>

Here is the easiest non-bioperl solution using executables provided
with ncbi's blast:

(1) format your multifasta file into a blast database

> /usr/local/ncbi/blast-2.2.16/bin/formatdb -i yourmultifastafile -t yourblastdb

(2) extract sequences from the newly created blast database with a
file containing a list of accession numbers (one on each line)

> /usr/local/ncib/blast-2.2.16/bin/fastacmd -d yourblastdb -i inputfilewithaccessionnumbers -o outputfile

Your outputfile should be a multifasta file of your list of accession numbers

blast executables are available from
http://www.ncbi.nlm.nih.gov/blast/download.shtml

Hope that helps.
Razi Khaja

On 10/2/07, outaleb Issame <outaleb at web.de> wrote:
> thx for this, but i want just create new fasta file with my accNumbers
> which i search in the FASTA file(localdbase).
> so --> just search this Numbers in the FASTA file, if yes then copy the
> Header and Sequence to other new fasta file .
> i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
> i get crazy guys.
> common some expert in this area??
>
>
>
> Smithies, Russell wrote:
>
> >I know this is the Bioperl list but how about just doing it with grep?
> >
> >       grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
> >
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: bioperl-l-bounces at lists.open-bio.org
> >>
> >>
> >[mailto:bioperl-l-bounces at lists.open-
> >
> >
> >>bio.org] On Behalf Of outaleb Issame
> >>Sent: Wednesday, 3 October 2007 3:51 a.m.
> >>To: outaleb Issame
> >>Cc: bioperl-l at lists.open-bio.org
> >>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> >>
> >>hi again,
> >>i think i can resolve this problem with the method : id_parser();
> >>how can i do that?
> >>any suggestion .or experience??
> >>ehx again
> >>
> >>
> >>
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>>thx for the help, but i got a empty output file,
> >>>i think its problem with matching the acc number, my fasta file look
> >>>
> >>>
> >like:
> >
> >
> >>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>
> >>>
> >>protein
> >>
> >>
> >>>DDHHHU...
> >>>
> >>>
> >>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>DDHHHU..
> >>>
> >>>
> >>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>MMMMM..*
> >>>
> >>>and my i Accnum File look like:
> >>>*IPI00177321
> >>>IPI00453473
> >>>
> >>>*i hopt it helps to understand.*
> >>>*.
> >>>
> >>>
> >>>Nathan S. Haigh wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>outaleb Issame wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>hi,
> >>>>>with this file i mean, i picked out this Accession Number from
> >>>>>IPI-Human Dbase,they come from a fasta file,
> >>>>>so they re under eachother like a i a table in separate file now.
> >>>>>what i want is how how can i check it in the fasta File (so in the
> >>>>>IPI-Human FAsta File), i they re really there;
> >>>>>if yes please copy the entire entry of this Number (>....the
> >>>>>
> >>>>>
> >sequence
> >
> >
> >>>>>also)in new fasta file.so that i get at the end a new
> >>>>>FASTA file with jus this IPI Accession Number.
> >>>>>thx and hope was clearly.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>Ok, first of all, I'd read the contents of your Accession numbers
> >>>>
> >>>>
> >into a
> >
> >
> >>>>hash, something like the following (this could be written in a
> >>>>
> >>>>
> >shorter
> >
> >
> >>>>form, but since you're a newbie I'll leave it in a longer form so
> >>>>
> >>>>
> >you
> >
> >
> >>>>can follow easier).
> >>>>
> >>>>-- start script --
> >>>>use strict;
> >>>>use Bio::SeqIO;
> >>>>
> >>>># change the following three lines to point to the relevant paths
> >>>># of your list of accessions file, your fasta file and your output
> >>>># fasta file
> >>>>my $acc_file = "/path/to/your/file";
> >>>>my $fasta_file_in = "/path/to/your/fasta/file";
> >>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>>>
> >>>># Use a hash to keep a record of accessions we want to find
> >>>>my %hash_of_req_acc;
> >>>>
> >>>># read all the required accessions from the file into the hash as
> >>>>
> >>>>
> >keys
> >
> >
> >>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>>>while (<ACC_FILE>) {
> >>>>my $line = $_;
> >>>>chomp $line;
> >>>>$hash_of_req_acc{$_} = 1;
> >>>>}
> >>>>close ACC_FILE;
> >>>>
> >>>>my $seqio_object_in = Bio::SeqIO->new(
> >>>>-file => $fasta_file_in,
> >>>>-format => 'fasta'
> >>>>);
> >>>>my $seqio_object_out = Bio::SeqIO->new(
> >>>>-file => $fasta_file_out,
> >>>>-format => 'fasta'
> >>>>);
> >>>>
> >>>># loop through all the sequences in the fasta file
> >>>>while (my $seq_object = $seqio_object_in->next_seq) {
> >>>># get the sequence accession for easy matching
> >>>>my $seq_acc = $seq_object->accession_number;
> >>>>
> >>>># write the sequence object to the output fasta file if we have a
> >>>>matching accession
> >>>>$seqio_object_out->write_seq($seq_object) if exists
> >>>>$hash_of_req_acc{$seq_acc};
> >>>>}
> >>>>-- end script --
> >>>>
> >>>>I haven't tested this, but it should at least get you started. Also,
> >>>>
> >>>>
> >the
> >
> >
> >>>>fasta description line in the output file may not be exactly as it
> >>>>
> >>>>
> >was
> >
> >
> >>>>in the input fasta file - if this really matters, you may need to
> >>>>
> >>>>
> >get
> >
> >
> >>>>back to us. Also, if the input fasta file is huge (many thousands of
> >>>>sequences) it may be wise to create an index of the fasta file in
> >>>>
> >>>>
> >order
> >
> >
> >>>>to speed up retrieval.
> >>>>
> >>>>You may find this page helpful:
> >>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>>>
> >>>>Anyway, hope this helps to get you started.
> >>>>Nath
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l at lists.open-bio.org
> >>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>_______________________________________________
> >>>Bioperl-l mailing list
> >>>Bioperl-l at lists.open-bio.org
> >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >=======================================================================
> >Attention: The information contained in this message and/or attachments
> >from AgResearch Limited is intended only for the persons or entities
> >to which it is addressed and may contain confidential and/or privileged
> >material. Any review, retransmission, dissemination or other use of, or
> >taking of any action in reliance upon, this information by persons or
> >entities other than the intended recipients is prohibited by AgResearch
> >Limited. If you have received this message in error, please notify the
> >sender immediately.
> >=======================================================================
> >
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jason at bioperl.org  Tue Oct  2 20:50:37 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 17:50:37 -0700
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
Message-ID: <CF48176B-CE5B-40EC-81DE-8C3114502ADE@bioperl.org>

http://bioperl.open-bio.org/wiki/ 
FAQ#How_do_I_use_Bio::Index::Fasta_and_index_on_different_ids.3F

On Oct 2, 2007, at 7:51 AM, outaleb Issame wrote:

> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
>
>
>
> outaleb Issame wrote:
>
>> thx for the help, but i got a empty output file,
>> i think its problem with matching the acc number, my fasta file  
>> look like:
>>
>> *>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to  
>> NOD3 protein
>> DDHHHU...
>>> IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> DDHHHU..
>>> IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> MMMMM..*
>>
>> and my i Accnum File look like:
>> *IPI00177321
>> IPI00453473
>>
>> *i hopt it helps to understand.*
>> *.
>>
>>
>> Nathan S. Haigh wrote:
>>
>>
>>
>>> outaleb Issame wrote:
>>>
>>>
>>>
>>>
>>>> hi,
>>>> with this file i mean, i picked out this Accession Number from
>>>> IPI-Human Dbase,they come from a fasta file,
>>>> so they re under eachother like a i a table in separate file now.
>>>> what i want is how how can i check it in the fasta File (so in the
>>>> IPI-Human FAsta File), i they re really there;
>>>> if yes please copy the entire entry of this Number (>....the  
>>>> sequence
>>>> also)in new fasta file.so that i get at the end a new
>>>> FASTA file with jus this IPI Accession Number.
>>>> thx and hope was clearly.
>>>>
>>>>
>>>>
>>>>
>>> Ok, first of all, I'd read the contents of your Accession numbers  
>>> into a
>>> hash, something like the following (this could be written in a  
>>> shorter
>>> form, but since you're a newbie I'll leave it in a longer form so  
>>> you
>>> can follow easier).
>>>
>>> -- start script --
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> # change the following three lines to point to the relevant paths
>>> # of your list of accessions file, your fasta file and your output
>>> # fasta file
>>> my $acc_file = "/path/to/your/file";
>>> my $fasta_file_in = "/path/to/your/fasta/file";
>>> my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>
>>> # Use a hash to keep a record of accessions we want to find
>>> my %hash_of_req_acc;
>>>
>>> # read all the required accessions from the file into the hash as  
>>> keys
>>> open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>> while (<ACC_FILE>) {
>>> my $line = $_;
>>> chomp $line;
>>> $hash_of_req_acc{$_} = 1;
>>> }
>>> close ACC_FILE;
>>>
>>> my $seqio_object_in = Bio::SeqIO->new(
>>> -file => $fasta_file_in,
>>> -format => 'fasta'
>>> );
>>> my $seqio_object_out = Bio::SeqIO->new(
>>> -file => $fasta_file_out,
>>> -format => 'fasta'
>>> );
>>>
>>> # loop through all the sequences in the fasta file
>>> while (my $seq_object = $seqio_object_in->next_seq) {
>>> # get the sequence accession for easy matching
>>> my $seq_acc = $seq_object->accession_number;
>>>
>>> # write the sequence object to the output fasta file if we have a
>>> matching accession
>>> $seqio_object_out->write_seq($seq_object) if exists
>>> $hash_of_req_acc{$seq_acc};
>>> }
>>> -- end script --
>>>
>>> I haven't tested this, but it should at least get you started.  
>>> Also, the
>>> fasta description line in the output file may not be exactly as  
>>> it was
>>> in the input fasta file - if this really matters, you may need to  
>>> get
>>> back to us. Also, if the input fasta file is huge (many thousands of
>>> sequences) it may be wise to create an index of the fasta file in  
>>> order
>>> to speed up retrieval.
>>>
>>> You may find this page helpful:
>>> http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>
>>> Anyway, hope this helps to get you started.
>>> Nath
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From Russell.Smithies at agresearch.co.nz  Tue Oct  2 21:05:25 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 14:05:25 +1300
Subject: [Bioperl-l] coloring of HSPs in blast panel
In-Reply-To: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk><47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de><D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz><4702BC5B.7040407@web.de>
	<62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDC73@imail.agresearch.co.nz>

Hi all,
I'm using a modified version of Lincoln's tutorial
(http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output)
and I'm colouring the HSPs by setting the -bgcolor by score with a sub
to give a similar image to that from NCBI but for some reason, my
colours are coming out wrong (see attached example)
They seem to be off by one but I can't see why.

Any ideas?

I can't be certain but I think it's only started doing this since our
BLAST upgrade to 2.2.17 a few weeks ago.

Here's the colouring code:
------------------------------------------------------------------------
-------
my $track = $panel->add_track(
                              -glyph       => 'segments',
                              -label       => 1,
                              -connector   => 'dashed',
                              -bgcolor     => sub {
                                my $feature = shift;
                                my $score = $feature->score;
			return 'red'       if $score >= 200;
                                    return 'fuchsia' if $score >= 80;
                                    return 'lime'      if $score >= 50;
			return 'blue'      if $score >= 40;
                                    return 'black';
                               },
                              -font2color  => 'gray',
                              -sort_order  => 'high_score',
                              -description => sub {
                                my $feature = shift;
                                return unless
$feature->has_tag('description');
                                my ($description) =
$feature->each_tag_value('description');
                                my $score = $feature->score;
                                "$description, score=$score";
                               },
                             );
------------------------------------------------------------------------
---------


Thanx,

Russell Smithies




=======================================================================
Attention: The information contained in this message and/or attachments
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From aaron.j.mackey at gsk.com  Tue Oct  2 21:40:14 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Tue, 2 Oct 2007 21:40:14 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
Message-ID: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>

Let me second Jason's comment that while BLAST is a great search program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with the 
FASTA package) is now vector-parallelized on most i386 architectures, it 
is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run 
BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 10:50:47 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 10:50:47 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
References: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
	<OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>

I agree that BLAST is not a very good alignment algorithm but believe
there are plenty of reasons to run BLAST, especially when placing a
contig /BAC/PAC to a genome. In those cases, fully implementation of SW
requires an unpractical matrix of n X m.   

Currently we are developing an algorithm which will run global alignment
after BLAST. Hopefully a Perl wrapper will become available next year.


Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Tuesday, October 02, 2007 9:40 PM
To: Jason Stajich
Cc: bioperl-l list; Thiago Venancio
Subject: Re: [Bioperl-l] frac_* methods

Let me second Jason's comment that while BLAST is a great search
program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
the 
FASTA package) is now vector-parallelized on most i386 architectures, it

is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run

BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From aaron.j.mackey at gsk.com  Wed Oct  3 11:53:12 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Wed, 3 Oct 2007 11:53:12 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
Message-ID: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are expected 
to occur naturally (i.e. are not an artifact of the experiment that in an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very 
good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical significance)

Please don't get me wrong, I think BLAST is an invaluable tool that fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures, it
> 
> is only about 10 times slower than BLAST for complete database searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> > Consider the -postsw option in WUBLAST as well as it will realign the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the 
> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From vebaev at gmail.com  Wed Oct  3 12:44:35 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 19:44:35 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
Message-ID: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>

Hi,
What methods should I use to draw a CG plot of a sequence (with
bio::graphics)?

Thanks

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 13:37:51 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 13:37:51 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
References: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
	<OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C36@NIHCESMLBX8.nih.gov>

I agree what you said. 

One of the reasons that we introduce 'BLAST-guided-global alignment
(NW)' is that a significant amount of clones are either of low quality,
partially sequenced, erroneously assembled, or come from non reference
strain.   

Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Wednesday, October 03, 2007 11:53 AM
To: Cui, Wenwu (NIH/NLM/NCBI) [C]
Cc: bioperl-l list; Jason Stajich; Thiago Venancio
Subject: RE: [Bioperl-l] frac_* methods

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance
for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling
algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are
expected 
to occur naturally (i.e. are not an artifact of the experiment that in
an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very

good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical
significance)

Please don't get me wrong, I think BLAST is an invaluable tool that
fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of
SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global
alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with
so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures,
it
> 
> is only about 10 times slower than BLAST for complete database
searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even
run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number
that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment.

> > Consider the -postsw option in WUBLAST as well as it will realign
the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single
HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the

> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs
individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at uiuc.edu  Wed Oct  3 14:19:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 13:19:43 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
Message-ID: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>

You should look at Bio::Graphics::Glyph::dna.  From the POD:

---------------------------

This glyph draws DNA sequences.  At high magnifications, this glyph
will draw the actual base pairs of the sequence (both strands).  At
low magnifications, the glyph will plot the GC content.  By default,
the GC calculation will use non-overlapping bins, but this can be
changed by specifying the gc_window option, in which case, a
sliding window calculation will be used.

For this glyph to work, the feature must return a DNA sequence string
in response to the dna() method. For example, you can use a
Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
like this:
     my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
     my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end  
=> 800 );
     $feature->attach_seq($dna);
     $panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used.

---------------------------

chris

On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:

> Hi,
> What methods should I use to draw a CG plot of a sequence (with
> bio::graphics)?
>
> Thanks
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From vebaev at gmail.com  Wed Oct  3 14:31:49 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 21:31:49 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
Message-ID: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>

Thanks,
I will use Bio::Graphics::Glyph::dna for the classical CG%
(this type is for C+G % or CpG)?


and if I want to draw a similar plot but for example for a % of dinucleotide
(NpN) occurrances in a sliding windiw, what should I use?


Thanks!




2007/10/3, Chris Fields <cjfields at uiuc.edu>:
>
> You should look at Bio::Graphics::Glyph::dna.  From the POD:
>
> ---------------------------
>
> This glyph draws DNA sequences.  At high magnifications, this glyph
> will draw the actual base pairs of the sequence (both strands).  At
> low magnifications, the glyph will plot the GC content.  By default,
> the GC calculation will use non-overlapping bins, but this can be
> changed by specifying the gc_window option, in which case, a
> sliding window calculation will be used.
>
> For this glyph to work, the feature must return a DNA sequence string
> in response to the dna() method. For example, you can use a
> Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
> like this:
>      my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
>      my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end
> => 800 );
>      $feature->attach_seq($dna);
>      $panel->add_track( $feature, -glyph => 'dna' );
>
> A Bio::Graphics::Feature object may also be used.
>
> ---------------------------
>
> chris
>
> On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:
>
> > Hi,
> > What methods should I use to draw a CG plot of a sequence (with
> > bio::graphics)?
> >
> > Thanks
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From dave at davemessina.com  Wed Oct  3 14:22:23 2007
From: dave at davemessina.com (Dave Messina)
Date: Wed, 3 Oct 2007 20:22:23 +0200
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <37574C6D-98BA-47A5-875E-9255377133B8@sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the  
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Panel.html

I think the example code will help you to do what you want.


Dave



From cjfields at uiuc.edu  Wed Oct  3 15:10:46 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 14:10:46 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
	<a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
Message-ID: <7B62B534-2A8C-4EAE-B956-F0FADB726195@uiuc.edu>

On Oct 3, 2007, at 1:31 PM, Vesselin Baev wrote:

> Thanks,
> I will use Bio::Graphics::Glyph::dna for the classical CG%
> (this type is for C+G % or CpG)?
>
>
> and if I want to draw a similar plot but for example for a % of  
> dinucleotide
> (NpN) occurrances in a sliding windiw, what should I use?
>
>
> Thanks!

It would be GC content, not CpG.  Not sure what you would use for  
dinucleotide content; you could look at the Bio::Graphics::Glyph::dna  
code and either subclass it for your needs (probably the best option)  
or add an extra parameter and 'rewire' the appropriate methods to do  
what you want.

chris


From dmessina at sbc.su.se  Wed Oct  3 14:55:10 2007
From: dmessina at sbc.su.se (dmessina at sbc.su.se)
Date: Wed, 3 Oct 2007 20:55:10 +0200 (CEST)
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <61118.217.213.158.117.1191437710.squirrel@mail.sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html

I think the example code will help you to do what you want.


Dave




From lzhtom at hotmail.com  Wed Oct  3 18:30:43 2007
From: lzhtom at hotmail.com (zhihuali)
Date: Wed, 3 Oct 2007 22:30:43 +0000
Subject: [Bioperl-l] Loading Blast Report in a minimal way
Message-ID: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>


Hi netters,

I'm using SearchIO to parse my blast reports. They are extremely huge, and not surprisingly, it's extremely slow and sometimes the system crashed due to memmory problem. As I can handle small reports quickly, it seems like a problem related to the way SearchIO works: it slurps the whole report into the memory and builds millions of objects.

I've checked old posts and some people used FastHitEventBuilder to build hit objects without any hsp objects. And some people suggested using tabular output of blast. But in my case I need to go to each of the hsps of each hit, parse the alignment, and gather the information needed if that hsp fits certain criteria, and then move on to the next hsp/or jump over to the next hit/ or exit the processing, according to the information I have already got. An ideal way would be to read one hsp at a time from the report to the memory.  Is there some way to modify SearchIO (or build another Search Event) to do this?

Thanks a lot!


Zhihua Li
_________________________________________________________________
?? Live Search ??????????????
http://www.live.com/?searchOnly=true


From budd at embl-heidelberg.de  Thu Oct  4 09:43:57 2007
From: budd at embl-heidelberg.de (Aidan Budd)
Date: Thu, 4 Oct 2007 15:43:57 +0200 (CEST)
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
Message-ID: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>

Hi bioperlers,

I've been trying to add info to a feature in a RichSeq object so that when 
the Seq is written in swissprot format I can put information in the final
field of the feature

FT   DOMAIN      208    392       Helicase ATP-binding.

i.e. where it says "Helicase ATP-binding."

I can control what goes in the primary field, and set the location, but 
haven't been able to work out how to add info to go in this final field.

Thanks,

Aidan

-- 
----------------------------------------------------------------------
Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
Meyerhofstr. 1, 69117 Heidelberg, Germany

URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html



From cjfields at uiuc.edu  Thu Oct  4 10:32:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 09:32:43 -0500
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
In-Reply-To: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
References: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
Message-ID: <84A6CB47-6890-476B-A375-6FCF37655330@uiuc.edu>

Try adding it as a tag value with the name 'description','note', or  
'product' (the first two are probably the best to use for most  
purposes).  There is a quick explanation here:

http://www.bioperl.org/wiki/HOWTO:Feature- 
Annotation#Building_Your_Own_Sequences

You can also do something like:

$sf->add_tag_value('description', 'Helicase ATP-binding');

See Bio::SeqFeature::Generic POD for more.

chris

On Oct 4, 2007, at 8:43 AM, Aidan Budd wrote:

> Hi bioperlers,
>
> I've been trying to add info to a feature in a RichSeq object so  
> that when
> the Seq is written in swissprot format I can put information in the  
> final
> field of the feature
>
> FT   DOMAIN      208    392       Helicase ATP-binding.
>
> i.e. where it says "Helicase ATP-binding."
>
> I can control what goes in the primary field, and set the location,  
> but
> haven't been able to work out how to add info to go in this final  
> field.
>
> Thanks,
>
> Aidan
>
> -- 
> ----------------------------------------------------------------------
> Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
> Meyerhofstr. 1, 69117 Heidelberg, Germany
>
> URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cain.cshl at gmail.com  Thu Oct  4 11:08:52 2007
From: cain.cshl at gmail.com (Scott Cain)
Date: Thu, 04 Oct 2007 11:08:52 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
Message-ID: <1191510532.2787.16.camel@localhost.localdomain>

Hi Chris,

I think adding the type=MYISAM is the right thing to do; please go ahead
and commit it.

Scott



On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
> Just thought I would forward this on to the GBrowse list as well in  
> case anyone has run into the same problem.  The issue pops up when  
> using bioperl from CVS and appears to be related to a fix Lincoln  
> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using  
> FULLTEXT, which only works for MyISAM currently.
> 
> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE  
> queries does work when InnoDB is set to the default.  Should I go  
> ahead and commit?
> 
> chris
> 
> Begin forwarded message:
> 
> > I'm getting the following error on my local MySQL (v 5.0.41) with
> > bp_seqfeature_load:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: The used table type doesn't support FULLTEXT indexes
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /Library/
> > Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
> > STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
> > Bio/DB/SeqFeature/Store.pm:382
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
> > 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
> > STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
> > SeqFeature/Store.pm:345
> > STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
> > -------------------------------------------
> >
> > The default setting for storage is InnoDB; switching to MyISAM fixes
> > the issue.  Should we specify TYPE = MyISAM with the various CREATE
> > TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
> > safe side?
> >
> > chris
> 
> 
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



From cjfields at uiuc.edu  Thu Oct  4 11:14:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 10:14:37 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <1191510532.2787.16.camel@localhost.localdomain>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
	<1191510532.2787.16.camel@localhost.localdomain>
Message-ID: <9DEFB5C1-6F79-465B-8FB4-68305C53E427@uiuc.edu>

Done.  If we run into issues and need to roll back let me know.

chris

On Oct 4, 2007, at 10:08 AM, Scott Cain wrote:

> Hi Chris,
>
> I think adding the type=MYISAM is the right thing to do; please go  
> ahead
> and commit it.
>
> Scott
>
>
>
> On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
>> Just thought I would forward this on to the GBrowse list as well in
>> case anyone has run into the same problem.  The issue pops up when
>> using bioperl from CVS and appears to be related to a fix Lincoln
>> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using
>> FULLTEXT, which only works for MyISAM currently.
>>
>> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE
>> queries does work when InnoDB is set to the default.  Should I go
>> ahead and commit?
>>
>> chris
>>
>> Begin forwarded message:
>>
>>> I'm getting the following error on my local MySQL (v 5.0.41) with
>>> bp_seqfeature_load:
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: The used table type doesn't support FULLTEXT indexes
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database / 
>>> Library/
>>> Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
>>> STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
>>> Bio/DB/SeqFeature/Store.pm:382
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
>>> 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
>>> STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
>>> SeqFeature/Store.pm:345
>>> STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
>>> -------------------------------------------
>>>
>>> The default setting for storage is InnoDB; switching to MyISAM fixes
>>> the issue.  Should we specify TYPE = MyISAM with the various CREATE
>>> TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
>>> safe side?
>>>
>>> chris
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.net email is sponsored by: Microsoft
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>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
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>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Thu Oct  4 15:30:48 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 14:30:48 -0500
Subject: [Bioperl-l] blastxml oddity
Message-ID: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>

Just noticed an oddity from BLASTXML output from the NCBI server; I'm  
cc'ing this to NCBI so maybe they can explain.  BTW, the following  
doesn't occur via URLAPI.

When running a standard BLAST query using the NCBI web page, if  
requesting XML output after the run I get the entire query seq masked  
out and no midline.  This occurs with all default settings except  
output type (set to XML).  Can anyone replicate this?

Here's a sample:

<Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
               <Hsp_bit-score>320.472</Hsp_bit-score>
               <Hsp_score>820</Hsp_score>
               <Hsp_evalue>2.17708e-86</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>181</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
               <Hsp_hit-to>181</Hsp_hit-to>
               <Hsp_query-frame>0</Hsp_query-frame>
               <Hsp_hit-frame>0</Hsp_hit-frame>
               <Hsp_identity>0</Hsp_identity>
               <Hsp_positive>0</Hsp_positive>
               <Hsp_gaps>0</Hsp_gaps>
               <Hsp_align-len>181</Hsp_align-len>
                
<Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
                
<Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPV 
TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAV 
LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
                
<Hsp_midline>                                                            
                                                                         
                                                    </Hsp_midline>
             </Hsp>
           </Hit_hsps>



<notblast>chris</notblast>


From cjfields at uiuc.edu  Thu Oct  4 16:36:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 15:36:25 -0500
Subject: [Bioperl-l] blastxml oddity
In-Reply-To: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
References: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
Message-ID: <86D7D694-1ACF-4D91-9FEC-0FEA21C1B689@uiuc.edu>

NCBI's BLAST team is working on this; it occurs only if you use an GI/ 
accession instead of a full sequence, and only for XML.

chris

On Oct 4, 2007, at 2:30 PM, Chris Fields wrote:

> Just noticed an oddity from BLASTXML output from the NCBI server; I'm
> cc'ing this to NCBI so maybe they can explain.  BTW, the following
> doesn't occur via URLAPI.
>
> When running a standard BLAST query using the NCBI web page, if
> requesting XML output after the run I get the entire query seq masked
> out and no midline.  This occurs with all default settings except
> output type (set to XML).  Can anyone replicate this?
>
> Here's a sample:
>
> <Hit_hsps>
>              <Hsp>
>                <Hsp_num>1</Hsp_num>
>                <Hsp_bit-score>320.472</Hsp_bit-score>
>                <Hsp_score>820</Hsp_score>
>                <Hsp_evalue>2.17708e-86</Hsp_evalue>
>                <Hsp_query-from>1</Hsp_query-from>
>                <Hsp_query-to>181</Hsp_query-to>
>                <Hsp_hit-from>1</Hsp_hit-from>
>                <Hsp_hit-to>181</Hsp_hit-to>
>                <Hsp_query-frame>0</Hsp_query-frame>
>                <Hsp_hit-frame>0</Hsp_hit-frame>
>                <Hsp_identity>0</Hsp_identity>
>                <Hsp_positive>0</Hsp_positive>
>                <Hsp_gaps>0</Hsp_gaps>
>                <Hsp_align-len>181</Hsp_align-len>
>
> <Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
>
> <Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGN 
> PV
> TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQL 
> AV
> LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
>
> <Hsp_midline>
>
>                                                     </Hsp_midline>
>              </Hsp>
>            </Hit_hsps>
>
>
>
> <notblast>chris</notblast>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 15:35:25 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 14:35:25 -0500
Subject: [Bioperl-l] bp_search2gff.pl
Message-ID: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>

Hello,

I have been playing with the bp_search2gff.pl script (on HEAD of
bioperl-live).    There are a couple of issues I was wondering about.

One is the ID that gets generated for a match feature when the --match
option is set.   The ID is  set to the ID of the query sequence.  This
can be problematic if you are representing the query sequence and the
blast hit in the same gff file.  When using the resultant gff file for
loading into Chado, it also creates a problem if you have more than
one hit for a given query sequence, for example if you ran two
different analyses that each had a hit for a given query.  Would it be
possible to have an option to create a unique ID for match features.
One suggestion could be to create an ID based on the ID of the query +
the id of the hit + the source

As long as two different analyses were loaded as different sources,
this would ensure unique IDs for the match features.


Also, is there a reason for writing the Target string as

Target=Sequence:SOME_ID

as opposed to

Target=SOME_ID


The latter seems a little more in line with the gff3 spec and plays a
little nicer with the GMOD tools.

Thanks for looking into this.

Eric


From cjfields at uiuc.edu  Fri Oct  5 15:51:20 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 5 Oct 2007 14:51:20 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
Message-ID: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>

We might want to file this as a bug so we can track it.

The core devs have been mulling over the state of GFF/GFF3 in  
BioPerl; proper handling of any SearchIO data is certainly included  
in that.  I believe some road forward is to be planned soon (after  
Genome Informatics).

chris

On Oct 5, 2007, at 2:35 PM, Eric Just wrote:

> Hello,
>
> I have been playing with the bp_search2gff.pl script (on HEAD of
> bioperl-live).    There are a couple of issues I was wondering about.
>
> One is the ID that gets generated for a match feature when the --match
> option is set.   The ID is  set to the ID of the query sequence.  This
> can be problematic if you are representing the query sequence and the
> blast hit in the same gff file.  When using the resultant gff file for
> loading into Chado, it also creates a problem if you have more than
> one hit for a given query sequence, for example if you ran two
> different analyses that each had a hit for a given query.  Would it be
> possible to have an option to create a unique ID for match features.
> One suggestion could be to create an ID based on the ID of the query +
> the id of the hit + the source
>
> As long as two different analyses were loaded as different sources,
> this would ensure unique IDs for the match features.
>
>
> Also, is there a reason for writing the Target string as
>
> Target=Sequence:SOME_ID
>
> as opposed to
>
> Target=SOME_ID
>
>
> The latter seems a little more in line with the gff3 spec and plays a
> little nicer with the GMOD tools.
>
> Thanks for looking into this.
>
> Eric
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 16:06:48 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 15:06:48 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
	<54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
Message-ID: <fa1fe35c0710051306v1636d6er6f02133f4ecef91c@mail.gmail.com>

Thanks Chris, I'll enter it as a bug.  I'd also be glad to help on the
solution if there is an executive decision made at some point.



On 10/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
> We might want to file this as a bug so we can track it.
>
> The core devs have been mulling over the state of GFF/GFF3 in
> BioPerl; proper handling of any SearchIO data is certainly included
> in that.  I believe some road forward is to be planned soon (after
> Genome Informatics).
>
> chris
>
> On Oct 5, 2007, at 2:35 PM, Eric Just wrote:
>
> > Hello,
> >
> > I have been playing with the bp_search2gff.pl script (on HEAD of
> > bioperl-live).    There are a couple of issues I was wondering about.
> >
> > One is the ID that gets generated for a match feature when the --match
> > option is set.   The ID is  set to the ID of the query sequence.  This
> > can be problematic if you are representing the query sequence and the
> > blast hit in the same gff file.  When using the resultant gff file for
> > loading into Chado, it also creates a problem if you have more than
> > one hit for a given query sequence, for example if you ran two
> > different analyses that each had a hit for a given query.  Would it be
> > possible to have an option to create a unique ID for match features.
> > One suggestion could be to create an ID based on the ID of the query +
> > the id of the hit + the source
> >
> > As long as two different analyses were loaded as different sources,
> > this would ensure unique IDs for the match features.
> >
> >
> > Also, is there a reason for writing the Target string as
> >
> > Target=Sequence:SOME_ID
> >
> > as opposed to
> >
> > Target=SOME_ID
> >
> >
> > The latter seems a little more in line with the gff3 spec and plays a
> > little nicer with the GMOD tools.
> >
> > Thanks for looking into this.
> >
> > Eric
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


From bix at sendu.me.uk  Sun Oct  7 08:40:44 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sun, 07 Oct 2007 13:40:44 +0100
Subject: [Bioperl-l] Bio::FeatureIO::gff bug?
In-Reply-To: <5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
References: <46F784EB.9050507@sendu.me.uk>	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>	<46F7B9A1.9080206@sendu.me.uk>	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>	<46F8DC34.6020908@sendu.me.uk>	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
Message-ID: <4708D3CC.60909@sendu.me.uk>

Hilmar Lapp wrote:
> On Sep 28, 2007, at 5:34 PM, Chris Fields wrote:
> 
>> The section writing the gff header info in _initialize() checks the  
>> file specifically for '>' prior to output; I think Sendu planned on  
>> changing that to use mode() instead.
> 
> What if we pass in a file handle?

mode() is supposed to work in that instance as well: it sees if the file 
handle is writable.


From er at xs4all.nl  Sun Oct  7 10:13:45 2007
From: er at xs4all.nl (Erik)
Date: Sun, 7 Oct 2007 16:13:45 +0200 (CEST)
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <4708D3CC.60909@sendu.me.uk>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
Message-ID: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>


http://bioperl.org/
http://www.bioperl.org/wiki/Main_Page

seems to be having problems - I only receive an empty
screen...

regards,
Erik






From cjfields at uiuc.edu  Sun Oct  7 17:16:02 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 7 Oct 2007 16:16:02 -0500
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
	<12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
Message-ID: <EBD33439-22B4-44FC-A60C-D3EC653EC363@uiuc.edu>

Should be back up.  Jason was running some wiki updates.

chris

On Oct 7, 2007, at 9:13 AM, Erik wrote:

>
> http://bioperl.org/
> http://www.bioperl.org/wiki/Main_Page
>
> seems to be having problems - I only receive an empty
> screen...
>
> regards,
> Erik




From alan at tll.org.sg  Mon Oct  8 01:02:45 2007
From: alan at tll.org.sg (alan)
Date: Mon, 8 Oct 2007 13:02:45 +0800
Subject: [Bioperl-l] exonerate
In-Reply-To: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
	<73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
Message-ID: <F5563806-FCAE-46C6-8EE3-3C55FCDD906C@tll.org.sg>

Hi Chris,

On 02 Oct 2007, at 11:03 PM, Chris Fields wrote:

> One option is to try running $run->cleanup() after you finish  
> parsing, which gets rid of the tempfiles on each run.
>

I tried this option in the past but it did not change anything.

I found a temporary solution: I am using tcsh and the ulimit for open  
files (descriptors) was set to 256. I changed this limit to 2000 and  
I got my code to run to completion. This imply that I am  
circumventing the real problem of open files. I will continue to look  
at the file closing step in bioperl but the ulimit or limit option  
allows me to get a quick work around for now.

for bash shell (ulimit -n [number])

for tcsh shell (limit descriptors [number])

alan




> chris
>
> On Sep 30, 2007, at 8:53 PM, alan wrote:
>
>> Hi,
>>
>>
>>>> I am calling exonerate.pm within my script while attempting to
>>>> align cDNA  to multiple genomic fragments. After processing about
>>>> 120+ genomic fragments my code crashes with the following error:
>>>>
>>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>>> aborting...
>>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>>
>>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>>> routine yet I get the error message about "too many open files".
>>>> Any suggestions on how I should be closing these files?
>>>>
>>>>
>>>> Extract from my code that runs exonerate is listed below.
>>>>
>>>> foreach my $f(@files) {
>>>>   next unless (-f  "$dir/$f");
>>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>>   my $query_obj = $q_in->next_seq();
>>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>>> format=>"Fasta");
>>>>   my $target_obj = $target_in->next_seq();
>>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>>
>>>>   [code for parsing the data.......]
>>>>
>>>>   $exonerate_io->close; #tried this line out of desperation but it
>>>> did not help :-)
>>>> }
>>>>
>>>> thanks
>>>> alan
>
>



From bix at sendu.me.uk  Mon Oct  8 05:54:15 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Mon, 08 Oct 2007 10:54:15 +0100
Subject: [Bioperl-l] Loading Blast Report in a minimal way
In-Reply-To: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
References: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
Message-ID: <4709FE47.3040103@sendu.me.uk>

zhihuali wrote:
> Hi netters,
> 
> I'm using SearchIO to parse my blast reports. They are extremely 
> huge, and not surprisingly, it's extremely slow and sometimes the 
> system crashed due to memmory problem. As I can handle small reports 
> quickly, it seems like a problem related to the way SearchIO works: 
> it slurps the whole report into the memory and builds millions of 
> objects.
> 
> I've checked old posts and some people used FastHitEventBuilder to 
> build hit objects without any hsp objects. And some people suggested 
> using tabular output of blast. But in my case I need to go to each of
>  the hsps of each hit, parse the alignment, and gather the
> information needed if that hsp fits certain criteria, and then move
> on to the next hsp/or jump over to the next hit/ or exit the
> processing, according to the information I have already got. An ideal
> way would be to read one hsp at a time from the report to the memory.
> Is there some way to modify SearchIO (or build another Search Event)
> to do this?

Use Bio::SearchIO::blast_pull

(ie.
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                             -file =>
't/data/new_blastn.txt');
)

It doesn't yet support all kinds of Blast report, however. Let me know
how you get on.

Cheers,
Sendu.


From bix at sendu.me.uk  Wed Oct 10 10:09:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 15:09:24 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
Message-ID: <470CDD14.4000005@sendu.me.uk>

Once I store a feature like so:

$db = Bio::DB::SeqFeature::Store->new( # mysql );
$db->new_feature(-primary_tag  => 'X',
                  -seq_id       => 'Y',
                  #...
		 -source       => 'Z');

How do I search for it again? I could have sworn that in the past the 
source somehow became one of the feature's attributes so that I could do:

@feats = $db->features(-attributes => {source => 'Z'});

(Or does/did some other feature-related module store source as an 
attribute, and in the past I stored those features in my db?)

The obvious isn't implemented:

@feats = $db->features(-source => 'Z');

Looking at the code I see I can do type and source at the same time:

@feats = $db->features(-type => 'X:Z');

which works, but how do I just search for all Z, regardless of type?


From lstein at cshl.edu  Wed Oct 10 10:20:33 2007
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 10 Oct 2007 10:20:33 -0400
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <470CDD14.4000005@sendu.me.uk>
References: <470CDD14.4000005@sendu.me.uk>
Message-ID: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>

Hi Sendu,

This may be a glaring omission on my part. Try searching for:

 @feats = $db->get_features_by_type(":$source");

Remove the colon in front of $source.

This might not work, but give it a try.

Lincoln

On 10/10/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> Once I store a feature like so:
>
> $db = Bio::DB::SeqFeature::Store->new( # mysql );
> $db->new_feature(-primary_tag  => 'X',
>                   -seq_id       => 'Y',
>                   #...
>                  -source       => 'Z');
>
> How do I search for it again? I could have sworn that in the past the
> source somehow became one of the feature's attributes so that I could do:
>
> @feats = $db->features(-attributes => {source => 'Z'});
>
> (Or does/did some other feature-related module store source as an
> attribute, and in the past I stored those features in my db?)
>
> The obvious isn't implemented:
>
> @feats = $db->features(-source => 'Z');
>
> Looking at the code I see I can do type and source at the same time:
>
> @feats = $db->features(-type => 'X:Z');
>
> which works, but how do I just search for all Z, regardless of type?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


From bix at sendu.me.uk  Wed Oct 10 11:10:45 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 16:10:45 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
References: <470CDD14.4000005@sendu.me.uk>
	<6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
Message-ID: <470CEB75.7050804@sendu.me.uk>

Lincoln Stein wrote:
> Hi Sendu,
> 
> This may be a glaring omission on my part. Try searching for:
> 
>  @feats = $db->get_features_by_type(":$source");
> 
> Remove the colon in front of $source.

It doesn't, unfortunately, colon or not. get_features_by_type is 
implemented using _features(-type => ), just like features(). In any 
case, I'm searching for multiple things at the same time so need to use 
the features() method.


The following patch seems to do the job in my hands, allowing:

@feats = $db->features(-source => 'Z');
to work as expected.

Also, we now have:
@feats = $db->features(-type => 'X', -source => 'Z');
as a nicer (ie. matching the syntax the user used to create the feature 
in the first place) alternative to:
@feats = $db->features(-type => 'X:Y');

Of course, this patch is specific to the mysql implementation. You may 
want to check it over to see if it is sane, see if there is a cleaner 
way to do it, or see if there's a more general way to apply it to all 
implementations.


RCS file: 
/home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.33
diff -r1.33 mysql.pm
724c724,725
<       $iterator
---
 >       $iterator,
 >       $sources
731a733
 >             ['SOURCE','SOURCES']
760c762,785
<
---
 >
 >   if (defined($sources)) {
 >     my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources);
 >     if (defined($types)) {
 >         my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types);
 >         my @final_types;
 >         foreach my $type (@types) {
 >             # *** not sure what to do if user supplies both -source
 >             #     and -type where the type includes a source!
 >             if ($type =~ /:/) {
 >                 push(@final_types, $type);
 >             }
 >             else {
 >                 foreach my $source (@sources) {
 >                     push(@final_types, $type.':'.$source);
 >                 }
 >             }
 >         }
 >         $types = \@final_types;
 >     }
 >     else {
 >         $types = [map { ':'.$_ } @sources];
 >     }
 >   }
939,940c964,971
<       push @matches,"tl.tag=?";
<       push @args,"$primary_tag:$source_tag";
---
 >       if (length($primary_tag)) {
 >         push @matches,"tl.tag=?";
 >         push @args,"$primary_tag:$source_tag";
 >       }
 >       else {
 >         push @matches,"tl.tag LIKE ?";
 >         push @args,"%:$source_tag";
 >       }


From bix at sendu.me.uk  Thu Oct 11 06:40:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 11 Oct 2007 11:40:24 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
Message-ID: <470DFD98.4030603@sendu.me.uk>

Following Chris's changes to SF::Annotated et al., lots of existing user 
code breaks. Also, at least some Bioperl code breaks, notably 
Bio::DB::SeqFeature::Store, which in mysql mode calls 
_get_location_and_bin() which calls $feature->seq_id which ends up 
storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
the database, instead of an actual sequence id (which completely breaks 
searching by seq_id).

I propose its API be changed to be more consistent with 
Bio::SeqFeatureI, eg. instead of:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : a Bio::Annotation::SimpleValue object representing the
            seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

we have:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : string representing the seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

This would apply to seq_id(), name(), type(), source(), phase() and 
frame(). Internally the implementation could store the string value in a 
SimpleValue object.


However, I'm obviously missing something, because I have no idea what 
the justification for returning SimpleValue objects was in the first 
place (what other module needs them?), nor even what the point of 
SimpleValue objects is in the first place.


From ULNJUJERYDIX at spammotel.com  Thu Oct 11 07:32:33 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Thu, 11 Oct 2007 19:32:33 +0800
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>

wow thanks for the replies!
I have gotten the answer from the blast help

Subsequence range can be specified by the ?L parameter. Please refer
to this web document for more information:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node60.html



Other end-user oriented standalone blast documents are at:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/


but will try this method as well to see which works better.

cheers!
kevin

There is a script that comes with the bioperl core distribution,

> bp_split_seq.pl, which does this.  Here's the CVS location:
>
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
> scripts/seq/?cvsroot=bioperl
>
> chris
>



From cjfields at uiuc.edu  Thu Oct 11 09:49:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 08:49:59 -0500
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
	<5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
Message-ID: <F866A1FE-EBC7-4722-A3E6-2F4A10FD0373@uiuc.edu>

Yep, started using this myself for mapping old predicted CDS onto new  
assemblies using BLASTX.  Works very well, particularly since it  
retains the seq position on hits, where using bp_slit_seq would  
require mapping to the correct coordinates.

chris

On Oct 11, 2007, at 6:32 AM, Kevin Lam wrote:

> wow thanks for the replies!
> I have gotten the answer from the blast help
>
> Subsequence range can be specified by the ?L parameter. Please refer
> to this web document for more information:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ 
> blastall_node60.html
>
>
>
> Other end-user oriented standalone blast documents are at:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
>
>
> but will try this method as well to see which works better.
>
> cheers!
> kevin
>
> There is a script that comes with the bioperl core distribution,
>
>> bp_split_seq.pl, which does this.  Here's the CVS location:
>>
>> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
>> scripts/seq/?cvsroot=bioperl
>>
>> chris
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From cjfields at uiuc.edu  Thu Oct 11 10:19:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 09:19:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>


On Oct 11, 2007, at 5:40 AM, Sendu Bala wrote:

> Following Chris's changes to SF::Annotated et al., lots of existing  
> user
> code breaks. Also, at least some Bioperl code breaks, notably
> Bio::DB::SeqFeature::Store, which in mysql mode calls
> _get_location_and_bin() which calls $feature->seq_id which ends up
> storing something like 'Bio::Annotation::SimpleValue=HASH 
> (0x1f435d0)' in
> the database, instead of an actual sequence id (which completely  
> breaks
> searching by seq_id).
>
> I propose its API be changed to be more consistent with
> Bio::SeqFeatureI, eg. instead of:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> we have:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> This would apply to seq_id(), name(), type(), source(), phase() and
> frame(). Internally the implementation could store the string value  
> in a
> SimpleValue object.

Agreed.  It would be easy to change over but we need to also make  
sure FeatureIO fixes are in place.  In reality all FeatureIO methods  
should be changed over to recognize any SeqFeatureI or (if we retain  
it) the stricter TypedSeqFeatureI.  Using only Bio::SF::Annotated  
limits other more lightweight implementations.  I simply haven't had  
time to work on it yet due to $job; if you want to make the necessary  
changes you are more than welcome; the few tests I found I moved into  
SeqFeatAnnotated.t, which likely expects the wrong behavior.

> However, I'm obviously missing something, because I have no idea what
> the justification for returning SimpleValue objects was in the first
> place (what other module needs them?), nor even what the point of
> SimpleValue objects is in the first place.

I believe it was to ensure any data stored or retrieved was strongly  
typed (i.e. scalars in SimpleValue, dbxrefs in DBLink, comments in  
Comment, etc).  Since B::SF::Generic is also AnnotatableI, it can  
store a mix of scalars in methods as well as Bio::Annotation data;  
this class attempts to lump them all together as Bio::Annotation in a  
Collection in a strongly typed, uniform way.  Hilmar's  
Bio::SF::AnnotationAdaptor frankly does a better job of describing  
the reasoning behind this and is more flexible; I use that now for  
typing via feature(), though I just realized it should be changed to  
be a singleton instance per class (oops!).

B::SF::A violated the SeqFeatureI interface from the get-go by  
returning objects.  To trick it's way around the issue it used  
overloading so that calling it in some contexts (print, comparison)  
returned a string or value; removing the overloads unmasked that  
behavior.  To me an object returned (regardless of overloading) is  
still an object and not a scalar, and still violates the interface  
methods where scalars are expected.  I can't fault the authors  
involved completely since the idea was to radically change the way  
SFs/Annotation worked together, but the implementation was never  
completed so I rolled it back and limited typing to B::SF::A until  
something else can be worked out.

Personally I think it's too 'heavy' and other options should be  
explored, such as abstracting out the type checking into a separate  
utility class which FeatureIO can use on any SeqFeatureI (TypeMapper  
does something like this for the primary_tag()).

chris


From jaudall at gmail.com  Thu Oct 11 20:51:50 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 18:51:50 -0600
Subject: [Bioperl-l] Hsp_hit-from
Message-ID: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>

Bioperl -

I'm parsing an XML blast output using SearchIO and the usual fields seem to
work fine.

print $result->query_name . "\t" . $hit->name . "\n";

However, I'm curious as to the 5' position distribution of my hits.  So I'd
like to access this data field <Hsp_query-from> in the xml output file.  I
searched both the mailing lists and the Search docs including
*Bio::Search::Hit::HitI,
*but I can't seem to find an example of someone accessing this data field.
Perhaps, I missed it, but do any of you have any suggestions as to how I
might get at the <Hsp_query-from> for each hit?  Thanks.

Josh


From cjfields at uiuc.edu  Thu Oct 11 22:14:21 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 21:14:21 -0500
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
Message-ID: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>


On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:

> Bioperl -
>
> I'm parsing an XML blast output using SearchIO and the usual fields  
> seem to
> work fine.
>
> print $result->query_name . "\t" . $hit->name . "\n";
>
> However, I'm curious as to the 5' position distribution of my  
> hits.  So I'd
> like to access this data field <Hsp_query-from> in the xml output  
> file.  I
> searched both the mailing lists and the Search docs including
> *Bio::Search::Hit::HitI,
> *but I can't seem to find an example of someone accessing this data  
> field.
> Perhaps, I missed it, but do any of you have any suggestions as to  
> how I
> might get at the <Hsp_query-from> for each hit?  Thanks.
>
> Josh

That tag (as well as related tags) are mapped to start(), end(), and  
strand() in the HSP objects.  To access the relevant data pass  
'query' or 'hit' to the method, so for the query use: $hsp->start 
('query') or $hsp->end('query').

Note: in BioPerl all location starts are less than the end (strand  
determines the orientation for DNA).

chris


From hlapp at gmx.net  Thu Oct 11 23:25:22 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 11 Oct 2007 23:25:22 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>


On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:

> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.

type() and source() should be ontology-typed in a TypedSeqFeatureI  
(and therefore be instances of Bio::Annotation::OntologyTerm, not  
Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't  
understand what the benefit of typing seq_id() any stronger than a  
string would be.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From jaudall at gmail.com  Thu Oct 11 23:34:18 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 20:34:18 -0700
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
	<162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
Message-ID: <52cea20c0710112034k60f14241k8884a07d26939e86@mail.gmail.com>

Thanks!  For some reason I was stuck on the idea that it would be different
with an xml file.  I'm glad it's not ...

On 10/11/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:
>
> > Bioperl -
> >
> > I'm parsing an XML blast output using SearchIO and the usual fields
> > seem to
> > work fine.
> >
> > print $result->query_name . "\t" . $hit->name . "\n";
> >
> > However, I'm curious as to the 5' position distribution of my
> > hits.  So I'd
> > like to access this data field <Hsp_query-from> in the xml output
> > file.  I
> > searched both the mailing lists and the Search docs including
> > *Bio::Search::Hit::HitI,
> > *but I can't seem to find an example of someone accessing this data
> > field.
> > Perhaps, I missed it, but do any of you have any suggestions as to
> > how I
> > might get at the <Hsp_query-from> for each hit?  Thanks.
> >
> > Josh
>
> That tag (as well as related tags) are mapped to start(), end(), and
> strand() in the HSP objects.  To access the relevant data pass
> 'query' or 'hit' to the method, so for the query use: $hsp->start
> ('query') or $hsp->end('query').
>
> Note: in BioPerl all location starts are less than the end (strand
> determines the orientation for DNA).
>
> chris
>


From pellet at cervi-lyon.inserm.fr  Fri Oct 12 04:48:06 2007
From: pellet at cervi-lyon.inserm.fr (Johann PELLET)
Date: Fri, 12 Oct 2007 10:48:06 +0200
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
Message-ID: <470F34C6.9050800@cervi-lyon.inserm.fr>

Hi,
I have two questions:
First, I have problems for example with this genbank entry: NC_008210. 
Indeed, for one CDS, the location is : 
join(161990..162784,complement(88222..88806),complement(86666..87448))

When I parse a genbank file with this entry.

my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
                               -file => $input_file);

while( my $seq = $seq_in->next_seq() ) {
    my @features = $seq->get_SeqFeatures();
    for ( my $i =0; $i < scalar @features; $i++ ){
        my $feat = @features[$i];
         if ( $feat->primary_tag eq 'CDS' ){


             my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
             my $seq_CDS=$seq_CDS_obj->seq;


I have this error:
Can't call method "isa" without a package or object reference at ....

Secondly, When location is like: 
join(complement(AY421753.1:1..6),complement(3813..5699)) I know that we 
must use spliced_seq with the argument db, but it's not working.
      my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
How can we valid a Bio::DB::RandomAccessI?

Thanks

-- 
Johann Pellet
phone (work): +33(0)4 37282352
E-mail:    pellet at cervi-lyon.inserm.fr
Centre d'Etudes et de Recherche en Virologie et Immunologie
INSERM U503
21, Avenue Tony Garnier
69365 Lyon cedex 07 France 



From bix at sendu.me.uk  Fri Oct 12 09:04:25 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 14:04:25 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
Message-ID: <470F70D9.6030108@sendu.me.uk>

Chris Fields wrote:
> B::SF::A violated the SeqFeatureI interface from the get-go by returning 
> objects.

On that note, the other major change I'd propose is to make B::SF::A 
inherit from B::SeqFeatureI. I really need this for RangeI methods.

Or, heck, since it's such a mess, do we just want to drop Annotated 
entirely and recommend using AnnotationAdaptor with Generic? What does 
Annotated bring to the table?

(Since its one of the modules added in 1.5 I think it's fair to drop it 
from the 1.6 release: stuff that doesn't work can and should be moved 
out of the path of stable branches.)


From hlapp at gmx.net  Fri Oct 12 10:46:19 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 10:46:19 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>


On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

My recollection may be wrong since it's been quite a while, but I  
believe one of the main motivations was to reflect the ontology- 
typing of feature type and other annotation that GFF3 requires.

The motivation of AnnotationAdaptor was primarily to provide a view  
onto a SeqFeatureI that makes tag/value annotation transparently  
appear as B:AnnotatableI and B:AnnotationCollectionI compliant, mixed  
in with the annotation collection that B:S:Generic may hold already.

Although sometimes confused, these are not the same motivations.  
AnnotationAdaptor provides a view - you use it when that's the view  
you need on a SeqFeatureI object you have in hand. For example,  
bioperl-db uses it so it doesn't have to bother about how to de/ 
serialize tag/value pairs, when it knows how to de/serialize  
annotation collections already from sequence objects.  
AnnotationAdaptor doesn't care whether the primary_tag, or any other  
tag, is from an ontology.

>
> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
>> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

I agree with that unless someone steps up and makes it work.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From cjfields at uiuc.edu  Fri Oct 12 10:49:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 09:49:25 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>


On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> B::SF::A violated the SeqFeatureI interface from the get-go by  
>> returning
>> objects.
>
> On that note, the other major change I'd propose is to make B::SF::A
> inherit from B::SeqFeatureI. I really need this for RangeI methods.

It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,  
which itself is-a SeqFeatureI.  We might want to run the tests on  
that but a quick inheritance tree check on my ends seems to confirm  
that.  If the Range methods don't work there may be an issue within  
B::SF::A (which wouldn't surprise me).

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

I agree about getting rid of B::SF::A, but if we do we will need a  
reasonable replacement for SFs in FeatureIO, as it relies directly on  
B::SF::A.  As for AnnotationAdaptor, it runs a simple type check on  
the data within a SF but I don't think it checks the primary_tag  
against the current SO or other ontologies for GFF3.

My inclination is to hold back FeatureIO from 1.6 and retool it to  
use any SeqFeatureI, then find a way to optionally type a  
SeqFeatureI.  This is so we don't have to completely retool every  
Bio::Tools* class.  For instance:

# a SF::Generic with a few type-related methods added to SeqFeatureI
$sf->type(); # undef, not checked
$sf->ontology_term; # undef, not checked

# call proper methods to type check
# or use a utility class dedicated to this function

$sf->validate_sf_type(); # or...
$util->validate_sf_type($sf);

$sf->type(); # returns string
$sf->ontology_term; # returns Bio::Ontology::TermI

My feeling is that FeatureIO needs the ability to validate SFs and  
maybe have it turned on by default, but it should be optional.  The  
TermI would be a Bio::Annotation::OntologyTerm if we insist on using  
AnnotationAdaptor for richly typed SFs, which may not be necessary  
(Hilmar?).  As not all SeqFeatureI are also AnnotatableI that should  
probably be optional anyway.

> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

Agreed.  If anyone wants to use experimental stuff they can always  
use bioperl-live.

chris


From cjfields at uiuc.edu  Fri Oct 12 11:02:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 10:02:03 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
Message-ID: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>


On Oct 12, 2007, at 9:46 AM, Hilmar Lapp wrote:

>
> On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:
>
>> Or, heck, since it's such a mess, do we just want to drop Annotated
>> entirely and recommend using AnnotationAdaptor with Generic? What  
>> does
>> Annotated bring to the table?
>
> My recollection may be wrong since it's been quite a while, but I  
> believe one of the main motivations was to reflect the ontology- 
> typing of feature type and other annotation that GFF3 requires.
>
> The motivation of AnnotationAdaptor was primarily to provide a view  
> onto a SeqFeatureI that makes tag/value annotation transparently  
> appear as B:AnnotatableI and B:AnnotationCollectionI compliant,  
> mixed in with the annotation collection that B:S:Generic may hold  
> already.
>
> Although sometimes confused, these are not the same motivations.  
> AnnotationAdaptor provides a view - you use it when that's the view  
> you need on a SeqFeatureI object you have in hand. For example,  
> bioperl-db uses it so it doesn't have to bother about how to de/ 
> serialize tag/value pairs, when it knows how to de/serialize  
> annotation collections already from sequence objects.  
> AnnotationAdaptor doesn't care whether the primary_tag, or any  
> other tag, is from an ontology.

Ah, forgot it returns a Collection.  It doesn't modify the SF I assume?

>> (Since its one of the modules added in 1.5 I think it's fair to  
>> drop it
>>> from the 1.6 release: stuff that doesn't work can and should be  
>>> moved
>> out of the path of stable branches.)
>
> I agree with that unless someone steps up and makes it work.
>
> 	-hilmar

Making it work may be more trouble than it's worth.  Sincerest  
apologies to the authors of the module but we should probably  
deprecate it in favor of something more flexible when we can.  It's  
obvious anything reliant on it would also have to be dropped.

The GMOD meeting is a few weeks away, where I assume some things will  
be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth  
saving; maybe retooling it would be in our best interests, but it  
needs a decent roadmap to move forward.

chris


From bix at sendu.me.uk  Fri Oct 12 11:06:30 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 16:06:30 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
Message-ID: <470F8D76.8080101@sendu.me.uk>

Chris Fields wrote:
> 
> On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:
> 
>> Chris Fields wrote:
>>> B::SF::A violated the SeqFeatureI interface from the get-go by
>>> returning objects.
>> 
>> On that note, the other major change I'd propose is to make
>> B::SF::A inherit from B::SeqFeatureI. I really need this for RangeI
>> methods.
> 
> It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,
> which itself is-a SeqFeatureI.  We might want to run the tests on
> that but a quick inheritance tree check on my ends seems to confirm
> that.  If the Range methods don't work there may be an issue within
> B::SF::A (which wouldn't surprise me).

Sorry, I was looking at the docs on the website and for whatever reason
its failing to display all the inherited modules. If RangeI methods
don't work I'll post back, but for now assume they do (I'm not in a
position to test right now).


> My inclination is [snip]

I still don't really understand what the deal is with all these modules,
so I'll leave it your hands to make further recommendations and take action.

 From my limited understanding what you said seems reasonable, except for
excluding FeatureIO completely. At least, I'd really like to see it in
1.6; it would be a shame to miss it just because of Annotated. Worst
case, isn't Generic 'good enough' as a replacement?


> The GMOD meeting is a few weeks away, where I assume some things will
> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
> saving; maybe retooling it would be in our best interests, but it
> needs a decent roadmap to move forward.

Agreed. I guess we'll wait for the results of that meeting? Is anyone 
going planning to discuss this issue?


From cjfields at uiuc.edu  Fri Oct 12 12:15:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 11:15:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F8D76.8080101@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
	<470F8D76.8080101@sendu.me.uk>
Message-ID: <EAD0DE5B-3E55-453B-A57B-C478F2BB9AE4@uiuc.edu>


On Oct 12, 2007, at 10:06 AM, Sendu Bala wrote:
...

>
> I still don't really understand what the deal is with all these  
> modules,
> so I'll leave it your hands to make further recommendations and  
> take action.
>
> From my limited understanding what you said seems reasonable,  
> except for
> excluding FeatureIO completely. At least, I'd really like to see it in
> 1.6; it would be a shame to miss it just because of Annotated. Worst
> case, isn't Generic 'good enough' as a replacement?

It probably could work, but type checking, ontology_term(), and SF  
data validation wouldn't be implemented immediately as it would  
require additional code.  I'll try looking into it this weekend to  
see what needs to be done and work from there.

>> The GMOD meeting is a few weeks away, where I assume some things will
>> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
>> saving; maybe retooling it would be in our best interests, but it
>> needs a decent roadmap to move forward.
>
> Agreed. I guess we'll wait for the results of that meeting? Is  
> anyone going planning to discuss this issue?

Jason is going to be there and intends to bring it up as it affects  
GBrowse/GMOD/Chado.

chris



From jason at bioperl.org  Fri Oct 12 12:18:15 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 12 Oct 2007 09:18:15 -0700
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
In-Reply-To: <470F34C6.9050800@cervi-lyon.inserm.fr>
References: <470F34C6.9050800@cervi-lyon.inserm.fr>
Message-ID: <90E849A1-C5AB-40B3-9AB1-2DC79EBF5C4C@bioperl.org>

1.

Always 'use strict;' in your code - you'll see the bug more clearly  
that you should use $feat not $cds in the if stmt.


2.
You should pass in an actual Bio::DB::GenBank object to the -db  
argument.

my $db = Bio::DB::GenBank->new;
my $cds = $seq->spliced_seq(-db => $db);

-jason
On Oct 12, 2007, at 1:48 AM, Johann PELLET wrote:

> Hi,
> I have two questions:
> First, I have problems for example with this genbank entry: NC_008210.
> Indeed, for one CDS, the location is :
> join(161990..162784,complement(88222..88806),complement(86666..87448))
>
> When I parse a genbank file with this entry.
>
> my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
>                                -file => $input_file);
>
> while( my $seq = $seq_in->next_seq() ) {
>     my @features = $seq->get_SeqFeatures();
>     for ( my $i =0; $i < scalar @features; $i++ ){
>         my $feat = @features[$i];
>          if ( $feat->primary_tag eq 'CDS' ){
>
>
>              my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
>              my $seq_CDS=$seq_CDS_obj->seq;
>


>
> I have this error:
> Can't call method "isa" without a package or object reference at ....
>
> Secondly, When location is like:
> join(complement(AY421753.1:1..6),complement(3813..5699)) I know  
> that we
> must use spliced_seq with the argument db, but it's not working.
>       my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
> How can we valid a Bio::DB::RandomAccessI?
>
> Thanks
>
> -- 
> Johann Pellet
> phone (work): +33(0)4 37282352
> E-mail:    pellet at cervi-lyon.inserm.fr
> Centre d'Etudes et de Recherche en Virologie et Immunologie
> INSERM U503
> 21, Avenue Tony Garnier
> 69365 Lyon cedex 07 France
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From hlapp at gmx.net  Fri Oct 12 13:22:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 13:22:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
	<D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
Message-ID: <9762F1F9-68C8-42E2-8488-6656C76D36B8@gmx.net>


On Oct 12, 2007, at 11:02 AM, Chris Fields wrote:

>> Although sometimes confused, these are not the same motivations.  
>> AnnotationAdaptor provides a view - you use it when that's the  
>> view you need on a SeqFeatureI object you have in hand. For  
>> example, bioperl-db uses it so it doesn't have to bother about how  
>> to de/serialize tag/value pairs, when it knows how to de/serialize  
>> annotation collections already from sequence objects.  
>> AnnotationAdaptor doesn't care whether the primary_tag, or any  
>> other tag, is from an ontology.
>
> Ah, forgot it returns a Collection.  It doesn't modify the SF I  
> assume?

No, not if you only use getters. It does support adding annotation  
too, though.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From smwilson at hpc.unm.edu  Fri Oct 12 13:45:41 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Fri, 12 Oct 2007 11:45:41 -0600
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
	against latest Homo_sapiens.ags file
Message-ID: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>

Hi,

I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
memory.  I get a simple "Out of memory" output even with the  
following code:

#!/usr/bin/perl
use strict;
use Bio::ASN1::EntrezGene;
   my $parser = Bio::ASN1::EntrezGene->new('file' =>  
"Homo_sapiens.xml");
   while(my $result = $parser->next_seq)
   {
   }



Thanks.
Susan





From arareko at campus.iztacala.unam.mx  Fri Oct 12 14:10:44 2007
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 12 Oct 2007 14:10:44 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FB8A4.2050601@campus.iztacala.unam.mx>

Hi Susan,

Bio::ASN1::EntrezGene is not part of the BioPerl distribution, even 
though it shares the same namespace and is used by BP. Maybe you'd want 
to contact Mingyi Liu who is the author of the module. for more info 
take a look here:

http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene/

Regards,
Mauricio.

Susan Wilson wrote:
> Hi,
> 
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
> 
> 
> 
> Thanks.
> Susan
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM



From Kevin.M.Brown at asu.edu  Fri Oct 12 14:19:48 2007
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 12 Oct 2007 11:19:48 -0700
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>

> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> machine with 256GB of memory.  I get a simple "Out of memory" 
> output even with the following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }

I think most systems have a per process memory limit (either hardcoded
in the OS or configured depending on the OS) and IIRC most of the IO
handlers for BioPerl load entire file contents into memory to process
them.  Some of the IO parsers have been changed recently (a new one
added for blast) so that it only pulls into memory as much as it needs
to process the next result rather than the whole file in one shebang.



From stefan.kirov at bms.com  Fri Oct 12 14:34:49 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:34:49 -0400
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <470FBE49.7010703@bms.com>

Kevin Brown wrote:
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
>> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
>> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
>> machine with 256GB of memory.  I get a simple "Out of memory" 
>> output even with the following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>     
>
> I think most systems have a per process memory limit (either hardcoded
> in the OS or configured depending on the OS) and IIRC most of the IO
> handlers for BioPerl load entire file contents into memory to process
> them.  Some of the IO parsers have been changed recently (a new one
> added for blast) so that it only pulls into memory as much as it needs
> to process the next result rather than the whole file in one shebang.
>   
The file is approx. 6GB, so on a 256GB machine this is not going to
create any problem. I think this might be deep not well controlled
recursion problem.
Stefan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From mingyi.liu at gpc-biotech.com  Fri Oct 12 15:06:25 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 15:06:25 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <470FC5B1.3090606@gpc-biotech.com>

BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi


From j_martin at lbl.gov  Fri Oct 12 14:58:41 2007
From: j_martin at lbl.gov (Joel Martin)
Date: Fri, 12 Oct 2007 11:58:41 -0700
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FBE49.7010703@bms.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
	<470FBE49.7010703@bms.com>
Message-ID: <20071012185841.GE13838@eniac.jgi-psf.org>

Hello,
    Just a suggestion, is /usr/bin/perl a 64 bit perl?
Even on our sun machines with 72+ GB memory, for some reason they're
distributed with a 32 bit perl which can handle large files but would
probably have out of memory errrors if trying to read one into memory.

% file /usr/bin/perl 
/usr/bin/perl:  ELF 32-bit MSB executable SPARC Version 1, dynamically
linked, stripped

Joel

On Fri, Oct 12, 2007 at 02:34:49PM -0400, Stefan Kirov wrote:
> Kevin Brown wrote:
> >> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> >> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> >> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> >> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> >> machine with 256GB of memory.  I get a simple "Out of memory" 
> >> output even with the following code:
> >>
> >> #!/usr/bin/perl
> >> use strict;
> >> use Bio::ASN1::EntrezGene;
> >>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> >> "Homo_sapiens.xml");
> >>    while(my $result = $parser->next_seq)
> >>    {
> >>    }
> >>     
> >
> > I think most systems have a per process memory limit (either hardcoded
> > in the OS or configured depending on the OS) and IIRC most of the IO
> > handlers for BioPerl load entire file contents into memory to process
> > them.  Some of the IO parsers have been changed recently (a new one
> > added for blast) so that it only pulls into memory as much as it needs
> > to process the next result rather than the whole file in one shebang.
> >   
> The file is approx. 6GB, so on a 256GB machine this is not going to
> create any problem. I think this might be deep not well controlled
> recursion problem.
> Stefan
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >   
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From stefan.kirov at bms.com  Fri Oct 12 14:20:38 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:20:38 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FBAF6.1050509@bms.com>

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   
Susan,
Are you running the latest version of Bio::ASN1::EntrezGene? You may
have a better chance of getting a fast (and useful) answer if you
contact Mingyi Liu (see on CPAN) directly- the module is not part of
Bioperl. Just to mention- I have also seen similar problems and there
seems to be particular problematic records. I think NCBI made some
changes/additions to their format (might have to do something with the
number/structure of contigs). I will have to run my pipeline soon again
and if I run into the same problem I will probably create bug report for
Mingyi. I hope you do it before me- it is boring and long process.
Stefan



From mingyi.liu at gpc-biotech.com  Fri Oct 12 14:50:08 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 14:50:08 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FC1E0.4070708@gpc-biotech.com>

Hi, Susan,

Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, it's better to directly contact me.  I actually deleted a few messages of this discussion before one caught my eye. Nowadays I'm working in some other areas and not tracking bioperl mailing list closely, a direct email to me would usually work out better.

As for the problem you mentioned, there could be two reasons: 1. It 
seems that you converted the file to XML file instead of ASN file. My 
parser is designed for ASN file, so please use gene2xml to convert the 
downloaded file to ASN file instead of XML file.  It is likely the wrong 
syntax of the file caused my parser to attempt to read the entire file 
as a string (because it couldn't find the start/end).  However, there's 
another minor possibility (which you might have taken care of already): 
2. Perl 5.8 added 64 bit support, but I don't know if you have perl 5.8 
64 bit installed on your system to support the 256 GB system memory you 
have?  If not, your >5 GB file is over the 4 GB 32 bit Perl limit.

Let me know if my suggestions work out for you.

Best,

Mingyi

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   



From gyang at plantbio.uga.edu  Fri Oct 12 16:52:06 2007
From: gyang at plantbio.uga.edu (Guojun Yang)
Date: Fri, 12 Oct 2007 16:52:06 -0400
Subject: [Bioperl-l] hide XML display on web
In-Reply-To: 41A08079-6EEC-4B62-8104-C41E70C03083@uiuc.edu
Message-ID: <20071012205206.9105fd09@dogwood.plantbio.uga.edu>

Hi, All,  
I have a cgi script that uses remoteblast (xml output). Every time, before and after the blast is finished, a lot of information is displayed on the client's screen, it's a nuisance but I am wondering if anyone knows how to rid of these. See below for examples:  
   
Thanks  
Guojun Yang  
_______________________example_____________________  
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>NCBI Blast:</title>
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
<!--[if lte IE 6]>
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
<![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="js/results.js"></script>
</head>

<body id="type-a" class="noToggleCheck" >
<div id="wrap">
   <div id="header">
  <div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span class="desc"> Basic Local Alignment Search Tool</span>
  </div>
  <div id="search">
  <div><script language="JavaScript" type="text/javascript"><!--
    var myncbi_xo = 0;
    var myncbi_x = MyNCBI_find();
    var myncbi_cu = unescape('http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3F');
    function MyNCBI_find()
    {
        var cs = document.cookie.split('; ');
        for(var i = 0; i < cs.length; i++) {
            // a name/value pair (a crumb) is separated by an equal sign
            var c = cs[i].split('=');
            if(c[0] == 'WebCubbyUser') { return c[1]; }
        }
        return '';
    }
.........


From hlapp at gmx.net  Sat Oct 13 17:49:49 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 13 Oct 2007 17:49:49 -0400
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <F2EFD76D-AA02-4FF7-8CAA-86AAC58E2D2E@gmx.net>


On Oct 12, 2007, at 2:19 PM, Kevin Brown wrote:

> IIRC most of the IO handlers for BioPerl load entire file contents  
> into memory to process them

As was determined already this most likely isn't the issue here, but  
I'm still confused by your statement. Most BioPerl Bio::SeqIO,  
Bio::ClusterIO, and Bio::OntologyIO parsers read an input file line  
by line, or at least by chunk.

Did you possibly mean something else?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From mingyi.liu at gpc-biotech.com  Sat Oct 13 23:28:09 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Sat, 13 Oct 2007 23:28:09 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <47118CC9.8090807@gpc-biotech.com>

Hi, Susan,

Let us know how my suggestions worked for you.  I replied to both you 
and the bioperl mailing list last Friday in the hope that my answer 
could be helpful for the list discussion, but it seems that the mailing 
list server had serious problems and dropped both of my emails.  I'm 
therefore replying again and combined the content of my 2 emails 
together below. Hopefully the email gets sent out to the mailing list.  
If not, would one of you please forward it out?  Thanks.

Mingyi Liu wrote:
> Hi, Susan,
>
> Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, 
> it's better to directly contact me.  I actually deleted a few messages 
> of this discussion before one caught my eye. Nowadays I'm working in 
> some other areas and not tracking bioperl mailing list closely, a 
> direct email to me would usually work out better.
>
> As for the problem you mentioned, there could be two reasons: 1. It 
> seems that you converted the file to XML file instead of ASN file. My 
> parser is designed for ASN file, so please use gene2xml to convert the 
> downloaded file to ASN file instead of XML file.  It is likely the 
> wrong syntax of the file caused my parser to attempt to read the 
> entire file as a string (because it couldn't find the start/end).  
> However, there's another minor possibility (which you might have taken 
> care of already): 2. Perl 5.8 added 64 bit support, but I don't know 
> if you have perl 5.8 64 bit installed on your system to support the 
> 256 GB system memory you have?  If not, your >5 GB file is over the 4 
> GB 32 bit Perl limit.
>
> Let me know if my suggestions work out for you.
>
> Best,
>
> Mingyi
>
BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped 
binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus 
SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi

> Susan Wilson wrote:
>> Hi,
>>
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
>> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
>> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB 
>> of  memory.  I get a simple "Out of memory" output even with the  
>> following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>
>>
>>
>> Thanks.
>> Susan
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>   
>
>



From smwilson at hpc.unm.edu  Mon Oct 15 11:08:55 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 15 Oct 2007 09:08:55 -0600
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC5B1.3090606@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
	<470FC5B1.3090606@gpc-biotech.com>
Message-ID: <72C50125-E169-448C-8F25-AB13A8AD308D@hpc.unm.edu>

Mingyi,

Thank you very much for your advice.  The text ASN file 1/4 the size  
of the (evil, evil) XML file and parsing it ran just fine.  We are  
still pursuing a 64-bit perl on our 256GB server and I will let you  
know how it works.

Thanks.
Susan



On Oct 12, 2007, at 1:06 PM, Mingyi Liu wrote:

> BTW, here's the syntax in one of my messages last year about how to  
> convert the compressed binary ASN format NCBI provides to the text  
> ASN format my module (or Stefan's SeqIO::entrezgene) expects (the - 
> x switch does the trick, overwriting the default option to produce  
> XML output):
>
> my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i  
> Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the  
> gzipped binary file directly downloaded from NCBI
>
> Same syntax should be used when you're using SeqIO (thus  
> SeqIO::entrezgene).
>
> BTW, text ASN is both smaller and faster to parse than XML format.
>
> Best,
>
> Mingyi



From wgallin at ualberta.ca  Mon Oct 15 18:25:14 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 15 Oct 2007 16:25:14 -0600
Subject: [Bioperl-l] Capturing Joined Sequence from two records
Message-ID: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>

I have encountered a case of a protein sequence record for which the  
coding sequence is a join with ranges from two nucleotide sequence  
records:

gi # is 7648673

Relevant annotation is:

   CDS             1..630
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"


Is there any way using Bio::Seq objects to seamlessly get the CDS  
nucleic acid sequence, or do I need to just treat it as an oddity and  
cobble together something manually?

Warren Gallin


From esnyder at vbi.vt.edu  Mon Oct 15 16:38:06 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 16:38:06 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713CFAE.7020007@vbi.vt.edu>

Hello Again,

I think I've discovered the problem.  Apparently I've got an old version 
of BioPerl which expected an array of arguments rather than a named 
list.  When I cut-and-pasted the new code for translate() into my 
distribution, the problem went away.

So, the next question is: how can I be sure that I have the most 
up-to-date distribution available (or at least the one that matches the 
BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within 
the last year but I don't know where it actually came from.

Thanks,
eesnyder

-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"




From jason at bioperl.org  Mon Oct 15 18:54:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 15 Oct 2007 15:54:38 -0700
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
Message-ID: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>

pass in a db handle to spliced_seq. There was a question about this  
on the list a few days ago.
http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html

  - does anyone want to add this solution in more example to FAQ?

-jason

On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:

> I have encountered a case of a protein sequence record for which the
> coding sequence is a join with ranges from two nucleotide sequence
> records:
>
> gi # is 7648673
>
> Relevant annotation is:
>
>    CDS             1..630
>                       /gene="KCND2"
>                       /coded_by="join
> (AF166007.1:430..1544,AF166008.1:345..507,
>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>                        
> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>
>
> Is there any way using Bio::Seq objects to seamlessly get the CDS
> nucleic acid sequence, or do I need to just treat it as an oddity and
> cobble together something manually?
>
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org

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From torsten.seemann at infotech.monash.edu.au  Mon Oct 15 20:49:16 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Tue, 16 Oct 2007 10:49:16 +1000
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <a79f6a4b0710151749o240a5e72j697a1cff6bf39baf@mail.gmail.com>

>  pass in a db handle to spliced_seq. There was a question about this on the
> list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?

Done.

http://www.bioperl.org/wiki/FAQ#How_do_I_get_the_complete_spliced_sequence_when_the_coordinates_refer_to_Genbank_identifiers.3F

If anyone spots any errors or wants to improve it, please do so.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From cjfields at uiuc.edu  Mon Oct 15 21:02:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:02:25 -0500
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
In-Reply-To: <4713CFAE.7020007@vbi.vt.edu>
References: <4713CFAE.7020007@vbi.vt.edu>
Message-ID: <67EBC789-C27F-4918-941C-46E62ACFE934@uiuc.edu>

http://www.bioperl.org/wiki/ 
FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F

If you installed BioPerl via CPAN you more than likely have 1.4.  The  
most recent dev release is 1.5.2.

chris

On Oct 15, 2007, at 3:38 PM, Eric E. Snyder wrote:

> Hello Again,
>
> I think I've discovered the problem.  Apparently I've got an old  
> version
> of BioPerl which expected an array of arguments rather than a named
> list.  When I cut-and-pasted the new code for translate() into my
> distribution, the problem went away.
>
> So, the next question is: how can I be sure that I have the most
> up-to-date distribution available (or at least the one that matches  
> the
> BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within
> the last year but I don't know where it actually came from.
>
> Thanks,
> eesnyder
>
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0447
> USA
>
> Office:    (540) 231-5428
> Mobile:    (540) 230-5225
> Fax:    (540) 231-2606
> Email:    eesnyder at vbi.vt.edu
> JDAM:    N 37 12'01.6", W 80 24'26.9"
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Oct 15 21:39:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:39:37 -0500
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>

Would spliced_seq() work with a protein sequence this way?  The  
location string is in a tag 'coded_by', which would require a little  
more work to get the sequence.

chris

On Oct 15, 2007, at 5:54 PM, Jason Stajich wrote:

> pass in a db handle to spliced_seq. There was a question about this  
> on the list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?
>
> -jason
>
> On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:
>
>> I have encountered a case of a protein sequence record for which the
>> coding sequence is a join with ranges from two nucleotide sequence
>> records:
>>
>> gi # is 7648673
>>
>> Relevant annotation is:
>>
>>    CDS             1..630
>>                       /gene="KCND2"
>>                       /coded_by="join
>> (AF166007.1:430..1544,AF166008.1:345..507,
>>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>>                        
>> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>>
>>
>> Is there any way using Bio::Seq objects to seamlessly get the CDS
>> nucleic acid sequence, or do I need to just treat it as an oddity and
>> cobble together something manually?
>>
>> Warren Gallin
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From Russell.Smithies at agresearch.co.nz  Mon Oct 15 23:51:40 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 16 Oct 2007 16:51:40 +1300
Subject: [Bioperl-l] Parsing EMBL records
In-Reply-To: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca><EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
	<50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05EFC097@imail.agresearch.co.nz>

I've got some output from "newcpgreport" that looks like embl format but
I'm having trouble parsing it.
One of the reasons might be because of this warning but I'm not sure.
	-------------------- WARNING ---------------------
	MSG: Got a sequence with no letters in it cannot guess alphabet
[]
	---------------------------------------------------

I need to get it into gff or tabbed format and don't want to have to
resort to Perl regexes to do it.
Has anyone got some example code for parsing embl or swiss output I
could borrow?

The "newcpgreport " output looks like this:
-----------------------------------------------------
ID   BTA28  46084206 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       181953..182223
FT                    /size=271
FT                    /Sum C+G=162
FT                    /Percent CG=59.78
FT                    /ObsExp=0.75
FT   CpG island       222609..223040
FT                    /size=432
FT                    /Sum C+G=290
FT                    /Percent CG=67.13
FT                    /ObsExp=0.97
FT   CpG island       288537..288741
FT                    /size=205
FT                    /Sum C+G=112
FT                    /Percent CG=54.63
FT                    /ObsExp=0.85 
------------------------------------------------------


Any help greatly appreciated  :-)

Russell Smithies

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From esnyder at vbi.vt.edu  Mon Oct 15 14:50:54 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 14:50:54 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713B68E.2040804@vbi.vt.edu>

Hello,

I am having trouble with translate() when supplying parameters such as 
-frame, -codontable_id, etc.  I am working straight out of the tutorial 
with a very simple program-- which has me stumped!

use Bio::SeqIO;
foreach my $file ( @ARGV ){
     my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
                                     -format =>  "fasta" );
     my $seq_obj = $seqio_obj->next_seq;

     print "loaded one sequence:\n\tdisplay_id\t" .
	   $seq_obj->display_id() . "\n" .
     	   "\tdescription\t" . $seq_obj->description() . "\n";

     foreach my $frame ( 0 .. 2){
         $prot_obj = $seq_obj->translate( '-frame' => $frame );
         print "translation = " . $prot_obj->seq . "\n";
     }
}

Everything works as expected until calling translate.  The output I get 
is the translation of my FASTA sequence (in frame zero, repeated three 
times) in which every "stop" is replaced with "-frame" (!!).  However, 
with no parameters, translate works as advertised.

This is getting me down because by using the full complement of 
translate options, including specifying frame, genetic code, alternative 
start codons, etc., BioPerl will save me a huge amount of time... but 
only if I can figure out how to use it properly!

Any assistance would be greatly appreciated!!!

Sincerely,
eesnyder


-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"



From bosborne11 at verizon.net  Tue Oct 16 08:57:46 2007
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 16 Oct 2007 08:57:46 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
 parameters
In-Reply-To: <4713B68E.2040804@vbi.vt.edu>
Message-ID: <C33A2D8A.FF00%bosborne11@verizon.net>

Eric,

I took your code, unmodified, and ran it using a file in the distribution.
The output looks OK, different frames are used and I don't see "-frame" in
the output sequence (see below). This is using the latest bioperl-live -
what version Bioperl are you using?

Brian O.


269 ~/bioperl-live>./test.pl t/data/HUMBETGLOA.fa
loaded one sequence:
        display_id      HUMBETGLOA
        description     Human haplotype C4 beta-globin gene, complete cds.
translation = 
TSYLTPLITPLIVTLWVVSDFLFICIFDCIKRSLVFYLLFPKT**VTNAQSTLICIYSIFRHNLLACMSKLRKTTT
NECIYMYMYVCTYTHIYIYIFFLFLPEGFNPNKEKICLELR*SFHPFCPVSILHILETQEEIHLHIPKLNYGRQNS
STFSASTSYLCNKKIGKTIFNMLTKL*FQILRKYTCKGGCF**QFVLMVWGQEIYLRGRAEGLKSNS*ASARRAKD
RYGCHHLDLTLWSHTLGLANLLPGAGRAGARAGHKSQGRAIYCLHLLLTQLCSLATSNRHHGASDS*GEVCRYCPV
GQGERG*SWW*GPGQVGIKVTRQV*GDQ*KLGMWRQRRLLGF**ALTLSAYWSIFPPLGCWWSTLGPRGSLSPLGI
CPLLMLLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWILRTSG*VYGTLDVFFPLLFYG*VH
VIGRG*VTGYSLEWETDE*LHQCGSLRIVLVSFICCS*QLFSFV*FLLSFFFFSAIFTIILNALTLCITKGNISEI
H*VT*KKTLHSLPSTLLFGIYVCLFAYS*SPYFIFFYF*LIHNHYTYLWVKV*CFNMCTHIDQIRVILHL*F*KML
SSFNILFCLSYF*YFP*SLSFRAIMIQCIMPLCTILKNNSDNFWVKAIAISLHINISAYKL*LM*EVSYC**QLQS
SYHSAFILWLG*GWIILSPS*ALLLIMFIPLIFLPQLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHK
YH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHCNDVFKLFLNILLKRECGRSVHLKHKEMKS
*FKPWENTLYLKLHERR*GCKQLMHIGNSPDAYALFIPQKRIQVEA*FGG*SFAMLYFTLLIVLAVLMNVFSLPIC
LSCISQP*LHSVLLLRDTTFPLKCSFHVLRRDGFSSPGHSALVVSVVL*RST*RRKNRGHGLTVL*ALLPCLPHSQ
*PGICSASLPELS
translation = 
PPI*HH*LPH**SHFGL*VTFYLFVFLTALRGL*FFTSCFPKPNK*LMHRAH*FVFILFLDIIY*HA*AN*EKQQQ
MNAYICICMCVHIHIYIYIYFFFSYQKVLIQIRRRYA*N*GRVFIHSVL*VFCIFWRRRKRSIYISQS*IMVDKTL
PLLVHQLLICVIRKLGKRSSICLPSCDSKYYVNTLAKEDVFSSNLY*WYGAKRYILEGGLRV*SPTPKPVPEEPRT
GTAVIT*TSPCGATP*GWPIYSQEQGGQEPGLGIKVRAEPSIAYICF*HNCVH*QPQTDTMVHLTPEEKSAVTALW
GKVNVDEVGGEALGRLVSRLQDRFKETNRNWACGDREDSWVSDRH*LSLPIGLFSHP*AAGGLPLDPEVL*VLWGS
VHS*CCYGQP*GEGSWQESARCL**WPGSPGQPQGHLCHTE*AAL*QAARGS*ELQGESMGPLMFSFPFFSMVKFM
S*EGDK*QGTV*NGKQTNDCISVEVSGSF*FLLFAVHNNCFLLFNSCFLFFSSPQFLLLYLMP*HCV*QKEISLRY
IK*LKKKLYTVCLVHYYLEYMCAYLHIHNLPTLFSFIFN*YIIIIHIYGLKCNVLICVHILTKSG*FCICNFKKCF
LLLIYFFVYLISNTFPNLFLSGQ**YNVSCLFAPF*RITVIISGLRQ*QYLCI*IFLHINCN*CKRFHIANSSYNP
ATILLLFYGWDKAGLF*VQARPFC*SCSYLLSSSHSSWATCWSVCWPITLAKNSPHQCRLPIRKWWLVWLMPWPTS
ITKLAFLLSNFY*RFLCSLSPTTKLGDIMKGLEHLDSA**KTFIFIAMMYLNYF*IFY*KGNVGGQCI*NIKK*RA
SSNLGKIHYILNSMKEGEAANS*CTLATALMHMPYSSLRKGFK*RLDLEVKVLLCCILHYLLF*LSS*MSFHYPFA
YPASLSLDSTQFSCLEIPPFP*SVPSMFYGEMVSPRLATQP*LSLLSYRGLLEEGKTGVMV*LSCEPFFPASPTHS
DPESAVLVSRNY
translation = 
LLFDTTDYPIDSHTLGCK*LFIYLYF*LH*EVSSFLPLVSQNLISN*CTEHIDLYLFYF*T*FISMHEQIKKNNNK
*MHIYVYVCVYIYTYIYIYIFSFLTRRF*SK*GEDMLRTEVEFSSILSCKYFAYSGDAGRDPSTYPKAELW*TKLF
HF*CINFLFV**ENWENDLQYAYQAVIPNIT*IHLQRRMFLVAICTDGMGPRDIS*REG*GFEVQLLSQCQKSQGQ
VRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQSHLLLTFASDTTVFTSNLKQTPWCI*LLRRSLPLLPCG
AR*TWMKLVVRPWAGWYQGYKTGLRRPIETGHVETEKTLGFLIGTDSLCLLVYFPTLRLLVVYPWTQRFFESFGDL
STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRVSLWDP*CFLSPSFLWLSSC
HRKGISNRVQFRMGNRRMIASVWKSQDRFSFFYLLFITIVFFCLILAFFFFLLRNFYYYT*CLNIVYNKRKYL*DT
LSNLKKNFTQSA*YITIWNICVLICIFIISLLYFLLFLIDT*SLYIFMG*SVMF*YVYTY*PNQGNFAFVILKNAF
FF*YTFLFILFLILSLISFFQGNNDTMYHASLHHSKE*Q**FLG*GNSNISAYKYFCI*IVTDVRGFILLIAATIQ
LPFCFYFMVGIRLDYSESKLGPFANHVHTSYLPPTAPGQRAGLCAGPSLWQRIHPTSAGCLSESGGWCG*CPGPQV
SLSSLSCCPISIKGSFVP*VQLLNWGIL*RALSIWILPNKKHLFSLQ*CI*IISEYFTKKGMWEVSAFKT*RNEEL
VQTLGKYTIS*TP*KKVRLQTANAHWQQP*CICLIHPSEKDSSRGLIWRLKFCYAVFYITYCFSCPHECLFTTHLL
ILHLSALTPLSSLA*RYHLSPEVFLPCFTARWFLLAWPLSLSCLCCLIEVYLKKEKQGSWFDCPVSPSSLPPPLTV
TRNLQC*SPGTI



On 10/15/07 2:50 PM, "Eric E. Snyder" <esnyder at vbi.vt.edu> wrote:

> Hello,
> 
> I am having trouble with translate() when supplying parameters such as
> -frame, -codontable_id, etc.  I am working straight out of the tutorial
> with a very simple program-- which has me stumped!
> 
> use Bio::SeqIO;
> foreach my $file ( @ARGV ){
>      my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
>                                      -format =>  "fasta" );
>      my $seq_obj = $seqio_obj->next_seq;
> 
>      print "loaded one sequence:\n\tdisplay_id\t" .
>   $seq_obj->display_id() . "\n" .
>   "\tdescription\t" . $seq_obj->description() . "\n";
> 
>      foreach my $frame ( 0 .. 2){
>          $prot_obj = $seq_obj->translate( '-frame' => $frame );
>          print "translation = " . $prot_obj->seq . "\n";
>      }
> }
> 
> Everything works as expected until calling translate.  The output I get
> is the translation of my FASTA sequence (in frame zero, repeated three
> times) in which every "stop" is replaced with "-frame" (!!).  However,
> with no parameters, translate works as advertised.
> 
> This is getting me down because by using the full complement of
> translate options, including specifying frame, genetic code, alternative
> start codons, etc., BioPerl will save me a huge amount of time... but
> only if I can figure out how to use it properly!
> 
> Any assistance would be greatly appreciated!!!
> 
> Sincerely,
> eesnyder
> 




From sheris at berkeley.edu  Tue Oct 16 19:15:43 2007
From: sheris at berkeley.edu (Sheri Simmons)
Date: Tue, 16 Oct 2007 16:15:43 -0700
Subject: [Bioperl-l] what are the key features of genbank file recognized by
	SeqIO?
Message-ID: <200710161615.43420.sheris@berkeley.edu>

I'm hoping someone can help me with figuring out how to generate genbank files 
from scratch that can be interpreted with SeqIO. The problem is that genbank 
files generated via the artemis program are not recognized by SeqIO, so I am 
attempting to generate SeqIO-compatible genbank files so they can be 
converted to other formats later. 
I produced a file which looks by eye exactly like standard genbank files, but 
which is not recognized by SeqIO. Could anyone tell me or refer me to a 
source that explains the exact format that SeqIO::genbank requires? 
FYI here's a snippet of the file generated by my program:

########
LOCUS   Contig2406              66712 bp        dna     linear  UNK
FEATURES             Location/Qualifiers
     CDS                 83..1222
                            /gene="org_2406_0001"
     CDS                1259..1576
                           /gene="org_2406_0002"
     CDS                complement(1830..3284)
                           /gene="org_2406_0003c"
(more CDS)
BASE COUNT      14091 a         19796 c         18841 g         13747 t
ORIGIN
        1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
      61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
(more sequence)
###########

Thanks,
Sheri

-- 
Sheri Simmons
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
http://webfiles.berkeley.edu/~sheris


From barry.moore at genetics.utah.edu  Tue Oct 16 19:47:56 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 16 Oct 2007 17:47:56 -0600
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>

Hi Sheri,

You would need to look at the source code for Bio::SeqIO::genbank.pm  
specifically the next_seq method.  If you let us know what kind of  
errors you're getting, or what data is missing in your seq object  
perhaps we could help you narrow it down.  You could also send one of  
your GenBank style files that isn't working and someone might be  
willing to take a stab at running it.

Barry

On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:

> I'm hoping someone can help me with figuring out how to generate  
> genbank files
> from scratch that can be interpreted with SeqIO. The problem is  
> that genbank
> files generated via the artemis program are not recognized by  
> SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank  
> files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me  
> to a
> source that explains the exact format that SeqIO::genbank requires?
> FYI here's a snippet of the file generated by my program:
>
> ########
> LOCUS   Contig2406              66712 bp        dna     linear  UNK
> FEATURES             Location/Qualifiers
>      CDS                 83..1222
>                             /gene="org_2406_0001"
>      CDS                1259..1576
>                            /gene="org_2406_0002"
>      CDS                complement(1830..3284)
>                            /gene="org_2406_0003c"
> (more CDS)
> BASE COUNT      14091 a         19796 c         18841 g          
> 13747 t
> ORIGIN
>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta  
> acatacacaa
>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg  
> ccgatatcaa
> (more sequence)
> ###########
>
> Thanks,
> Sheri
>
> --
> Sheri Simmons
> Department of Earth and Planetary Sciences
> University of California, Berkeley
> Berkeley, CA 94720-4767
> http://webfiles.berkeley.edu/~sheris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Tue Oct 16 19:58:46 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Oct 2007 16:58:46 -0700
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
References: <200710161615.43420.sheris@berkeley.edu>
	<020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
Message-ID: <74393EF9-C4B9-4F3B-8150-E22BECE81587@bioperl.org>

I am sure we should also let the Artemis developers know what is  
going on so they can help fix the bug on their end as well.

Have you also tried dumping EMBL from Artemis, a format I assume they  
are more likely to use, and seeing if that parses fine in BioPerl?

-jason
On Oct 16, 2007, at 4:47 PM, Barry Moore wrote:

> Hi Sheri,
>
> You would need to look at the source code for Bio::SeqIO::genbank.pm
> specifically the next_seq method.  If you let us know what kind of
> errors you're getting, or what data is missing in your seq object
> perhaps we could help you narrow it down.  You could also send one of
> your GenBank style files that isn't working and someone might be
> willing to take a stab at running it.
>
> Barry
>
> On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:
>
>> I'm hoping someone can help me with figuring out how to generate
>> genbank files
>> from scratch that can be interpreted with SeqIO. The problem is
>> that genbank
>> files generated via the artemis program are not recognized by
>> SeqIO, so I am
>> attempting to generate SeqIO-compatible genbank files so they can be
>> converted to other formats later.
>> I produced a file which looks by eye exactly like standard genbank
>> files, but
>> which is not recognized by SeqIO. Could anyone tell me or refer me
>> to a
>> source that explains the exact format that SeqIO::genbank requires?
>> FYI here's a snippet of the file generated by my program:
>>
>> ########
>> LOCUS   Contig2406              66712 bp        dna     linear  UNK
>> FEATURES             Location/Qualifiers
>>      CDS                 83..1222
>>                             /gene="org_2406_0001"
>>      CDS                1259..1576
>>                            /gene="org_2406_0002"
>>      CDS                complement(1830..3284)
>>                            /gene="org_2406_0003c"
>> (more CDS)
>> BASE COUNT      14091 a         19796 c         18841 g
>> 13747 t
>> ORIGIN
>>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta
>> acatacacaa
>>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg
>> ccgatatcaa
>> (more sequence)
>> ###########
>>
>> Thanks,
>> Sheri
>>
>> --
>> Sheri Simmons
>> Department of Earth and Planetary Sciences
>> University of California, Berkeley
>> Berkeley, CA 94720-4767
>> http://webfiles.berkeley.edu/~sheris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From torsten.seemann at infotech.monash.edu.au  Tue Oct 16 21:31:03 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Wed, 17 Oct 2007 11:31:03 +1000
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <a79f6a4b0710161831x30efa062oacc64844706e8a96@mail.gmail.com>

On 17/10/2007, Sheri Simmons <sheris at berkeley.edu> wrote:
> I'm hoping someone can help me with figuring out how to generate genbank files
> from scratch that can be interpreted with SeqIO. The problem is that genbank
> files generated via the artemis program are not recognized by SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me to a
> source that explains the exact format that SeqIO::genbank requires?

Here is NCBI's documentation on the feature table format.
http://www.ncbi.nlm.nih.gov/collab/FT/

Regarding Artemis: if you load an EMBL file, then save as EMBL, it
seems to keep the header. If you save it as Genbank though, it
discards the header and only outputs the feature table and sequence.
Also, Artemis for many of its Save options only saves the feature
table. Both of these last two can't be read by BioPerl. At one stage I
had some code to whack in a fake header and empty sequence at the end
to get it to load.

Now, regarding your example output. I'm never sure if the first line
is LOCUS or ID, I guess one is deprecated. You also don't have a Date
at the end of the first line, but maybe it is optional. You are also
missing the "//" on the final line. Finally, Genbank is strict on
correct spacing etc, but I'm sure the Bioperl parser is written
relatively defensively here, so that might not be the problem.

Hope this helps,

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From wgallin at ualberta.ca  Wed Oct 17 21:42:54 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Wed, 17 Oct 2007 19:42:54 -0600
Subject: [Bioperl-l] Still trouble with remote joined records
Message-ID: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>

I must be missing something, but I can not get the procedure outlined  
in FAQ 5.5 to do what I think it should (maybe my expectations are  
incorrect.

I think I have an up-to-date release:

GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print  
$Bio::Root::Version::VERSION,"\n"'
1.005002102


If I run the following script (not that gi7648673 is a protein record):
___________________________________________________________
#! /usr/bin/perl

#071017 - Small script to test the method for getting the ORF sequence
#using dbh passing into the sequence method.


use strict;
use warnings;
use LWP::Simple;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::Seq;

#Create handles to GenBank and GenPept

my $gbh = Bio::DB::GenBank -> new;
my $gph = Bio::DB::GenPept -> new;

#This is the gi number of the entry being tested

my $test_gi = 7648673;

#Get the protein sequence file from GENBANK

my $test_na_record = $gph -> get_Seq_by_gi ($test_gi);

#Go through the features - when the CDS feature is found splice  
together the sequence and translate.


   for my $feat ( $test_na_record->get_SeqFeatures ) {
     if ( $feat->primary_tag eq 'CDS' ) {
        my $cds = $feat->spliced_seq(-db => $gbh, -nosort => 1);
        print $cds->translate->seq, "\n";
     }
   }


exit;
_______________________________________________________________________
I get an error that a protein sequence can not be translated.  I  
thought that by feeding the handle to GenBank into the spliced_seq  
method that it would retrieve the necessary nucleic acid sequence  
records and splice together the specified ranges.

So I tried using the corresponding nucleic acid record, gi7648671,  
which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).

That yielded the correct amino acid sequence for the first half the  
protein, encoded by the sequence in the record itself, but it did not  
retrieve the other nucleic acid record that is specified to contain  
the 3' end of the sequence.

So, as far as I can see, passing the DB handle isn't causing the  
spliced_seq method to go elsewhere for the nucleic acid sequence data.

I thought that was the purpose.

Can anyone enlighten me, or is this a bug?

Warren Gallin



From cjfields at uiuc.edu  Wed Oct 17 22:49:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 21:49:37 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
Message-ID: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>

On Oct 17, 2007, at 8:42 PM, Warren Gallin wrote:

> I must be missing something, but I can not get the procedure outlined
> in FAQ 5.5 to do what I think it should (maybe my expectations are
> incorrect.
>
> I think I have an up-to-date release:
>
> GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print
> $Bio::Root::Version::VERSION,"\n"'
> 1.005002102
> ...
> I get an error that a protein sequence can not be translated.  I
> thought that by feeding the handle to GenBank into the spliced_seq
> method that it would retrieve the necessary nucleic acid sequence
> records and splice together the specified ranges.

No, the error is expected:

MSG: Can't translate an amino acid sequence.

The record in question is a protein record, so you are retrieving a  
protein sequence, which can't be translated (the exception is valid,  
in other words).  Note that the 'CDS' feature in this case has a  
specified location of 1..630 (indicated by arrow):

      CDS             1..630   <---------
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"

The tag name 'coded_by' has the data you want; however it is stored  
as a string only.

> So I tried using the corresponding nucleic acid record, gi7648671,
> which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).
>
> That yielded the correct amino acid sequence for the first half the
> protein, encoded by the sequence in the record itself, but it did not
> retrieve the other nucleic acid record that is specified to contain
> the 3' end of the sequence.
> ...
> So, as far as I can see, passing the DB handle isn't causing the
> spliced_seq method to go elsewhere for the nucleic acid sequence data.
>
> I thought that was the purpose.
>
> Can anyone enlighten me, or is this a bug?
>
> Warren Gallin

This appears to be a bug.  The remote sequence is designated in the  
feature:

      CDS             join 
(430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
                      AF166008.1:9952..10044,AF166008.1:13222..13469,
                      AF166008.1:15123..15300)
                      /gene="KCND2"
                      /codon_start=1
                      /product="voltage-gated potassium channel Kv4.2"
                      /protein_id="AAF65618.1"
                      /db_xref="GI:7648673"

but the location is truncated when passed through SeqIO to genbank  
output, which explains the spliced_seq() problem:

      CDS             430..1544
                      /db_xref="GI:7648673"
                      /codon_start=1
                      /protein_id="AAF65618.1"
                      /gene="KCND2"

I'll try looking into this; if I can't get to it immediately I'll  
file a bug report.  Thanks!

chris


From cjfields at uiuc.edu  Wed Oct 17 23:45:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 22:45:55 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
	<8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
Message-ID: <872F9A22-AC32-4381-B7FE-4554943C8D75@uiuc.edu>


On Oct 17, 2007, at 9:49 PM, Chris Fields wrote:

> ...
>> So, as far as I can see, passing the DB handle isn't causing the
>> spliced_seq method to go elsewhere for the nucleic acid sequence  
>> data.
>>
>> I thought that was the purpose.
>>
>> Can anyone enlighten me, or is this a bug?
>>
>> Warren Gallin
>
> This appears to be a bug.  The remote sequence is designated in the
> feature:
>
>       CDS             join
> (430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
>                       AF166008.1:9952..10044,AF166008.1:13222..13469,
>                       AF166008.1:15123..15300)
>                       /gene="KCND2"
>                       /codon_start=1
>                       /product="voltage-gated potassium channel Kv4.2"
>                       /protein_id="AAF65618.1"
>                       /db_xref="GI:7648673"
>
> but the location is truncated when passed through SeqIO to genbank
> output, which explains the spliced_seq() problem:
>
>       CDS             430..1544
>                       /db_xref="GI:7648673"
>                       /codon_start=1
>                       /protein_id="AAF65618.1"
>                       /gene="KCND2"
>
> I'll try looking into this; if I can't get to it immediately I'll
> file a bug report.  Thanks!
>
> chris

Looked into it and there isn't a problem with BioPerl, but there  
appears to be an error on NCBI's end with some full GenBank seqs and  
remote locations.  The default return type for records using  
Bio::DB::GenBank is 'gbwithparts' (which retrieves full records for  
everything), but this particular record version has a truncated  
location.  You can see the truncated version here via eutils:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
db=nucleotide&retmode=text&id=7648671&rettype=gbwithparts

You can get around this in your script by changing the requested  
format to 'gb', which has the correct location string and returns the  
full protein seq:

my $gbh = Bio::DB::GenBank->new(-format => 'gb');

chris


From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From smei_26 at yahoo.com  Thu Oct 18 23:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From cjfields at uiuc.edu  Fri Oct 19 00:47:12 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 18 Oct 2007 23:47:12 -0500
Subject: [Bioperl-l] Bioperl DB RefSeq
In-Reply-To: <534058.73546.qm@web38804.mail.mud.yahoo.com>
References: <534058.73546.qm@web38804.mail.mud.yahoo.com>
Message-ID: <744D3248-EA8E-4832-847D-4434DFF258E6@uiuc.edu>

Use an eval {} block, described here:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Error_Handling

my $seq;
eval {
   $seq =  $seq = $seq_refseq->get_Seq_by_id("$acc");
};

print "ID does not exist!\n" if $@;

chris

On Oct 18, 2007, at 10:11 PM, Steven Mei wrote:

> Hi,
>
> I have a list of refseq accession  numbers and  wish  to get  their  
> sequences. I used Bio::DB:: RefSeq module
>
> However, if the $acc is bad (such as deleted accession), an  
> exception  would  printed out  and the script stops execution.
>
>
> ---------------EXCEPTION-------------------
> MSG: id does not exist
> ...
> ----------------------------------------------------
>
> my $seq = $seq_refseq->get_Seq_by_id("$acc");
>
>
> What I wish to happen is the script would handle the next accession  
> (bypass the bad accession) and continue until all the accessions  
> have been processed.
>
> Anyone have idea how to handle this issue? Thanks
>
> -- Mike



From j.s.soares at gmail.com  Fri Oct 19 08:45:25 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 05:45:25 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of the gene. This is the thing where the script goes weird. It doesn't
reset the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need to know how
many repetitions of the pattern there are in each gene, as above, it does
not reset the counting of repetitions and istead gives me the repitions in
the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;

#print "What is the pattern you're looking for?";
#chomp (my $pat = <>);# Taking the pattern input from the user and cuting
the new line character in the end

#print "How many letters in the pattern?";
#chomp (my $patlen = <>);# Taking the length of the pattern input from the
user and cuting the new line character in the end

print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";# Taking the file to analyse
input from the user and cuting the new line character in the end

print "Where do you want to store the rough file?";
chomp (my $rough = <>);# Taking the rough file input from the user and
cuting the new line character in the end

print "Where do you want to store the final file?";
chomp (my $final = <>);# Taking the clean file input from the user and
cuting the new line character in the end

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0,
0);#Initialization of the variables common to the whole script:
#$count_of_pat3 is used to count how many times the pattern appears in a DNA
sequence.
#$position states the location in number of bases from the start of the
sequence to the first base of the pattern. 
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');#A
BioPerl module was used here (Bio::Tools::SeqPattern in order to give the
program a better direction telling it what exactly the pattern is about. If
it's DNA, RNA or Protein. In this case it's DNA.

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {#Using
BioPerl module Bio::SeqIO to open the file that contains the sequences to be
analysed
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
#Using Perl's simple default function open to create the rough file and make
it writable

        while (my $seq_obj = $in->next_seq) {
#This while loop uses BioPerl objects: $seq_obj and next_seq. It basically
states that for each sequence in the Sequences file it will run the lines
that follow and after that it will pick up the next sequence

        	#my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE
=>'Dna');#A BioPerl module was used here (Bio::Tools::SeqPattern in order to
give the program a better direction telling it what exactly the pattern is
about. If it's DNA, RNA or Protein. In this case it's DNA.

                my $id1 = $seq_obj->display_id();
#We use the $seq_obj->display_id() object here to be able to chop the fasta
header from each sequence and store it as the variable $id1

                     
				foreach ($seq_obj->seq =~ m/$pat/g){#for each sequence that contains the
pattern we are looking for, we start the count of the times the pattern
repeats itself
								++$count_of_pat;
							
							print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",#The Fasta Header,
the number of pattern repitions and the position where each repition was
found in each sequence is printed on the rough file
							$position + $-[0] + 1, "\n"; #This resets the position for the next
repetition
							$position = $position + length($seq_obj) - $patlen + 1;
							#print $-;
							#print "$count_of_pat\n";
							#print "$position\n";
							#print $seq_obj->seq, "\n";
							}#The positon is set to start from 1 rather than the default Perl
start position 0.
				
							
					}
					
					
        close MOTIFCOUNT;#With the file completelly scanned, the rough file
is closed

        open (SYM, "+< $rough") or die "The file doesn't exist";#The rough
file is open again and if it hasn't been created it prints out that it
doesn't exist

        open (TAB, ">> $final") or die "The gene list wasn't
transformed";#Another file is created and made writable, the final file.
This is done as can be seen in the following lines in order to substitute
any space by a tab and to print, as a header in the file, the motif we were
looking for.

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;#The regexp that substitutes each space
for a tab 
        		print TAB "$line";
        	}
        }
        close (SYM);#Closing both files the rough and the final
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;


Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
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From j.s.soares at gmail.com  Fri Oct 19 09:10:18 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 06:10:18 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of each gene. This is where the script goes weird. It doesn't reset
the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need the
information on how many repetitions of the pattern there are in each gene,
as above, it does not reset the counting of repetitions and instead gives me
the repitions in the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Perl;
use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;




print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";
print "Where do you want to store the rough file?";
chomp (my $rough = <>);
print "Where do you want to store the final file?";
chomp (my $final = <>);

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";


        while (my $seq_obj = $in->next_seq) {

                #my $id1 = $seq_obj->display_id();
				my $seq_length = length($seq_obj);
				#print "$seq_length\n";
				foreach ($seq_obj->seq =~ m/$pat/g){
								++$count_of_pat;
								
								my $id1 = $seq_obj->display_id();
								print $seq_obj->seq, "\n";							
								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
								$position + $-[0] + 1, "\n";
								$position = $position + length($seq_obj) - $patlen + 1;
								#print "$id1\n";
								#print "$count_of_pat\n";
								#print "$position\n";
								
								}
					
					#print "$seq_length\n";
					print $seq_obj->seq, "\n";
					}
					
					
        close MOTIFCOUNT;

        open (SYM, "+< $rough") or die "The file doesn't exist";

        open (TAB, ">> $final") or die "The gene list wasn't transformed";

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;
        		print TAB "$line";
        	}
        }
        close (SYM);
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;



Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From chemmeri at cgb.indiana.edu  Fri Oct 19 09:40:22 2007
From: chemmeri at cgb.indiana.edu (Chris Hemmerich)
Date: Fri, 19 Oct 2007 09:40:22 -0400 (EDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <13293737.post@talk.nabble.com>
References: <13293737.post@talk.nabble.com>
Message-ID: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>



Djoja,

Perhaps this is a problem with scope. Since you declare $position outside 
of

         while (my $seq_obj = $in->next_seq) {

it will not be reset for each sequence.  The line

 		$position = $position + length($seq_obj) - $patlen + 1;

will continue to increase $position for each sequence processed. From a 
quick look, I don't think you need $position at all in this script and can 
just print $-[0]+1.

Hope this helps,

  Chris


On Fri, 19 Oct 2007, Djodja wrote:

>
> Hi all,
>
> This is my first post. I am very puzzeled about a script that i wrote last
> year, that was working fine, and all of sudden, with no change to the code
> it just stopped doing what it was supposed to do. Basically I'm searching
> for patterns on a whole genome database.
>
> The pattern that I'm searching for at the moment is AACAAAG.
>
> My script finds the pattern, no problem on regexps or anything. It also
> searches the whole genome divided in fasta headers for each gene. The
> problem is that I need to know the position of the pattern, relative to the
> start of each gene. This is where the script goes weird. It doesn't reset
> the counter to the start of each gene. It instead continues to count
> patterns as if the genes aren't separated at all. Also I need the
> information on how many repetitions of the pattern there are in each gene,
> as above, it does not reset the counting of repetitions and instead gives me
> the repitions in the whole genome.
>
> here is the code:
>
> #!/usr/lib/perl -w
>
> use Bio::Perl;
> use Bio::Seq ();
> use Bio::SeqIO ();
> use Bio::Tools::SeqPattern ();
> use strict;
> use warnings;
>
>
>
>
> print 'Where is the file that you want to analise?';
> chomp (my $Fasfile = <>) or die "No such file";
> print "Where do you want to store the rough file?";
> chomp (my $rough = <>);
> print "Where do you want to store the final file?";
> chomp (my $final = <>);
>
> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>
> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>
>
>        while (my $seq_obj = $in->next_seq) {
>
>                #my $id1 = $seq_obj->display_id();
> 				my $seq_length = length($seq_obj);
> 				#print "$seq_length\n";
> 				foreach ($seq_obj->seq =~ m/$pat/g){
> 								++$count_of_pat;
>
> 								my $id1 = $seq_obj->display_id();
> 								print $seq_obj->seq, "\n";
> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
> 								$position + $-[0] + 1, "\n";
> 								$position = $position + length($seq_obj) - $patlen + 1;
> 								#print "$id1\n";
> 								#print "$count_of_pat\n";
> 								#print "$position\n";
>
> 								}
>
> 					#print "$seq_length\n";
> 					print $seq_obj->seq, "\n";
> 					}
>
>
>        close MOTIFCOUNT;
>
>        open (SYM, "+< $rough") or die "The file doesn't exist";
>
>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>
> 	print TAB "Motif: $pat\n";
>        while (my $line = <SYM>){
>
>        	foreach ($line){
>                	$line =~ s/\|/\t/g;
>        		print TAB "$line";
>        	}
>        }
>        close (SYM);
>        close(TAB);
>
>        print "The gene list was created and transformed successfully.\n\a"
> }
> exit;
>
>
>
> Can anyone help me out? This is kind of in the way of my PhD progression.
>
> All the best,
>
> Djodja
> -- 
> View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From smei_26 at yahoo.com  Fri Oct 19 13:51:48 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Fri, 19 Oct 2007 10:51:48 -0700 (PDT)
Subject: [Bioperl-l] Please help: GenBank ID map
Message-ID: <560962.35266.qm@web38802.mail.mud.yahoo.com>

Hi, 

I have list of GenBank ID inlcuding ids for EST, gemonics sequence and UniGene. I wish to map these ids to RefSeq Ids using BioPerl. Anyone know how to do this? Thanks

example of the GenBank Id list: 

NM_000137
BC004558
BF939919
AL031588
AI673812
NM_006024
AK024914
AK026008
NM_014823
AA523958
NM_001677
AW291083
AL049246
AF116615
AI672084


-- Mike

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From j.s.soares at gmail.com  Sat Oct 20 03:11:17 2007
From: j.s.soares at gmail.com (Djodja)
Date: Sat, 20 Oct 2007 00:11:17 -0700 (PDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
References: <13293737.post@talk.nabble.com>
	<Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
Message-ID: <13307407.post@talk.nabble.com>


I will have to give you the credit here as well!

THank you so much Chris.

I have declared both $position and $count_of_pat inside the while loop.

Will rearrange the script and I'm going to make it a subroutine as I have
many other patterns to search for.

Thank you thank you thankyou.

Also, I am in England in Exeter. If you want I could look on ways to get you
here for a nice talk for you to expose your work.

Let me know.

Djodja

Chris Hemmerich wrote:
> 
> 
> 
> Djoja,
> 
> Perhaps this is a problem with scope. Since you declare $position outside 
> of
> 
>          while (my $seq_obj = $in->next_seq) {
> 
> it will not be reset for each sequence.  The line
> 
>  		$position = $position + length($seq_obj) - $patlen + 1;
> 
> will continue to increase $position for each sequence processed. From a 
> quick look, I don't think you need $position at all in this script and can 
> just print $-[0]+1.
> 
> Hope this helps,
> 
>   Chris
> 
> 
> On Fri, 19 Oct 2007, Djodja wrote:
> 
>>
>> Hi all,
>>
>> This is my first post. I am very puzzeled about a script that i wrote
>> last
>> year, that was working fine, and all of sudden, with no change to the
>> code
>> it just stopped doing what it was supposed to do. Basically I'm searching
>> for patterns on a whole genome database.
>>
>> The pattern that I'm searching for at the moment is AACAAAG.
>>
>> My script finds the pattern, no problem on regexps or anything. It also
>> searches the whole genome divided in fasta headers for each gene. The
>> problem is that I need to know the position of the pattern, relative to
>> the
>> start of each gene. This is where the script goes weird. It doesn't reset
>> the counter to the start of each gene. It instead continues to count
>> patterns as if the genes aren't separated at all. Also I need the
>> information on how many repetitions of the pattern there are in each
>> gene,
>> as above, it does not reset the counting of repetitions and instead gives
>> me
>> the repitions in the whole genome.
>>
>> here is the code:
>>
>> #!/usr/lib/perl -w
>>
>> use Bio::Perl;
>> use Bio::Seq ();
>> use Bio::SeqIO ();
>> use Bio::Tools::SeqPattern ();
>> use strict;
>> use warnings;
>>
>>
>>
>>
>> print 'Where is the file that you want to analise?';
>> chomp (my $Fasfile = <>) or die "No such file";
>> print "Where do you want to store the rough file?";
>> chomp (my $rough = <>);
>> print "Where do you want to store the final file?";
>> chomp (my $final = <>);
>>
>> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
>> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>>
>> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>>
>>
>>        while (my $seq_obj = $in->next_seq) {
>>
>>                #my $id1 = $seq_obj->display_id();
>> 				my $seq_length = length($seq_obj);
>> 				#print "$seq_length\n";
>> 				foreach ($seq_obj->seq =~ m/$pat/g){
>> 								++$count_of_pat;
>>
>> 								my $id1 = $seq_obj->display_id();
>> 								print $seq_obj->seq, "\n";
>> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
>> 								$position + $-[0] + 1, "\n";
>> 								$position = $position + length($seq_obj) - $patlen + 1;
>> 								#print "$id1\n";
>> 								#print "$count_of_pat\n";
>> 								#print "$position\n";
>>
>> 								}
>>
>> 					#print "$seq_length\n";
>> 					print $seq_obj->seq, "\n";
>> 					}
>>
>>
>>        close MOTIFCOUNT;
>>
>>        open (SYM, "+< $rough") or die "The file doesn't exist";
>>
>>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>>
>> 	print TAB "Motif: $pat\n";
>>        while (my $line = <SYM>){
>>
>>        	foreach ($line){
>>                	$line =~ s/\|/\t/g;
>>        		print TAB "$line";
>>        	}
>>        }
>>        close (SYM);
>>        close(TAB);
>>
>>        print "The gene list was created and transformed
>> successfully.\n\a"
>> }
>> exit;
>>
>>
>>
>> Can anyone help me out? This is kind of in the way of my PhD progression.
>>
>> All the best,
>>
>> Djodja
>> -- 
>> View this message in context:
>> http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13307407
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From avilella at gmail.com  Mon Oct 22 04:53:45 2007
From: avilella at gmail.com (Albert Vilella)
Date: Mon, 22 Oct 2007 09:53:45 +0100
Subject: [Bioperl-l] java runnables
Message-ID: <358f4d650710220153o4a941088qd5a109d546a1e140@mail.gmail.com>

Hi all,

A question related to java runnables in bioperl-run:

I would like to have a Pecan (http://www.bioperl.org/wiki/PECAN) runnable in
bioperl-run,
and there are a couple of java runnables already written, eponine and vista.

I was wondering if the current state of the java runnables satifies
everybody or if people
can think of a more clean or generic way of calling java from bioperl-run.

Comments?

Cheers,

    Albert.


From wgallin at ualberta.ca  Mon Oct 22 13:53:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 11:53:24 -0600
Subject: [Bioperl-l] Problem with EUtilities
Message-ID: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>

I've encountered a problem with retrieving a set of records using  
efetch.

Code snippet:

     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'efetch',
         -db      => 'protein',
         -rettype => 'genbank',
         -id      => \@ginumber_search
     );
     $file = 'temp_hold.gb';

     $gpeptfactory->get_Response( -file => $file );



If the array of gi numbers that I submit is large (482 elements does  
not give the problem but 1517 does) I am getting an error at the  
get_response step:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:144
-----------------------------------------------------------


Am I correct in thinking that the individual array elements are being  
submitted as part of the URI, and therefore a large array is  
exceeding the acceptable size limit for a URI?

If so, is there a workaround?  Breaking the large request into a set  
of smaller requests?
Or is there a way of submitting a file of gi numbers using  
EUtilities, rather than an array?

Warren Gallin


From cjfields at uiuc.edu  Mon Oct 22 14:16:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 13:16:19 -0500
Subject: [Bioperl-l] Problem with EUtilities
In-Reply-To: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
References: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
Message-ID: <DB401D8A-0DC9-46EB-89A9-58093B8FB171@uiuc.edu>


On Oct 22, 2007, at 12:53 PM, Warren Gallin wrote:

> I've encountered a problem with retrieving a set of records using
> efetch.
>
> Code snippet:
>
>      my $gpeptfactory = Bio::DB::EUtilities->new(
>          -eutil   => 'efetch',
>          -db      => 'protein',
>          -rettype => 'genbank',
>          -id      => \@ginumber_search
>      );
>      $file = 'temp_hold.gb';
>
>      $gpeptfactory->get_Response( -file => $file );
>
>
>
> If the array of gi numbers that I submit is large (482 elements does
> not give the problem but 1517 does) I am getting an error at the
> get_response step:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:144
> -----------------------------------------------------------
>
>
> Am I correct in thinking that the individual array elements are being
> submitted as part of the URI, and therefore a large array is
> exceeding the acceptable size limit for a URI?

Yes.

> If so, is there a workaround?  Breaking the large request into a set
> of smaller requests?
> Or is there a way of submitting a file of gi numbers using
> EUtilities, rather than an array?
>
> Warren Gallin

You can use epost and post your IDs first, then retrieve them.   
Alternatively, you can fetch them in small batches.  The following  
two code bits should help:

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_post_a_specific_list_of_UIDs_to_NCBI. 
27s_history_server.3F

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_usi 
ng_a_query.3F

chris


From er at xs4all.nl  Mon Oct 22 12:05:29 2007
From: er at xs4all.nl (Erikjan)
Date: Mon, 22 Oct 2007 18:05:29 +0200 (CEST)
Subject: [Bioperl-l] postgres datatype: VARCHAR to TEXT - patch
Message-ID: <22811.156.83.0.216.1193069129.squirrel@webmail.xs4all.nl>

Hello,

Using load_seqdatabase.pl to load uniprot_sprot.dat into
postgres (8.2.5), biosql gave me:

ERROR:  value too long for type character varying(40)

(all fresh from cvs)

Changing 'VARCHAR(N)' to 'TEXT' fixed those errors.

Generally, VARCHAR[(N)], (=character varying) are probably
better replaced with 'TEXT' as VARCHAR(N) is implemented
as TEXT with a check on length.



Attached is a patch for the table definitions in
biosqldb-pg.sql; I haven't changed the other scripts, as I
don't know if you will agree with this improvement.

(The other table-creating scripts are probably also better
off with a change from VARCHAR (=character varying) to the
text datatype.)

(loading uniprot_sprot.dat took 20 hours to load, but now
without errors, so I won't complain :)


Thanks,

Erik



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From hangsyin at gmail.com  Mon Oct 22 18:30:10 2007
From: hangsyin at gmail.com (Hang)
Date: Mon, 22 Oct 2007 22:30:10 +0000 (UTC)
Subject: [Bioperl-l] Extract features from GFF
Message-ID: <loom.20071022T221835-291@post.gmane.org>

Hello,

I have a list of about 100,000 short genomic regions with paired start and end
coordinations on reference fly genome (R5.3). I also have GFF files from the
same genome release. I wonder how I can extract all overlapping features from
these regions.

For example:

region A is on chromosome 2L between 123,456 bp to 123,489 bp. What code should
I use to extract feature, like gene, CDS etc., that overlaps with this region?

Thank you in advance!

-- Hang



From wgallin at ualberta.ca  Mon Oct 22 20:28:55 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 18:28:55 -0600
Subject: [Bioperl-l] More on EUtilities problem
Message-ID: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>

I seem to be missing something here.

I took the code from the HOWTO as a template and wrote the following  
code snippet (@gisearch_number is an array of gi numbers, prints out  
as expected and can be used to successfully download the relevant  
records using Batch Entrez):
______________________________________________________________

#Create new EUTILS  history object for submitting a large array of gi  
numbers
     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'epost',
         -db      => 'protein',
         -id      => \@ginumber_search,
         -keep_histories => 1
     );

     my $count = @ginumber_search;


     my $history;
     if ($history = $gpeptfactory -> next_History){
    		print "Posted successfully\n";                            
#Prints as expected for successful history
     	print "WebEnv    : ", $history -> get_webenv,"\n";
     	print "Query_key : ",$history->get_query_key,"\n";
     }
     $file = 'temp_hold.gb';

     $gpeptfactory->set_parameters (-eutil => 'efetch',
     							   -rettype => 'genbank',
     							   -history => $history,
     							
	);
	my ($retmax, $retstart) = (300,0);
	my $retry = 0;
RETRIEVE_SEQS: while ($retstart < $count) {
	
     $gpeptfactory->set_parameters(
     						-retmax => $retmax,
                             -retstart => $retstart,
                             );
     eval{
         $gpeptfactory->get_Response(-file => $file);
         print "Output file is $file.\n";
     };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++ && goto RETRIEVE_SEQS;
     }
     else{
     	
     	my $retend = $retstart + $ retmax;
     	print "Loaded entries $retstart through $retend on retry # 
$retry.\n";

     	$retstart += $retmax;
     	$retry = 0;
     }
}

         $retr_seq = Bio::SeqIO->new(
             -file   => $file,
             -format => 'genbank'
         );

________________________________________________
At this point the program fails because there is no file written.

It appears that the get_Response method is not doing its thing.

Also, on each iteration of the loop enclosing the eval the first pass  
fails with the following error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:177
-----------------------------------------------------------
  and then the second pass evaluates as correct - but the output file  
is never opened or written to.

I've tried to pass $file,  "$file" , ">>$file"  and a literal string  
of a file name, with and without the >>, but to no avail.

So I think that I must be missing something basic here, but I am  
unable to see what.

Any advice would be most welcome.

Warren Gallin




From cjfields at uiuc.edu  Mon Oct 22 20:43:31 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 19:43:31 -0500
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>


On Oct 22, 2007, at 5:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang

Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
depend on the GFF version of the data you have.

chris


From cjfields at uiuc.edu  Mon Oct 22 23:50:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 22:50:19 -0500
Subject: [Bioperl-l] More on EUtilities problem
In-Reply-To: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
References: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
Message-ID: <52D724FE-A586-489A-81BE-F9AAA6963435@uiuc.edu>


On Oct 22, 2007, at 7:28 PM, Warren Gallin wrote:

> I seem to be missing something here.
>
> I took the code from the HOWTO as a template and wrote the following
> code snippet (@gisearch_number is an array of gi numbers, prints out
> as expected and can be used to successfully download the relevant
> records using Batch Entrez):
> ...

One problem (but not the main one):

>      $file = 'temp_hold.gb';

You don't indicate the file needs appending (such as when rewriting  
to the same file in the loop below); you should change it to:

$file = '>>temp_hold.gb';

The below section is the main issue:

>      $gpeptfactory->set_parameters (-eutil => 'efetch',
>      							   -rettype => 'genbank',
>      							   -history => $history,
>      							
> 	);

In general, unless you're absolutely sure you want to carry over  
parameters from the previous eutil search (such as when you are  
looping through and changing the retmax/retstart parameters below),  
use reset_parameters():

$gpeptfactory->reset_parameters(
        -eutil => 'efetch',
        -db  => 'protein',
        -rettype => 'genbank',
        -history => $history
);

What's I believe is happening is the id parameter setting from your  
first eutil search is carried over and is reposted in the URL (thus  
getting the error).  reset_parameters() resets all parameters to  
undef unless new parameter args are passed in, in which case those  
are set to the new values, so nothing carries over.

 From that point on everything works fine (though again you'll want  
to specify that you are appending to a file instead of overwriting it  
within the loop).

chris

> 	my ($retmax, $retstart) = (300,0);
> 	my $retry = 0;
> RETRIEVE_SEQS: while ($retstart < $count) {
> 	
>      $gpeptfactory->set_parameters(
>      						-retmax => $retmax,
>                              -retstart => $retstart,
>                              );
>      eval{
>          $gpeptfactory->get_Response(-file => $file);
>          print "Output file is $file.\n";
>      };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++ && goto RETRIEVE_SEQS;
>      }
>      else{
>      	
>      	my $retend = $retstart + $ retmax;
>      	print "Loaded entries $retstart through $retend on retry #
> $retry.\n";
>
>      	$retstart += $retmax;
>      	$retry = 0;
>      }
> }
>
>          $retr_seq = Bio::SeqIO->new(
>              -file   => $file,
>              -format => 'genbank'
>          );
>
> ________________________________________________
> At this point the program fails because there is no file written.
>
> It appears that the get_Response method is not doing its thing.
>
> Also, on each iteration of the loop enclosing the eval the first pass
> fails with the following error message:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:177
> -----------------------------------------------------------
>   and then the second pass evaluates as correct - but the output file
> is never opened or written to.
>
> I've tried to pass $file,  "$file" , ">>$file"  and a literal string
> of a file name, with and without the >>, but to no avail.
>
> So I think that I must be missing something basic here, but I am
> unable to see what.
>
> Any advice would be most welcome.
>
> Warren Gallin
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From barry.moore at genetics.utah.edu  Tue Oct 23 00:09:05 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:09:05 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <7691F0B8-9771-477F-A982-21360F769D4A@genetics.utah.edu>

Hang-

Something like this would work, although for simply querying the  
coordinates on GFF like that you could iterate over the file with  
your own while loop, split the columns and do the same thing with  
about as many lines.  You'll need to do each chromosome as a separate  
GFF file or add some code to the loop to check the chromosome  
($feature->seq_id I think).

     use Bio::Tools::GFF;

     my $coord_start = 12345;
     my $coord_end  = 67890;

     # specify input via -fh or -file
     my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version =>  
2);
     my $feature;
     # loop over the input stream
     while($feature = $gffio->next_feature()) {
	 if ($coord_start <= $feature->start && $coord_end >= $feature->end) {
	 	print $feature->gff_string;
	}
     }
     $gffio->close();

Barry

On Oct 22, 2007, at 4:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From barry.moore at genetics.utah.edu  Tue Oct 23 00:37:07 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:37:07 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <C837CA5E-4E55-4B23-8451-27E74426BB52@genetics.utah.edu>

Oh yeah, much better option if you've got a database running.  Look  
at the docs for the modules Chris suggested.  Something like:

my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                  -dsn     =>  
'dbi:mysql:test',
                                                  -write   => 1 );
# load an entire GFF3 file, using the GFF3 loader...
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    =>  
$db,
							   -verbose  => 1,
							   -fast     => 1);

$loader->load('./my_genome.gff3');

@features = $db->get_features_by_location(-seq_id=>'Chr1',- 
start=>4000,-end=>600000);

Barry

On Oct 22, 2007, at 6:43 PM, Chris Fields wrote:

>
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
>
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files
>> from the
>> same genome release. I wonder how I can extract all overlapping
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
>
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will
> depend on the GFF version of the data you have.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sdavis2 at mail.nih.gov  Tue Oct 23 07:00:12 2007
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 23 Oct 2007 07:00:12 -0400
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <471DD43C.8060203@mail.nih.gov>

Chris Fields wrote:
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
> 
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired  
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files  
>> from the
>> same genome release. I wonder how I can extract all overlapping  
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with  
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
> 
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
> depend on the GFF version of the data you have.
> 
> chris

Not a bioperl solution, but still a very cool application, see:

http://main.g2.bx.psu.edu/

It is web-based and allows for set operations (intersection, union,
etc.) on genomic coordinates.  If you have two sets of regions of
interest, you can then ask (very quickly) for all regions that overlap,
contain, are distinct, etc.

Sean


From forrest_zhang at 163.com  Tue Oct 23 23:27:00 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Wed, 24 Oct 2007 11:27:00 +0800
Subject: [Bioperl-l]
	=?gb2312?B?tPC4tDogW0Jpb3BlcmwtbF0gbG9hZF9zZXFkYXRhYmFzZS5wbCBlcnJvcg==?=
In-Reply-To: <FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
Message-ID: <000101c815ed$bdafb2e0$390f18a0$@com>

Dear Chris:
	What's the result of test? In my computer, the test haven't been
passed.

Forrest Zhang

-----????????-----
??????: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] ???? Chris Fields
????????: 2007??9??29?? 6:03
??????: Forrest Zhang
????: bioperl-l at bioperl.org BioPerl
????: Re: [Bioperl-l] load_seqdatabase.pl error

Okay, fixed the recursion (extra copy of a BasePersistentAdaptor  
module I was working which tripped it, so nothing in CVS).

Forrest, I get all tests passing.  I used a database without taxonomy  
loaded with bioperl-db and bioperl from cvs and it worked w/o  
problems.  I'll try working with your sequence when I have time this  
weekend.

chris

On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:

> I'm actually getting some odd recursion issues again; not sure what's
> causing it, but a reinstall of both bioperl and bioperl-db fixed it
> last time.  It may be related to the rollback, just not sure yet.
>
> I'll try tracking it down if it persists (bad pun).
>
> t/04swiss....ok 3/52
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
> t/04swiss....ok
> All tests successful.
> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
> CPU)
>
> The specific error under verbose running is:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:680
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:658
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:252
> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> PrimarySeqAdaptor.pm:229
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/src/
> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:213
> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
> STACK toplevel t/04swiss.t:37
> ---------------------------------------------------
>
>
> chris
>
> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>
>> Chris let me know if you get stumped. I'm surprised that the special
>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>> assign ranks to them? I thought I filter them out. Needs to be looked
>> into too.), but at any rate I don't understand why they aren't being
>> accepted.
>>
>> Also, maybe we need a more verbose output here - Forrest, can you run
>> this with adding a --printerror argument. (I'm embarrassed to find
>> that this doesn't seem to be documented. Sigh.)
>>
>> 	-hilmar
>>
>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>
>>> If this is occurring using bioperl from CVS then I'll try taking a
>>> look at it.
>>>
>>> chris
>>>
>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>
>>>> Hilmar,
>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I
>>>> was
>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>> | rosids
>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>> Euphyllophyta |
>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>> ---------------------------------------------------
>>>> Could not store Q40784:
>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>> by unique
>>>> key
>>>> STACK: Error::throw
>>>> STACK: Bio::Root::Root::throw
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:206
>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:244
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:169
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:251
>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:271
>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>> -----------------------------------------------------------
>>>> Sigh~~~~~~
>>>>
>>>> Forrest Zhang
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>> Lapp
>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>> To: Forrest
>>>> Cc: bioperl-l at bioperl.org
>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>
>>>> Forrest,
>>>>
>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>> the
>>>> code will try to use it to look up species and their lineage,  
>>>> rather
>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>> sequence record.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>
>>>>> Hi, all
>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>> swissport data.
>>>>> But the programe show some error as below:
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>> mysql
>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>> Could not store Q6DAH5:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>> subsp.
>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>> Pectobacterium |
>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>> Proteobacteria | Bacteria')
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>> STACK: Bio::Species::classification
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:552
>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:1305
>>>>> STACK:  
>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:973
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:852
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:182
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: load_seqdatabase.pl:620
>>>>> -----------------------------------------------------------
>>>>>
>>>>>  at load_seqdatabase.pl line 633
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>
>>>>> How can I solve it, please help me, Thank you.
>>>>>
>>>>> Thanks
>>>>> Forrest zhang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From cjfields at uiuc.edu  Wed Oct 24 00:21:00 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 23 Oct 2007 23:21:00 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000101c815ed$bdafb2e0$390f18a0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
Message-ID: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From martin.burkert at uni-bielefeld.de  Wed Oct 24 08:25:13 2007
From: martin.burkert at uni-bielefeld.de (Martin Burkert)
Date: Wed, 24 Oct 2007 14:25:13 +0200
Subject: [Bioperl-l] Problems parsing Glimmer output
Message-ID: <471F39A9.6050909@uni-bielefeld.de>

Hello,

i can't figure out why my Glimmer files can not be parsed from
Bio::Tools::Glimmer.

---- pbglimmer.pl ----
use strict;
use Bio::Tools::Glimmer;

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
my $predictionCount = 0;

while(my $gene = $parser->next_prediction()) {
	$predictionCount++;
	print $predictionCount.	':' .$gene->display_name().
				', '.$gene->start().
				', '.$gene->stop()."\n";
}
print "Total predictions: ".$predictionCount;

---- pb4.predict ----
>pb4
orf00001     1022     1138  +2     0.90
orf00002     1655     1131  -3     2.77
orf00003     1638     2390  +3     3.59
orf00004     3176     3472  +2     0.30
orf00006     4395     5561  +3     2.96
orf00008     5576     8719  +2     2.98
orf00012     8725    10152  +1     2.96
orf00013    10906    11019  +1     0.21
orf00014    12188    12292  +2     2.41
orf00017    12518    14077  +2     2.97
orf00019    15356    15246  -3     2.21
orf00020    17864    17748  -3     0.23
orf00021    18153    18037  -1     0.32
orf00023    19253    19462  +2     0.48
orf00025    21018    20902  -1     0.23
orf00027    21658    24708  +1     2.92
orf00030    26115    24898  -1     2.96
orf00031    26414    26112  -3     3.21
orf00032    28015    28473  +1     3.54
orf00033    28044    27223  -1     2.85
orf00037    30137    30033  -3     2.80
orf00041    30183    33152  +3     2.98
orf00045    34860    33637  -1     2.96
orf00047    35142    34909  -1     2.54
orf00050    36606    36737  +3     1.44
orf00052    37616    37789  +2     2.23
orf00054    37786    40344  +1     2.98
orf00056    40624    40505  -2     0.79
orf00057    42508    43890  +1     2.96
orf00059    44183    44680  +2     1.49
orf00060    44705    44908  +2     0.05
orf00063    44920    46632  +1     2.97
orf00068    47296    47865  +1     0.39
orf00071    47953    49134  +1     2.90
orf00072    49208    49318  +2     1.15
orf00074    51139    51270  +1     1.16
orf00083    58362    53767  -1     2.99
orf00088    60846    58783  -1     2.98
orf00090    63298    61394  -2     2.97
orf00093    65553    63295  -1     2.98
orf00095    65959    65588  -2     1.13
orf00096    66185    65964  -3     2.98
orf00098    66610    66933  +1     0.11
orf00099    67371    67658  +3     0.27
orf00102    71019    68134  -1     2.98
orf00103    71825    72628  +2     2.71
orf00105    75062    73740  -3     2.96
orf00106    75817    76221  +1     0.73
orf00109    78206    76734  -3     2.92
orf00113      198    79299  -3     4.22


The program always outputs "Total predictions: 0".

I also tried to force the parsing format to be just 'Glimmer'
(prokaryotic) and not 'GlimmerHmm'  with:

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', -format =>
'Glimmer');

The pb4.predict was generated by glimmer3.02. I also tried to parse an
output from glimmer2.X, but without success.

Printing $parser with Data::Dumper outputs:

$VAR1 = bless( {
                 '_file' => 'pb4.predict',
                 '_preds_parsed' => 0,
                 '_analysis_date' => undef,
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_analysis_sbjct' => undef,
                 '_analysis_progVersion' => undef,
                 '_flush_on_write' => 1,
                 '_analysis_prog' => undef,
                 '_filehandle' => \*Symbol::GEN0,
                 '_analysis_query' => undef,
                 '_root_verbose' => 0,
                 '_preds' => []
               }, 'Bio::Tools::Glimmer' );

My installation:

Perl v5.8.8 built for MSWin32-x86-multi-thread
Bioperl 1.4

Thank you.

-- 
Viele Gr??e,

MARTIN BURKERT
mailto:martin.burkert at uni-bielefeld.de


From cjfields at uiuc.edu  Wed Oct 24 09:38:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 08:38:03 -0500
Subject: [Bioperl-l] Problems parsing Glimmer output
In-Reply-To: <471F39A9.6050909@uni-bielefeld.de>
References: <471F39A9.6050909@uni-bielefeld.de>
Message-ID: <37465B90-4A03-4A53-B4EF-BCC8296BAE2C@uiuc.edu>

Update to bioperl-live (from CVS).  The Glimmer parser was recently  
revised by Mark Johnson for Glimmer3 output.  I added a few fixes  
myself to correct start/end issues.

chris

On Oct 24, 2007, at 7:25 AM, Martin Burkert wrote:

> Hello,
>
> i can't figure out why my Glimmer files can not be parsed from
> Bio::Tools::Glimmer.
>
> ---- pbglimmer.pl ----
> use strict;
> use Bio::Tools::Glimmer;
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
> my $predictionCount = 0;
>
> while(my $gene = $parser->next_prediction()) {
> 	$predictionCount++;
> 	print $predictionCount.	':' .$gene->display_name().
> 				', '.$gene->start().
> 				', '.$gene->stop()."\n";
> }
> print "Total predictions: ".$predictionCount;
>
> ---- pb4.predict ----
>> pb4
> orf00001     1022     1138  +2     0.90
> orf00002     1655     1131  -3     2.77
> orf00003     1638     2390  +3     3.59
> orf00004     3176     3472  +2     0.30
> orf00006     4395     5561  +3     2.96
> orf00008     5576     8719  +2     2.98
> orf00012     8725    10152  +1     2.96
> orf00013    10906    11019  +1     0.21
> orf00014    12188    12292  +2     2.41
> orf00017    12518    14077  +2     2.97
> orf00019    15356    15246  -3     2.21
> orf00020    17864    17748  -3     0.23
> orf00021    18153    18037  -1     0.32
> orf00023    19253    19462  +2     0.48
> orf00025    21018    20902  -1     0.23
> orf00027    21658    24708  +1     2.92
> orf00030    26115    24898  -1     2.96
> orf00031    26414    26112  -3     3.21
> orf00032    28015    28473  +1     3.54
> orf00033    28044    27223  -1     2.85
> orf00037    30137    30033  -3     2.80
> orf00041    30183    33152  +3     2.98
> orf00045    34860    33637  -1     2.96
> orf00047    35142    34909  -1     2.54
> orf00050    36606    36737  +3     1.44
> orf00052    37616    37789  +2     2.23
> orf00054    37786    40344  +1     2.98
> orf00056    40624    40505  -2     0.79
> orf00057    42508    43890  +1     2.96
> orf00059    44183    44680  +2     1.49
> orf00060    44705    44908  +2     0.05
> orf00063    44920    46632  +1     2.97
> orf00068    47296    47865  +1     0.39
> orf00071    47953    49134  +1     2.90
> orf00072    49208    49318  +2     1.15
> orf00074    51139    51270  +1     1.16
> orf00083    58362    53767  -1     2.99
> orf00088    60846    58783  -1     2.98
> orf00090    63298    61394  -2     2.97
> orf00093    65553    63295  -1     2.98
> orf00095    65959    65588  -2     1.13
> orf00096    66185    65964  -3     2.98
> orf00098    66610    66933  +1     0.11
> orf00099    67371    67658  +3     0.27
> orf00102    71019    68134  -1     2.98
> orf00103    71825    72628  +2     2.71
> orf00105    75062    73740  -3     2.96
> orf00106    75817    76221  +1     0.73
> orf00109    78206    76734  -3     2.92
> orf00113      198    79299  -3     4.22
>
>
> The program always outputs "Total predictions: 0".
>
> I also tried to force the parsing format to be just 'Glimmer'
> (prokaryotic) and not 'GlimmerHmm'  with:
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', - 
> format =>
> 'Glimmer');
>
> The pb4.predict was generated by glimmer3.02. I also tried to parse an
> output from glimmer2.X, but without success.
>
> Printing $parser with Data::Dumper outputs:
>
> $VAR1 = bless( {
>                  '_file' => 'pb4.predict',
>                  '_preds_parsed' => 0,
>                  '_analysis_date' => undef,
>                  '_root_cleanup_methods' => [
>                                               sub { "DUMMY" }
>                                             ],
>                  '_analysis_sbjct' => undef,
>                  '_analysis_progVersion' => undef,
>                  '_flush_on_write' => 1,
>                  '_analysis_prog' => undef,
>                  '_filehandle' => \*Symbol::GEN0,
>                  '_analysis_query' => undef,
>                  '_root_verbose' => 0,
>                  '_preds' => []
>                }, 'Bio::Tools::Glimmer' );
>
> My installation:
>
> Perl v5.8.8 built for MSWin32-x86-multi-thread
> Bioperl 1.4
>
> Thank you.
>
> -- 
> Viele Gr??e,
>
> MARTIN BURKERT
> mailto:martin.burkert at uni-bielefeld.de
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From forrest_zhang at 163.com  Wed Oct 24 12:00:24 2007
From: forrest_zhang at 163.com (Forrest)
Date: Thu, 25 Oct 2007 00:00:24 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
Message-ID: <000001c81657$0067fd40$0137f7c0$@com>

Dear Chris,
	I was using different swissprot data all of the have some error about the taxon.
Maybe I should re-install bioperl and biosql. Could you give me the install protocol 
what you used.


Forrest Zhang

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Wednesday, October 24, 2007 12:21 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign









From cjfields at uiuc.edu  Wed Oct 24 12:47:45 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 11:47:45 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000001c81657$0067fd40$0137f7c0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
	<000001c81657$0067fd40$0137f7c0$@com>
Message-ID: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Wed Oct 24 14:56:55 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 11:56:55 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
Message-ID: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>

Has anyone else encountered a problem parsing wu-blast output with
Bio::SearchIO ?

The ->next_hit method first returns the "unfiltered+1" sequence; that is,
the plus strand representation of the query sequence that is listed (before
the minus strand) before the summary of hits and e-values.

Then, the next time the next_hit method is called, it returns the second hit
on the list.

The only caveat to my "bug" report here is that I was searching a database
that included the query sequence, so the first hit was identical to the
query (and maybe somehow retained the "unfiltered+1" tag?) ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 15:39:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 12:39:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
Message-ID: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>

I'm relatively new to both objects and bioperl, and I'm having trouble
finding documentation on what values an attribute can have.  For example, in
Bio::Assembly::Contig the example script invokes the 'new' method with an
example filename and assigns the -format attribute (I think that's the
correct terminology) a value of 'phrap' ...

now, I'm wanting to process contig output from the cap3 program, so I'll try
assigning 'cap3' to the -format attribute (haven't tried yet so I don't know
if it will work), but where do I look for a complete list of what possible
values I can use?  I can't find it via either the Pdoc or CPAN documentation
links from the bioperl wiki pages.  Any help would be appreciated ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From David.Messina at sbc.su.se  Wed Oct 24 16:35:48 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:35:48 +0200
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
Message-ID: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>

Hi Joseph,

Could you post the blast report that's giving you trouble? And also could
you tell us what version of WU-BLAST you're running and what version of
BioPerl you're using?

I'd like to try and reproduce your problem.

Thanks,
Dave


From David.Messina at sbc.su.se  Wed Oct 24 16:59:12 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:59:12 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
Message-ID: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>

I couldn't find the formats for Bio::Assembly::Contig in any of the
documentation either.

In situations like these, I poke around in the code for methods that deal
with whatever I'm looking for. In this case, I went to the pdoc for
Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
_guess_format method:

sub _guess_format {

   my $class = shift;
   my $arg   = shift;


return unless defined($arg);
   return 'ace'
 if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap'
 if ($arg =~ /\.phrap\.out$/i);

}

So it looks like 'ace' and 'phrap' are the two assembly formats that are
supported.

The other place where the question of formats often comes up is with
sequence formats. Those are better documented, in the SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats


Dave


From florent.angly at gmail.com  Wed Oct 24 17:25:25 2007
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 24 Oct 2007 14:25:25 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
Message-ID: <471FB845.2080201@gmail.com>

Dave,
Have a look in Bio::Assembly::Contig::IO, that's where all the supported 
assembly input/output formats are located. It's convenient to use the 
BioPerl Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query 
<http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query>
'ace' and 'phrap' are the supported formats. The 'tigr' assembler format 
has been added in the CVS version recently too.
Florent


Dave Messina wrote:
> I couldn't find the formats for Bio::Assembly::Contig in any of the
> documentation either.
>
> In situations like these, I poke around in the code for methods that deal
> with whatever I'm looking for. In this case, I went to the pdoc for
> Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> _guess_format method:
>
> sub _guess_format {
>
>    my $class = shift;
>    my $arg   = shift;
>
>
> return unless defined($arg);
>    return 'ace'
>  if ($arg =~ /\.ace\.\d+$/i);
>    return 'phrap'
>  if ($arg =~ /\.phrap\.out$/i);
>
> }
>
> So it looks like 'ace' and 'phrap' are the two assembly formats that are
> supported.
>
> The other place where the question of formats often comes up is with
> sequence formats. Those are better documented, in the SeqIO HOWTO:
>
> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
>
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From joseph.fass at gmail.com  Wed Oct 24 17:43:08 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:43:08 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
Message-ID: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 17:45:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:45:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <471FB845.2080201@gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
Message-ID: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>

thanks, both of you!

On 10/24/07, Florent Angly <florent.angly at gmail.com> wrote:
>
> Dave,
> Have a look in Bio::Assembly::Contig::IO, that's where all the supported
> assembly input/output formats are located. It's convenient to use the
> BioPerl Deobfuscator:
>
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> <
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> >
> 'ace' and 'phrap' are the supported formats. The 'tigr' assembler format
> has been added in the CVS version recently too.
> Florent
>
>
> Dave Messina wrote:
> > I couldn't find the formats for Bio::Assembly::Contig in any of the
> > documentation either.
> >
> > In situations like these, I poke around in the code for methods that
> deal
> > with whatever I'm looking for. In this case, I went to the pdoc for
> > Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> > Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> > _guess_format method:
> >
> > sub _guess_format {
> >
> >    my $class = shift;
> >    my $arg   = shift;
> >
> >
> > return unless defined($arg);
> >    return 'ace'
> >  if ($arg =~ /\.ace\.\d+$/i);
> >    return 'phrap'
> >  if ($arg =~ /\.phrap\.out$/i);
> >
> > }
> >
> > So it looks like 'ace' and 'phrap' are the two assembly formats that are
> > supported.
> >
> > The other place where the question of formats often comes up is with
> > sequence formats. Those are better documented, in the SeqIO HOWTO:
> >
> > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
> >
> >
> > Dave
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From jason at bioperl.org  Wed Oct 24 18:18:09 2007
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Oct 2007 18:18:09 -0400
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
Message-ID: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>

I'm pretty sure we fixed this problem after 1.4 so current "unstable"  
code a try first and let us know nif that solves the problem.

also - copy+paste of BLAST files on mailing list doesn't work so well  
so either a link to  URL or posting the file in a bugzilla bug  
(bugzilla.open-bio.org) make it easier for someone to try this at home.

-jason
On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:

> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what  
> you find.
>
> Joe
>
[SNIP]
--
Jason Stajich
jason at bioperl.org



From joseph.fass at gmail.com  Wed Oct 24 18:53:41 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 15:53:41 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
Message-ID: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>

I just updated to 1.5.2 via CPAN, and verified that that worked, and re-ran
my code ... same problem: it's still picking up "unfiltered+1" as the first
->next_hit result from wu-blast output.  This is a different issue than the
fixed bug (ID: 1649) I just found on bugzilla; that bug concerned the hit
sequences.  I'll post a report on bugzilla along with some files to try it
with (please let me know if what I upload there is incomplete).

Thanks for the quick attention, all!

~joe




On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I'm pretty sure we fixed this problem after 1.4 so current "unstable" code
> a try first and let us know nif that solves the problem.
>
> also - copy+paste of BLAST files on mailing list doesn't work so well so
> either a link to  URL or posting the file in a bugzilla bug (
> bugzilla.open-bio.org) make it easier for someone to try this at home.
>
> -jason
> On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
>
> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what you find.
>
> Joe
>
> [SNIP]
> --
> Jason Stajich
> jason at bioperl.org
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 19:25:50 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 16:25:50 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
	<195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
Message-ID: <195e25cb0710241625o8b92fe0y65925025fc9144c0@mail.gmail.com>

There's a script and sample input file to demonstrate this in Bugzilla, bug#
2388 <http://bugzilla.open-bio.org/show_bug.cgi?id=2388>

~joe



On 10/24/07, Joseph Fass <joseph.fass at gmail.com> wrote:
>
> I just updated to 1.5.2 via CPAN, and verified that that worked, and
> re-ran my code ... same problem: it's still picking up "unfiltered+1" as the
> first ->next_hit result from wu-blast output.  This is a different issue
> than the fixed bug (ID: 1649) I just found on bugzilla; that bug concerned
> the hit sequences.  I'll post a report on bugzilla along with some files to
> try it with (please let me know if what I upload there is incomplete).
>
> Thanks for the quick attention, all!
>
> ~joe
>
>
>
>
> On 10/24/07, Jason Stajich <jason at bioperl.org > wrote:
> >
> >  I'm pretty sure we fixed this problem after 1.4 so current "unstable"
> > code a try first and let us know nif that solves the problem.
> >
> > also - copy+paste of BLAST files on mailing list doesn't work so well so
> > either a link to  URL or posting the file in a bugzilla bug (
> > bugzilla.open-bio.org) make it easier for someone to try this at home.
> >
> > -jason
> > On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
> >
> > Hi Dave,
> >
> > here's my code, followed by a sample wu-blast report (below).
> > I'm using bioperl version 1.4
> > Thanks for looking into it, and I'd be very curious to know what you
> > find.
> >
> > Joe
> >
> > [SNIP]
> > --
> > Jason Stajich
> > jason at bioperl.org
> >
> >
>
>
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
>



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From simona_bazzocchi at yahoo.it  Wed Oct 24 23:46:53 2007
From: simona_bazzocchi at yahoo.it (simona bazzocchi)
Date: Thu, 25 Oct 2007 05:46:53 +0200 (CEST)
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
Message-ID: <594278.55585.qm@web27710.mail.ukl.yahoo.com>

Hi all, 
I'd like to parse my blast file to outuput in a html file filtering on percent identity, (75% identical or better). So I've just copied and pasted to create my perl file.
I launched this command:
perl searchIO.pl blast_file.txt
But it returned this error: "t
Bareword found where operator expected at searchIO.pl line 26, near "->length E"
        (Missing operator before E?)
syntax error at searchIO.pl line 26, near "->length E"
syntax error at searchIO.pl line 30, near "<gt"
Execution of searchIO.pl aborted due to compilation errors."
Here below you can find searchIO.pl
thanks



#!/usr/bin/perl
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);


# to filter your output
my $MinLength = 100; # need a variable with scope outside the method
sub hsp_filter { 
      my $hsp = shift;
      return 1 if $hsp->length('total') > $MinLength;
  }
sub result_filter { 
      my $result = shift;
      return $hsp->num_hits > 0;
  }

  sub hit_filter { 
      my $hit = shift;
      return $hit->length E<gt> 100; # test if length of the hit sequence
                                     # long enough    
  }
  my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HIT' =E<gt> \&hit_filter }  
      );


my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);

# can also set the filter via the writer object
$writer->filter('RESULT', \&result_filter);


 		
---------------------------------
Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3


From torsten.seemann at infotech.monash.edu.au  Thu Oct 25 00:20:13 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 25 Oct 2007 14:20:13 +1000
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
In-Reply-To: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
References: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
Message-ID: <a79f6a4b0710242120g13e9a55dq710d004745b7e68b@mail.gmail.com>

Simona

> So I've just copied and pasted to create my perl file.
> syntax error at searchIO.pl line 26, near "->length E"
> syntax error at searchIO.pl line 30, near "<gt"
>   sub hit_filter {
>       my $hit = shift;
>       return $hit->length E<gt> 100; # test if length of the hit sequence

You have a Perl syntax error due to cutting and pasting from code in
PerlDoc format. It should read:

  return $hit->length > 100;  # not "E<gt>

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From forrest_zhang at 163.com  Thu Oct 25 02:35:19 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 14:35:19 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>	<000101c815ed$bdafb2e0$390f18a0$@com>	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>	<000001c81657$0067fd40$0137f7c0$@com>
	<D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
Message-ID: <000001c816d1$38d70250$aa8506f0$@com>

Dear Chris,
	I try you protocol, but the taxonomy problem is still existent. And the new problem about " The table 'comment' is full" is coming.
The error example like below:
	
Could not store Q6DA52: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp. atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium | Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria | Proteobacteria | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Species::classification /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("-!- CATALYTIC ACTIVITY: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
-!- PATHWAY: Metabolic intermediate biosynthesis; chorismate
    biosynthesis; chorismate from D-erythrose 4-phosphate and PEP:
    step 3/7.
-!- PATHWAY: Context: Aromatic amino acids biosynthesis.
-!- SUBUNIT: Homodimer (By similarity).
-!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
","1") FKs (12352)
The table 'comment' is full
---------------------------------------------------
Could not store Q723F8: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Comment) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

 at load_seqdatabase.pl line 643
	

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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Bioperl-l at lists.open-bio.org
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From forrest_zhang at 163.com  Thu Oct 25 04:16:34 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:34 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000101c816df$600c5c40$202514c0$@com>



-----Original Message-----
From: Forrest Zhang [mailto:forrest_zhang at 163.com] 
Sent: Thursday, October 25, 2007 4:16 PM
To: 'Chris Fields'
Subject: RE: [Bioperl-l] ??: load_seqdatabase.pl error

Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:16:58 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:58 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000201c816df$6c956fb0$45c04f10$@com>


Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 04:06:27 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:06:27 +0800
Subject: [Bioperl-l] FW:  problem parsing WU-blast output
Message-ID: <000201c816dd$f5c5e5f0$e151b1d0$@com>

Hi, Joe
	My this script(wublast.pl) maybe is useful for you. You can get the
subsequence by using query range and hit range.
	The script is below, and the file name is wublast.pl.

use strict;
use Bio::SearchIO;

die "Usage:perl wublast <File>\n"
      unless @ARGV==1;
my $inputfile = $ARGV[0];
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => $inputfile);
print "query","\t","hit","\t","total_length","\t",
      "query_lenth","\t","hit_length","\t",
      "percent_identity","\t","score","\t","evalue","\t","rank",
      "\t","query range","\t","hit range","\n";

while( my $result = $in->next_result ) {
    my $image=$result->query_name;

    while( my $hit = $result->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {

	print $image,"\t",$hit->name,"\t",$hsp->length('total'),"\t",
	      $hsp->length('query'),"\t",$hsp->length('hit'),"\t",
	    $hsp->percent_identity,"\t",$hsp->score,"\t",$hsp->evalue,"\t",
 
$hsp->rank,"\t",$hsp->start('query'),",",$hsp->end('query'),"\t",
            $hsp->start('hit'),",",$hsp->end('hit'),"\n";

	}  
    }
}


Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
Sent: Thursday, October 25, 2007 5:43 AM
To: Dave Messina
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] problem parsing WU-blast output

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
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From David.Messina at sbc.su.se  Thu Oct 25 04:52:14 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 25 Oct 2007 10:52:14 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
	<195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
Message-ID: <628aabb70710250152l6218fa1as78b9ab23731f1530@mail.gmail.com>

Ah, wonderful -- thanks Florent! Man, that Deobfuscator sure is useful. :)

Dave


From cjfields at uiuc.edu  Thu Oct 25 09:07:23 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 25 Oct 2007 08:07:23 -0500
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
 =?utf-8?q?=2Epl_error?=
In-Reply-To: <000201c816df$6c956fb0$45c04f10$@com>
References: <000201c816df$6c956fb0$45c04f10$@com>
Message-ID: <F7F03A54-34F1-45A8-8141-7E785F0FB555@uiuc.edu>

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Thu Oct 25 17:50:02 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Thu, 25 Oct 2007 14:50:02 -0700
Subject: [Bioperl-l] what's the optimal way to search a fasta file for
	matching ID's?
Message-ID: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>

I would appreciate any advice, big or small, on this ...

I've got a decent-sized database ... 90,000 sequences or so in a single
fasta-format file.  Then, I've got sequence ID's from that database that
show up in blast reports.  I want to collect those ID's and their sequences
(for the purposes of exploring possible contigs).  Since the blast report
only includes sub-sequences (from alignments) of my sequences, I want to
parse the report, then match each hit ID against an ID in the database, so I
can pull out its full sequence.  Is there a faster way to do this than
opening the database file each time I have a new hit ID, so I can search it
from beginning to end?  If I push each sequence onto a list or hash, it's
liable to chew up a lot of RAM, I'm guessing.  Any suggestions?

Thanks in advance,
~joe

-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From MEC at stowers-institute.org  Thu Oct 25 18:17:04 2007
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Thu, 25 Oct 2007 17:17:04 -0500
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
Message-ID: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>

If you have the fasta database already indexed for blast searching, then
you should use fastacmd, which comes with the blast package, for
extracting (sub)sequences based on ID (and indices).

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
> Sent: Thursday, October 25, 2007 4:50 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] what's the optimal way to search a fasta 
> file formatching ID's?
> 
> I would appreciate any advice, big or small, on this ...
> 
> I've got a decent-sized database ... 90,000 sequences or so 
> in a single fasta-format file.  Then, I've got sequence ID's 
> from that database that show up in blast reports.  I want to 
> collect those ID's and their sequences (for the purposes of 
> exploring possible contigs).  Since the blast report only 
> includes sub-sequences (from alignments) of my sequences, I 
> want to parse the report, then match each hit ID against an 
> ID in the database, so I can pull out its full sequence.  Is 
> there a faster way to do this than opening the database file 
> each time I have a new hit ID, so I can search it from 
> beginning to end?  If I push each sequence onto a list or 
> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any 
> suggestions?
> 
> Thanks in advance,
> ~joe
> 
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From jason at bioperl.org  Fri Oct 26 00:57:52 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 00:57:52 -0400
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
	<CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
Message-ID: <8F627E8A-EE44-4953-9A90-F82BC69C15D9@bioperl.org>

or see Bio::DB::Fasta if you want a bioperl soln.

On Oct 25, 2007, at 6:17 PM, Cook, Malcolm wrote:

> If you have the fasta database already indexed for blast searching,  
> then
> you should use fastacmd, which comes with the blast package, for
> extracting (sub)sequences based on ID (and indices).
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph  
>> Fass
>> Sent: Thursday, October 25, 2007 4:50 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] what's the optimal way to search a fasta
>> file formatching ID's?
>>
>> I would appreciate any advice, big or small, on this ...
>>
>> I've got a decent-sized database ... 90,000 sequences or so
>> in a single fasta-format file.  Then, I've got sequence ID's
>> from that database that show up in blast reports.  I want to
>> collect those ID's and their sequences (for the purposes of
>> exploring possible contigs).  Since the blast report only
>> includes sub-sequences (from alignments) of my sequences, I
>> want to parse the report, then match each hit ID against an
>> ID in the database, so I can pull out its full sequence.  Is
>> there a faster way to do this than opening the database file
>> each time I have a new hit ID, so I can search it from
>> beginning to end?  If I push each sequence onto a list or
>> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any
>> suggestions?
>>
>> Thanks in advance,
>> ~joe
>>
>> --
>> Joseph Fass
>> joseph.fass at gmail.com  ||  joefass at hotmail.com
>> 970.227.5928 (c)  ||  530.754.7978 (w)
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From forrest_zhang at 163.com  Fri Oct 26 04:21:56 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Fri, 26 Oct 2007 16:21:56 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICBGVzogIOetlOWkjTogIGxvYWRfc2VxZGF0?=
	=?utf-8?q?abase=2Epl_error?=
Message-ID: <000701c817a9$4733fb40$d59bf1c0$@com>

Chris,
	I am using --safe to loading sequence. Maybe I would load species data one by one.
It seem be OK now.

	Thanks for your help so much Chris.

Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 9:07 PM
To: Forrest Zhang; BioSQL
Cc: bioperl-l at bioperl.org BioPerl
Subject: Re: [Bioperl-l] FW: ??: load_seqdatabase.pl error

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From avilella at gmail.com  Fri Oct 26 05:33:09 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 10:33:09 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
Message-ID: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>

Hi all,

I was looking at the Gumby runnable, which is pretty cool. But I got an
error
when running the tests (see below). Can other people reproduce this?

It seems to me that the runnable is expecting a tree object, not the
filename for a tree...

avilella at magneto:~/bioperl/vanilla/bioperl-run$ perl t/Gumby.t
1..124
ok 1 - use Bio::Tools::Run::Phylo::Gumby;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::TreeIO;
ok 4 - use Bio::DB::Taxonomy;
ok 5 - use Bio::Tools::GFF;
ok 6 - Found input alignment file
ok 7 - Found input tree file
ok 8 - Found input gff file
ok 9 - The object isa Bio::Tools::Run::Phylo::Gumby
ok 10 - has a created method not in args
ok 11 - quiet was set
ok 12 - program_dir returned correct default
ok 13 - Correct exe default name
Can't call method "value" without a package or object reference at
/home/avilella/bioperl/vanilla/bioperl-live/Bio/Tools/Phylo/Gumby.pm line
136, <GEN2> line 6.
# Looks like you planned 124 tests but only ran 13.
# Looks like your test died just after 13.


From bix at sendu.me.uk  Fri Oct 26 06:10:41 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 11:10:41 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <4721BD21.9060805@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got
> an error when running the tests (see below). Can other people
> reproduce this?
> 
> It seems to me that the runnable is expecting a tree object, not the 
> filename for a tree...

No, most likely this is another thing broken by the SeqFeature changes.
I'm going to go ahead and try out some of my proposals in the
'Bio::SeqFeature::Annotated API change' thread.


From Rohit.Ghai at mikrobio.med.uni-giessen.de  Fri Oct 26 07:30:43 2007
From: Rohit.Ghai at mikrobio.med.uni-giessen.de (Rohit Ghai)
Date: Fri, 26 Oct 2007 13:30:43 +0200
Subject: [Bioperl-l] cannot run emboss from bioperl on windows
Message-ID: <4721CFE3.4060805@mikrobio.med.uni-giessen.de>

Dear all,

I have emboss installed on a windows machine. (Embosswin). I can run
this from the dos command line and the path is present. However, when I 
try to call
an emboss application from bioperl I get a "Application not found error"


   my $f = Bio::Factory::EMBOSS->new();
   # get an EMBOSS application  object from the factory
   my $fuzznuc = $f->program('fuzznuc');
     $fuzznuc->run(
                   { -sequence  => $infile,
                         -pattern   => $motif,
                        -outfile   => $outfile                       
               });
  gives the following error

-------------------- WARNING ---------------------
MSG: Application [fuzznuc] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at searchPatterns.pl line 
102.

Can somebody help me fix this ?

best regards
Rohit

-- 

Dr. Rohit Ghai
Institute of Medical Microbiology
Faculty of Medicine
Justus-Liebig University
Frankfurter Strasse 107
35392 - Giessen
GERMANY

Tel  :	0049 (0)641-9946413
Fax  :	0049 (0)641-9946409
Email:  Rohit.Ghai at mikrobio.med.uni-giessen.de



From cjfields at uiuc.edu  Fri Oct 26 08:51:26 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 07:51:26 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <4721BD21.9060805@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<4721BD21.9060805@sendu.me.uk>
Message-ID: <D2A5B64D-9534-4421-A6B5-6EA607F3D649@uiuc.edu>


On Oct 26, 2007, at 5:10 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I got
>> an error when running the tests (see below). Can other people
>> reproduce this?
>>
>> It seems to me that the runnable is expecting a tree object, not the
>> filename for a tree...
>
> No, most likely this is another thing broken by the SeqFeature  
> changes.
> I'm going to go ahead and try out some of my proposals in the
> 'Bio::SeqFeature::Annotated API change' thread.

I was able to repeat it on my end.  If you have a fix for it  
involving B::SF::A then definitely go ahead.

chris


From bix at sendu.me.uk  Fri Oct 26 10:48:27 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 15:48:27 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
Message-ID: <4721FE3B.2080507@sendu.me.uk>

Hilmar Lapp wrote:
> 
> On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:
> 
>> seq_id()
>>   Usage   : $obj->seq_id($newval)
>>   Function: holds a string corresponding to the unique
>>             seq_id of the sequence underlying the feature
>>             (e.g. database accession or primary key).
>>   Returns : a Bio::Annotation::SimpleValue object representing the
>>             seq_id.
> 
> type() and source() should be ontology-typed in a TypedSeqFeatureI (and 
> therefore be instances of Bio::Annotation::OntologyTerm, not 
> Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't 
> understand what the benefit of typing seq_id() any stronger than a 
> string would be.

Would there be any problem with having source() return a string, but 
still allow access to the OntologyTerm object via 
get_Annotations('source')? (Ditto with type?)

I think that's the way I'm going to go for now.


From bix at sendu.me.uk  Fri Oct 26 12:52:59 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:52:59 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
 problem with Genewise.t
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <47221B6B.5000604@sendu.me.uk>

Sendu Bala wrote:
> Following Chris's changes to SF::Annotated et al., lots of existing user 
> code breaks. Also, at least some Bioperl code breaks, notably 
> Bio::DB::SeqFeature::Store, which in mysql mode calls 
> _get_location_and_bin() which calls $feature->seq_id which ends up 
> storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
> the database, instead of an actual sequence id (which completely breaks 
> searching by seq_id).
> 
> I propose its API be changed to be more consistent with 
> Bio::SeqFeatureI, eg. instead of:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> we have:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> This would apply to seq_id(), name(), type(), source(), phase() and 
> frame(). Internally the implementation could store the string value in a 
> SimpleValue object.

I've now done this except for type() and source(), since these aren't in 
Generic. Instead we have source_tag() and primary_tag() accepting and 
returning strings.

source() and type() return objects as before, but now only accept 
objects when setting for consistency.


One test that pops up with an error is t/Genewise.t
I don't understand what's causing the problem. Can anyone help?


From bix at sendu.me.uk  Fri Oct 26 12:53:43 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:53:43 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <47221B97.10209@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got an
> error

This should now be fixed (update live and run). If you run into any 
other problems please let me know.


From cjfields at uiuc.edu  Fri Oct 26 13:48:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 12:48:55 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <47221B97.10209@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
Message-ID: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>


On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I  
>> got an
>> error
>
> This should now be fixed (update live and run). If you run into any
> other problems please let me know.

Works now!

chris


From jason at bioperl.org  Fri Oct 26 14:22:42 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 14:22:42 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
	problem with Genewise.t
In-Reply-To: <47221B6B.5000604@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk> <47221B6B.5000604@sendu.me.uk>
Message-ID: <053BEEDD-9C6A-4FE8-BCFD-6FD9C70537DB@bioperl.org>

fixed

> One test that pops up with an error is t/Genewise.t
> I don't understand what's causing the problem. Can anyone help?

--
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Fri Oct 26 14:29:37 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:29:37 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
	<34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
Message-ID: <358f4d650710261129v13758f55g2dbc6d788f0e7618@mail.gmail.com>

for me too, thanks Sendu :)

On 10/26/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:
>
> > Albert Vilella wrote:
> >> Hi all,
> >>
> >> I was looking at the Gumby runnable, which is pretty cool. But I
> >> got an
> >> error
> >
> > This should now be fixed (update live and run). If you run into any
> > other problems please let me know.
>
> Works now!
>
> chris
>


From avilella at gmail.com  Fri Oct 26 14:45:29 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:45:29 +0100
Subject: [Bioperl-l] problems to use parsing of rst in
	Bio::Tools::Run::Phylo::PAML::Codeml
In-Reply-To: <41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
References: <471CD625.7090605@rennes.inra.fr>
	<41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
Message-ID: <358f4d650710261145k3e174c5aj94cd69b9ef9a356f@mail.gmail.com>

Hi Claude,

Did you submit the bug in bugzilla?

Or if you want, can you attach me a tar.gz with your script and input file
so I can have a look at this?

Cheers,

    Albert.

On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Claude - Will try and take a look when I have time, but pretty overwhelmed
> with other things for the time being - best bet is to also submit this as a
> bug to bugzilla.open-bio.org
>
> -jason
> On Oct 22, 2007, at 12:56 PM, Claude Rispe wrote:
>
> Dear Dr Stajich
> We have difficulty using this bioperl module to run Paml, when we try to
> parse the reconstruction of ancestral sites (rst). I send a workable extract
> of our program,  and two example fasta files (alignments). The program
> seems to work fine (at least for running codeml) and generates a correct rst
> file (by visual inspection) but we have two problems when we try to parse
> the results.
>
> 1/ we have 36 taxa and 11 internal nodes (see attached .nwk file).
> However, when we use the functions of "get_rst_persite", they do not work
> for node 36 (the last terminal node) and for node 47 (the last internal
> node): they return errors. However, inspecting visually the rst file, there
> are no problemes with these sequences.
>
> 2/ if alignments contain gaps (as eg. the file b1630.fas-GBL), the
> get_rst_persite returns wrong values.It seems the references are not
> correct (gaps being ignored ?) and so we obtain codons which are different
> from those actually expected for most sequences!
>
> May be you will have a bit of time to have a glance at our code and
> example files. We might have not written the code correctly (I am not an
> expert at this task). Thanks a lot in advance for any advice or feedback,
> Claude Rispe
> #!usr/bin/perl -w
>
> use Bio::SeqIO;
> use Bio::AlignIO;
> use Bio::Tools::Phylo::PAML;
> use Bio::Tools::Run::Phylo::PAML::Codeml;
> use Bio::TreeIO;
> use Bio::Tree::TreeI;
>
> use strict;
>
>
> my $treeio=Bio::TreeIO->new(-file =>"entero_topo.nwk", -format=>"newick");
> my $tree=$treeio->next_tree();
>
>
>    # runs PAML and gets encestral sequences (for internal nodes)
> ------------------------------------------------------------
>       my $in=Bio::AlignIO->new(-file => "b3298.fas-GBL",-format  =>
> 'fasta');
>       while ( my $aln=$in->next_aln() ) {
>          my $kaks_factory=new Bio::Tools::Run::Phylo::PAML::Codeml (
> -tree=> $tree, -save_tempfiles=> 'TRUE', -dir=>'/tmp', -params=>
> {'runmode'=>0,'seqtype'=>1,'model'=>0,'RateAncestor'=>1} );
>          $kaks_factory->alignment($aln);
>          my($rc,$parser)= $kaks_factory->run();
>  my $result=$parser->next_result;
>
>
>          # parsing of ancestral states and of mutations along branches
> ------------------------------------------------------------
>  my @trees = $result->get_rst_trees;
>  my $persite = $result->get_rst_persite;
>  my $nbsites=scalar(@$persite)-1;
>  print "$nbsites\n";
>     for my $t ( @trees ) {
>                for my $node ( $t->get_nodes ) {
>                    next unless $node->ancestor; # skip root node
>    printf "node:%s     ancestor: %s  node is leaf?
> %s\n",$node->id,$node->ancestor->id,$node->is_Leaf;
>    if ($node->id=~/^(\d*)/) {
>        for( my $i=1;$i<=$nbsites;$i++) {
>          print " $i ",$persite->[$i]->[$1]->{'codon'}, '
> ',$persite->[$i]->[$1]->{'aa'}," ";
>          unless ($node->is_Leaf) {print "
> ",$persite->[$i]->[$1]->{'prob'}," ";}
>
>
>        }
>    }
>            print "\n";
>                }
>
>
>            }
>
>
>
>
>       }
>
> Eco3
>
> GTCGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Erwca
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCGTTAACG
> TCAATTTTCG GTATCGGTAA AACTCGGTCG CAGGCTATTT GTGCTGCAAC GGAGATTGCC
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG ATAAGCTGCG TGACGAAGTT
> GCCAAGTTTG TTGTAGAAGG TGATCTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTT
> ATGGACCTTG GTACTTATCG TGGTTTGCGT CATCGTCGTG GTCTGCCGGT TCGCGGTCAG
> CGTACCAAGA CTAACGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGTCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Klebs
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCACAAAC ATACCGTTAT CGCTTTAACC
> GCTATTTTCG GTATCGGCAA AACCCGTTCT AAAGCCATCT GCGCTGAAAC GGGCATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATTG ATATTCTGCG TGAAGCAGTA
> GGTAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GTTGCTACCG TGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yent
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCGTTAACT
> GCGATCTACG GCATCGGTAA GACCCGTTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Eco10
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Styphim
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Enterob
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAAAAAC ATGCTGTGAT CGCATTAACT
> TCGATCTATG GCGTCGGCAA GACCCGTTCC AAAGCCATTT TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAGTTA GCATGAGCAT CAAGCGCCTT
> ATGGACCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGCCAG
> CGCACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Eco5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco7
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Serrp
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTAAT CGCCTTAACG
> TCGATCTTCG GAATCGGTAA AACCCGCTCA CAGTCTATCT GTGCGTCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATTG AACAGCTGCG TGAAGCAGTC
> GCCAAATTCA CTGTAGAAGG TGATTTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTG
> ATGGATCTTG GTACTTACCG TGGTTTGCGT CATCGTCGTG GTCTGCCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCAATCAA GAAA
>
> Sodalis
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCCCTAACG
> TCAATCTACG GTATCGGCAA AACCCGCTCG CAGCACATCT GCGCGGCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAGATTG ACACGCTGCG TGAAGCAGTT
> ACCAAGTTTG TTGTCGAAGG CGATCTGCGC CGTGAAGTCA CCCTGAGTAT CAAGCGTCTG
> ATGGACCTTG GTACCTATCG TGGTTTGCGT CATCGTCGTG GTCTTCCGGT TCGCGGTCAG
> CGTACCAAGA CCAATGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGCCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Pholu
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAGC ATACCGTGAT CGCTTTAACA
> TCGATCTACG GAATTGGCAA AACTCGCTCC CAAGCCATTT GTGCTGCGGC GGGTATTGCT
> GAGCATGTTA AGATCAGCGA GCTGTCTGAA GAGCAAATTG ATAAGCTGCG TGACGAAGTT
> GCCAAATACG TTGTAGAAGG CGATTTGCGT CGTGAAGTAA CCCTGAGCAT CAAACGTCTG
> ATGGATCTTG GTACTTATCG TGGTTTACGT CACCGTCGTG GTCTACCTGT TCGCGGCCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCACGTA AGCCGATCAA GAAA
>
> Eco9
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco8
>
> GTAGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTAT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TTCTGGCCGA AGCTCTCGTC
> CTCAAACTAC GCAAGCAGTC GGTAGCTGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGT
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGT TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TGTGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTGGCGGG CTTATTAGTC TGGATGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTTG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig6
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig4
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig5
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig2
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGCT GATATGAACA CACTACACTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Erwca
>
> ATGGCTTTTA TTGCGAGTTC ACCGTTCACA CATAACCAGC AGCGCACGCA GCGCATCATG
> CTGTGGGTTA TTCTGGCCTG CCTGCCGGGC ATGTTGGCGC AGGTCTATTT CTTTGGCTAC
> GGCAACCTGA TTCAGGTCGG GCTGGCGTCT GCCACCGCAC TCATTGCGGA AGGCGTGACG
> CTGTCACTGA GGAAATTTGC GGTTCGTACC ACCCTGGCTG ATAATTCCGC GTTACTGACC
> GCCGTGCTGC TCGGAATCAG TCTACCGCCA TTAGCGCCCT GGTGGATGGT GGTCATGGCA
> ACCGTCTTCG CTATCATTAT CGCTAAACAG CTGTATGGCG GATTAGGGCA AAATCCCTTT
> AACCCCGCGA TGATTGGTTA TGTGGTGTTG CTGATCTCTT TCCCTGTCCA GATGACGAGC
> TGGCTGCCAC CCGAGCCGCT GCAAACCATC TCGCTTAGTT TCCATGACTC GCTAGTCATC
> ATTTTTACCG GACACACGCC TGACGGGCAT ACCATGCAGC AGCTGATGCA CAATGTTGAT
> GGCGTGAGTC AGGCCACCCC GCTGGATACG TTTAAAACCA GCTTACGTTC CGGCCAAACG
> CCACAGAACA TCCTGCAACA GCCGATGTTT GCACAATCAC TGTCTGGTAT TGGCTGGCAG
> TGGGTTAATA TCGGTTTTCT CATCGGCGGG CTGTTCTTGC TGATGCGCGG CACGATTCGC
> TGGCATATTC CAGTCAGTTT CCTGCTGTCG CTGATGTTCT GCGCCCTGCT AAGCTGGATC
> ATCGCGCCGG ATAAATTTGC CCAACCGATG TTACATCTGT TGTCCGGTGC GACCATGCTC
> GGCGCATTTT TCATCGCCAC AGATCCCGTT ACAGCATCAA CCACGAACCG GGGCCGTCTG
> ATTTTCGGTG CGTTGATTGG GTTACTGGTG TGGCTGATTC GCACCTATGG CGGCTACCCA
> GACGGCGTTG CCTTTGCCGT TCTACTGGCG AACATCACCG TCCCGCTGAT CGACTATTAC
> ACCAAGCCAC GTGCTTACGG CCACCATCGC
>
> Shig3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGGT GATATGAACA CACTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig1
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAACAGTC GGTAGCCGCC ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTATATGGCG GTCTGGGACA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCTTGGTT TTATCGACGC CATCCAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Yep2
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep3
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Klebs
>
> ATGGTTTTCA TCGCAAGCTC CCCCTATACC CATAACCAGC GGCAGACCTC GCGTATTATG
> CTGCTGGTGC TGCTCGCCGC TGTGCCTGGC ATTGTGGTCC AGACCTGGTT TTTCGGCTGG
> GGCACCGTAC TGCAGATTGT CCTCGCCGCC CTGACGGCCT GGGCGACCGA AGCCGCTATT
> CTCAAACTGC GTAAACAGCC TGTTGCTGCC ACGCTGAAAG ATAATTCCGC CCTGCTCACC
> GGCCTGCTGC TGGCGGTGAG TATTCCGCCA CTGGCCCCGT GGTGGATGGT GGTGCTCGGC
> ACTGCCTTTG CCGTAGTCAT TGCCAAGCAG TTGTACGGAG GCCTGGGCCA TAACCCCTTC
> AACCCGGCAA TGATCGGCTA TGTCGTGCTG CTGATTTCGT TCCCGGTGCA GATGACCTCC
> TGGCTGCCTT CCTATGAGAT AGCCGCCCAT ATCCCGGCAT TCAGCGACGC GCTGCAGATG
> ATCTTCACCG GTCATACCGC CGCCGGAGGC GACATGGCCA GTCTGCGGCT GGGTATCGAC
> GGCGTCAGCC AGGCCACCCC GCTGGATACC TTTAAAACCT CCCTGCATGC CGGACATAGC
> GTTCAGCAGG TGCTGCAATT GCCGGTCTAC GGCGGCGTGC TGGCAGGTCT GGGCTGGCAG
> TGGGTGAATA TCGCCTGGCT GGCAGGCGGC CTTTTCCTGC TGTGGCAGAA GGCGATCCGC
> TGGCATATCC CGGTCAGCTT CCTTGTTAGC CTCGGCCTGT GCGCCACCCT CGGCTGGATT
> TTTTCGCCGC AGAGCCTGGC CTCACCGCAG ATGCATTTGC TCTCCGGGGC GACCATGCTT
> GGCGCCTTCT TTATCCTGAC CGATCCGGTG ACGGCCTCAA CAACCAACCG CGGCCGTCTG
> ATCTTTGGCG CCCTCGCTGG CCTGCTGGTC TGGCTCATCC GCAGCTTCGG TGGTTATCCG
> GACGGCGTGG CGTTTGCCGT TCTGCTGGCG AATATTACCG TGCCGCTGAT CGATTACTAC
> ACGCGCCCGC GCGTATATGG CCACCGT---
>
> Yep1
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yent
>
> ---------A TAGCCAGTTC CCCTTTTACG CATAATCAAC GTAGCACCCG CAGTATTATG
> CTGCTGGTTA TTTTAGCCTG CATTCCGGGG ATTATCGCCC AGACTTACTT CTTTGGTTAT
> GGCAGCCTAA TCCAAGTTGC ACTGGCTATA ATGACCGCCG TGCTGGCCGA AGGCGCTGTC
> TTGCATTTAC GTAAACAGCC GGTACTGACA CGATTACAGG ATAACTCTGC CCTGCTCACT
> GGCTTATTGT TAGGTATCAG TCTGCCGCCA CTTGCCCCTT GGTGGATGAT TGTTCTGGGT
> ACGGCATTTG CCATTATTAT TGCCAAACAA CTTTACGGCG GTTTAGGTCA GAATCCGTTT
> AATCCTGCCA TGGTCGGCTA TGTTGTACTA CTGATTTCAT TCCCAGTACA AATGACCAGT
> TGGCTTCCTC CTCTGCCATT ACAGGGAACG CCGGTTGGAT TCTATGACAG CTTATTAACT
> ATTTTCACCG GATTCACCCA AAATGGTGCC GATATTCACC AACTGCAGAT TGGCTATGAT
> GGGATAAGTC AGGCCACGCC TCTCGATAAC TTTAAAACCT CACTGCGCTC C---CAACCC
> GTGGAACAGA TTCTGCAACA ACCGATTTTT ACCGCGGGGC TGGCGGGTAT TGGTTGGCAA
> TGGATTAACC TCGGTTTTCT GGCGGGCGGT CTGTTGCTGC TATGGCGTAA AGCCATCCAC
> TGGCATATTC CGGTGAGTTT CCTATTGGCT TTGGCAGGTT GTGCTGCTAT CAGTTGGATG
> ATTGCGCCAC ACAGCTTCGC CCCCCCTATG TTGCATCTGT TTTCCGGTGC CACCATGTTG
> GGTGCTTTCT TTATTGCCAC CGATCCGGTC AGCGCCTCGA CAACACCTCG TGGTCGGCTG
> ATTTTCGGCG CATTGATTGG TATTTTGGTG TGGCTGATTC GCGTTTACGG CGGTTATCCC
> GATGGGGTAG CATTTGCGGT GCTGCTGGCC AACATCTGTG TTCCACTGAT TGATCACTAC
> ACTCAACCAC GCGTTTATGG TCATCAGCGC
>
> Yep4
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep5
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yeps2
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTGCTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATC TCGGCTTTCT GGTTGGCGGT TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
>
> ...
>
> [Message clipped]


From hlapp at gmx.net  Fri Oct 26 19:32:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 26 Oct 2007 19:32:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4721FE3B.2080507@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
Message-ID: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>


On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:

> Would there be any problem with having source() return a string,  
> but still allow access to the OntologyTerm object via  
> get_Annotations('source')? (Ditto with type?)

Do I interpret your second email that you abandoned this plan? I.e.,  
source() and type() return objects? I think that's the right way.  
(Otherwise source() is redundant with source_tag().)

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From bix at sendu.me.uk  Fri Oct 26 19:47:11 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 00:47:11 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
Message-ID: <47227C7F.9010709@sendu.me.uk>

Hilmar Lapp wrote:
> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
> 
>> Would there be any problem with having source() return a string,  
>> but still allow access to the OntologyTerm object via  
>> get_Annotations('source')? (Ditto with type?)
> 
> Do I interpret your second email that you abandoned this plan? I.e.,  
> source() and type() return objects? I think that's the right way.  
> (Otherwise source() is redundant with source_tag().)

Yes, I abandoned the above plan. I've left source() as a SimpleValue, at 
least until issues with DB::Store are resolved wrt ontologies (it stores 
the entire ontology for each feature in the database, increasing storage 
requirments > 800x).


From cjfields at uiuc.edu  Fri Oct 26 23:39:09 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 22:39:09 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <47227C7F.9010709@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
Message-ID: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>


On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
>>
>>> Would there be any problem with having source() return a string,
>>> but still allow access to the OntologyTerm object via
>>> get_Annotations('source')? (Ditto with type?)
>>
>> Do I interpret your second email that you abandoned this plan? I.e.,
>> source() and type() return objects? I think that's the right way.
>> (Otherwise source() is redundant with source_tag().)
>
> Yes, I abandoned the above plan. I've left source() as a  
> SimpleValue, at
> least until issues with DB::Store are resolved wrt ontologies (it  
> stores
> the entire ontology for each feature in the database, increasing  
> storage
> requirments > 800x).

Do you mean SeqFeature::Store or OntologyStore (I'm guessing the  
latter)?

chris


From bix at sendu.me.uk  Sat Oct 27 03:03:12 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 08:03:12 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
Message-ID: <4722E2B0.3050503@sendu.me.uk>

Chris Fields wrote:
> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>> I've left source() as a SimpleValue, at least until issues with
>> DB::Store are resolved wrt ontologies (it stores the entire
>> ontology for each feature in the database, increasing storage 
>> requirments > 800x).
> 
> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the 
> latter)?

Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you 
set the type() as well of course; the only reason I don't suffer from 
that is that I deliberately avoid setting the type on my features.


From cjfields at uiuc.edu  Sat Oct 27 10:53:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sat, 27 Oct 2007 09:53:59 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4722E2B0.3050503@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
	<4722E2B0.3050503@sendu.me.uk>
Message-ID: <C69BF9A1-1B61-4CE6-80F2-0941D6DB31AB@uiuc.edu>


On Oct 27, 2007, at 2:03 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>>> I've left source() as a SimpleValue, at least until issues with
>>> DB::Store are resolved wrt ontologies (it stores the entire
>>> ontology for each feature in the database, increasing storage
>>> requirments > 800x).
>>
>> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the
>> latter)?
>
> Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you
> set the type() as well of course; the only reason I don't suffer from
> that is that I deliberately avoid setting the type on my features.

Makes sense if you're using $store->add_SeqFeatures (it stores a  
serializized SF along with the data via Storable, so the  
OntologyStore probably goes along for the ride).  If we make type  
checking optional and lazily create the OntologyStore singleton it  
would probably reduce the space, as you wouldn't create it unless  
needed.  Or you could map it over to a DB::SeqFeature after  
validating the type.

Just noticed something: DB::SeqFeature uses type() and source() as  
synonyms of primary_tag() and source_tag(); both use strings instead  
of SimpleValues.

chris


From snaphit at planet.nl  Thu Oct 25 04:07:00 2007
From: snaphit at planet.nl (Jelle86)
Date: Thu, 25 Oct 2007 01:07:00 -0700 (PDT)
Subject: [Bioperl-l]  get_Stream_by_gi: Memory going up every call.
Message-ID: <13401838.post@talk.nabble.com>


Hi, 
I have a problem when using Bio::DB::GenBank->get_Stream_by_gi . My usage
memory for the perl script keeps going up each time a piece of the list is
downloaded. 
I have a gilist, that consist of about 1300 gi's, and i split it in pieces
of 100gi's since get_stream_by_gi doesn't work on more than 300 or so (don't
know why..). 
But either way, using this constructing makes the script take more and more
memory each time 100entries are downloaded. For 1300 gi's not a problem, but
i'm planning on doing it for at least 200.000 gi's.
How can i solve it. At the end of the end of the loops and end of the usage
of the package genbankQuery I empty all the used objects with undef. 
Below are some snippets of my code. Is there a way to find out what actually
causes the problem and more how to solve it?


I use:
perl 5.8.8.822
bioper1.5.2
winxp
behind a proxy


=========
ESTdownload;
makeChunks(){
  while (@small_list = splice(@{$gilist_ref->{gilist}}, 0, 100)) {
        $self->callStream(\@small_list);
 }
}
callStream(){
  $smallref=shift;#contains @small_list ref.
  my $query = genbankQuery->new(ids=>$smallref);
  my $part_result = $query->streamQuery();
}
=========
genbankQuery;
new{
  
  my $self = {
			ids => '',			
			@_,					
		    };
  $self->{gb}=Bio::DB::GenBank->new();
}
streamQuery(){
  my $stream_obj = $self->{gb}->get_Stream_by_gi(\@ids);
  my $seq_obj;       
  #Step through the results 
  while ($seq_obj = $stream_obj->next_seq) {
    #make lines from features and return them in an array ref
  }
}
_____________
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13401838
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From snaphit at planet.nl  Fri Oct 26 08:42:13 2007
From: snaphit at planet.nl (Jelle86)
Date: Fri, 26 Oct 2007 05:42:13 -0700 (PDT)
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13401838.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com>
Message-ID: <13426480.post@talk.nabble.com>


Ok I stripped a lot. And this is causing the problem:

use Bio::DB::Genbank;
sub new(){
  my $invocant = shift;
  my $class = ref($invocant) || $invocant;
  my $self = {@_};
  $self->{gb} = Bio::DB::GenBank->new();
  bless $self, $class;
  return $self;
}

sub streamQuery(){
	my $self = shift;        
	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
        while (my $seq_obj = $stream_obj->next_seq) {
                
        }
}

Both subs (new and streamQuery) are called several times with a new
accessionlist. 
Removing the while loop, will use a bit less memory. But the memory usage is
still going up.
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13426480
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From wgallin at ualberta.ca  Mon Oct 29 00:03:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Sun, 28 Oct 2007 22:03:24 -0600
Subject: [Bioperl-l] Not catching an error in EUtilities
Message-ID: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>

I've been having an intermittent problem, when the NCBI service that  
is accessed by EUtilities (in particular efetch) is not available.

I have the calls enclosed in eval statements, but an exception is not  
thrown.  Instead I find that the  file that should contain the  
results of the efetch only has the following text:

Error: The resource is temporarily unavailable

So it appears that this is not generating an exception (maybe that is  
not desireable in general, but it would be useful in my case).

The result is that my script tries to access the file using  
Bio::Seq::IO, and the expected text is not there.

The relevant snippet of code and the output are copied below.

The only way that I can think of to catch this outcome is to open the  
file and check the firt three lines for this text, and then go back  
and redo the efetch if this particular text is found.

Is this behaviour considered a bug, or just an outcome that needs to  
be checked for when code is written using efetch?

If so, is there a standard way of checking for this?

Thanks,

Warren Gallin

[Code that successfully executes an epost and retrieves the history]

   RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
         -eutil   => 'efetch',
         -rettype => 'genbank',
         -db      => 'protein',
         -history => $history
     );};
     if ($@){
     	print "efetch error trapped\n$@\n";
     	goto RETRIEVE_LIST;

     }

     $file1 = ">" . $file1;
     $retry = 0;
     eval { $prot_eutil->get_Response( -file => $file1 ); };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++;
         sleep(5);
         goto RETRIEVE_LIST;
     }
     else {
         print "efetch ran on $loop_bottom through $loop_top.\n";
     }

The output to the terminal from this part of the code is:

efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 11:42:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 10:42:43 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <5AEAE8C4-2E18-4BBE-A470-8CB398949BEA@uiuc.edu>


On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
>
> Error: The resource is temporarily unavailable
>
> So it appears that this is not generating an exception (maybe that is
> not desireable in general, but it would be useful in my case).
>
> The result is that my script tries to access the file using
> Bio::Seq::IO, and the expected text is not there.
>
> The relevant snippet of code and the output are copied below.
>
> The only way that I can think of to catch this outcome is to open the
> file and check the firt three lines for this text, and then go back
> and redo the efetch if this particular text is found.
>
> Is this behaviour considered a bug, or just an outcome that needs to
> be checked for when code is written using efetch?
...
> If so, is there a standard way of checking for this?

I may have already mentioned this (it is mentioned in the POD), but  
it's worth repeating: if you running a script to post more than 100  
requests you should be running it btwn 9pm and 5am ET per NCBI's rules:

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

I have built in a way to pass in an LWP::UserAgent-related callback  
to get_Response() using the -cb parameter, primarily to allow piping  
data to a child process for instance.  This could also be used for  
checking the initial data retrieved and throwing if an error is  
returned.  I haven't extensively tested this yet; I can try running a  
stress test to see if I can trigger an efetch error and catch it in  
the callback.  If I can get something working I'll post it later  
today and may incorporate it into EUtilities in CVS.

A bit of background: efetch is the only eutil that doesn't have a  
specific parser (Bio::Tools::EUtilities) attached to it, primarily b/ 
c the data retrieved is very diverse (seq/pubmed/snp/etc data in XML,  
asn.1, text, HTML).  All other eutils besides efetch generate error  
codes via the HTTP::Response header (the norm) or in the XML  
returned; both of the previous types are errors that EUtilities  
catches and throws, so an eval{} works.  efetch errors seen to be  
atypical and may be related to the server load or specific database  
availability.

chris

> Thanks,
>
> Warren Gallin
>
> [Code that successfully executes an epost and retrieves the history]
>
>    RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
>          -eutil   => 'efetch',
>          -rettype => 'genbank',
>          -db      => 'protein',
>          -history => $history
>      );};
>      if ($@){
>      	print "efetch error trapped\n$@\n";
>      	goto RETRIEVE_LIST;
>
>      }
>
>      $file1 = ">" . $file1;
>      $retry = 0;
>      eval { $prot_eutil->get_Response( -file => $file1 ); };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++;
>          sleep(5);
>          goto RETRIEVE_LIST;
>      }
>      else {
>          print "efetch ran on $loop_bottom through $loop_top.\n";
>      }
>
> The output to the terminal from this part of the code is:
>
> efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 12:06:24 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 11:06:24 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13426480.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
Message-ID: <8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>

It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Oct 29 16:45:53 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 15:45:53 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <A5708C31-CA39-43D8-ADE2-E1791D3332C7@uiuc.edu>

Warren,

For efetch the following works for me; it include a simple callback  
to check the initial data chunk (note the die in the callback and the  
extra call to check the header) and prints to the file if no error is  
detected, otherwise it retries.  I'll see if there is an easy way to  
integrate this into EUtilities.


# after eutil calls

open (my $SEQFILE, '>', $file) || die "Can't write to file:$!";
my $expected;
my $bytes = 0;

RETRIEVE_SEQS:
while ($retstart < $count) {
      $gpeptfactory->set_parameters(
		-retmax => $retmax,
                 -retstart => $retstart,
                              );
      my $response;
      eval{
         $response= $gpeptfactory->get_Response(-cb => sub {
            my ($chunk, $res) = @_;
             if ($bytes == 0 && $chunk =~ m{^Error:(.*)}i) {
                 die "$1\n";
             }
             $bytes += length($chunk);
             print $SEQFILE $chunk;
         });
      };
      if ($@ || $response->header('x-died')) {
          my $error = $@ || $response->header('x-died');
          die "Server error: $error.  Try again later" if $retry == 5;
          print STDERR "$error\n";
          print STDERR "Server error, redo #$retry\n";
          $retry++ && redo RETRIEVE_SEQS;
      } else  {
      	my $retend = $retstart + $retmax;
      	print "Loaded entries ",$retstart+1," through $retend on retry  
# $retry.\n";
      	$retstart += $retmax;
      	$retry = 0;
         $bytes = 0; # important!
         undef $expected ;
      }
}

close $SEQFILE;

chris

On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
> ...
> If so, is there a standard way of checking for this?
>
> Thanks,
>
> Warren Gallin
...


From wenbinye at gmail.com  Tue Oct 30 07:46:55 2007
From: wenbinye at gmail.com (Ye Wenbin)
Date: Tue, 30 Oct 2007 19:46:55 +0800
Subject: [Bioperl-l] console version of Deobfuscator
Message-ID: <op.t00dohrc52p72k@tsinghua-64dc66>

Hi, all.
I wrote a console version of Deobfuscator. I think it is easy to
use and more efficient to query and search.
Hope it is helpful!
You can download it from:
http://search.cpan.org/CPAN/authors/id/Y/YE/YEWENBIN/deob-0.02.tar.gz

-- 
Best regards.
Ye Wenbin


From cjfields at uiuc.edu  Tue Oct 30 08:10:41 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 07:10:41 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
Message-ID: <2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>

What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From snaphit at planet.nl  Tue Oct 30 04:51:40 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 09:51:40 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>

This doesn't seem to work. It still keeps using more memory. I already tried it once and didn't seem to make a difference. But gave it another try. But as I said, it doesn't solve the problem.


-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Mon 10/29/2007 5:06 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From jason at bioperl.org  Tue Oct 30 11:16:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Oct 2007 11:16:59 -0400
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>

Denis -
Not sure - the list members will know more.

-jason
Begin forwarded message:

> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
> Date: October 30, 2007 7:41:29 AM EDT
> To: <jason at bioperl.org>
> Subject: Pairwaise_kaks.pl
>
> Good morning,
>
> I'm attempting to set up the pairwise_kaks script here.
>
> I have successfully used an older version in a previous position so  
> I am
> somewhat familiar with it.
>
> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
> And have bioperl             in /usr/local/bioperl-1.5.2_100
>
>
> When I try to run the script I get the following
>
> Can't locate object method "_set_from_args" via package
> "Bio::Tools::Run::Alignment::Clustalw" at
> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>
> I'm not sure how to resolve this so I refer to a higher authority
>
> Merci
>
> Dennis Prickett
>
> Institute for Animal Health
> Compton nr Newbury
> Berkshire
> RG20 7NN
>
> Switchboard: +44  (0)1635 578411
> Central Fax: +44  (0)1635 57723
>

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct 30 11:33:34 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 10:33:34 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
Message-ID: <2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>

It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From bix at sendu.me.uk  Tue Oct 30 12:10:42 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Tue, 30 Oct 2007 16:10:42 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
Message-ID: <47275782.2010200@sendu.me.uk>

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably 
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the 
same place. Ie. 1.5.2 release packages or CVS, not both.


From bix at sendu.me.uk  Wed Oct 31 07:36:09 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 31 Oct 2007 11:36:09 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
	<8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <472868A9.2090706@sendu.me.uk>

dennis prickett (IAH-C) wrote:
> Sendu
> 
> Thanks for the quick response.  
> 
> Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
> the bioperl core package.
> 
> But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

No, that's still 1.5.2 with minor installation-related patches ( 
http://www.bioperl.org/wiki/Release_1.5.2#Updates ). You'll need to 
install bioperl-live from CVS, or bioperl-run-1.5.2_100.


From dennis.prickett at bbsrc.ac.uk  Wed Oct 31 07:32:35 2007
From: dennis.prickett at bbsrc.ac.uk (dennis prickett (IAH-C))
Date: Wed, 31 Oct 2007 11:32:35 -0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <47275782.2010200@sendu.me.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>

Sendu

Thanks for the quick response.  

Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
the bioperl core package.

But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

Thanks 

Dennis Prickett

-----Original Message-----
From: Sendu Bala [mailto:bix at sendu.me.uk] 
Sent: 30 October 2007 16:11
To: Jason Stajich
Cc: bioperl-l list; dennis prickett (IAH-C)
Subject: Re: [Bioperl-l] Fwd: Pairwaise_kaks.pl

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package 
>> "Bio::Tools::Run::Alignment::Clustalw" at 
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the
same place. Ie. 1.5.2 release packages or CVS, not both.



From snaphit at planet.nl  Tue Oct 30 10:56:10 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 15:56:10 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>

I just made a test script which shows the problem.
The second while loop will cause the program to use more and more memory without releasing it.

I will post the bug later today.

Jelle

code:
use Bio::DB::GenBank;
use strict;
use warnings;
my @arraylist = (157043286,157043285,157043189); #use couple of hundreds gi's to see the issue
while (my @small_list = splice(@arraylist, 0, 100)) {
        my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
        my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);        
        while (my $seq_obj = $stream_obj->next_seq) {
            #this is what causes the problem...
        }        
}

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 1:10 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From snaphit at planet.nl  Wed Oct 31 06:07:38 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Wed, 31 Oct 2007 11:07:38 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
	<2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F1A@CPEXBE-EML18.kpnsp.local>

I installed S/SE/SENDU/bioperl-1.5.2_102.tar.gz using cpan -force -notest.
And now running the script doesn't use that much memory. Although it keeps going up, but just a little bit every call. For 14000 +/-20mb (starts at 16mb).

Before I used this bioperl version (only one I was able to install using PPM):
Bioinformatics Toolkit 1.5.2 RC2
Version:	1.5.1.9992
Released:	2006-10-02

I first replaced the modules you mentioned, but it didn't help. So I thought before I report the bug, I will try to install the package with cpan. It gave some errors at first, so I used force and notest. And now it seems to work. I get the output I expect and a lot less memory usage. 

So if you don't see anything on your windows machine, I won't report the bug.

Thanks,
Jelle



-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 4:33 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From swapnatbhat at gmail.com  Wed Oct 31 17:34:38 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 14:34:38 -0700 (PDT)
Subject: [Bioperl-l]  BLAST output parsing
Message-ID: <13519112.post@talk.nabble.com>


Hi all,

I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
it.  I did use -m 9 option to get a tabular information of the blast data. 
But it does not include the gene names or the names of the organisms of each
hit.  Are there any parsers that can do this job ??

I would really appreciate if anybody can help me with this.

Swapna
-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13519112
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From torsten.seemann at infotech.monash.edu.au  Wed Oct 31 21:27:29 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 1 Nov 2007 12:27:29 +1100
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <13519112.post@talk.nabble.com>
References: <13519112.post@talk.nabble.com>
Message-ID: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>

Swapna,

> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
> it.  I did use -m 9 option to get a tabular information of the blast data.
> But it does not include the gene names or the names of the organisms of each
> hit.  Are there any parsers that can do this job ??

The -m 9 tabular output does not include gene descriptions and
organisms. It only includes the "gene id" that was present immediately
after the ">" sign in the FASTA file that was used to create the BLAST
database you specified with the -d option when you ran BLAST.

Hence, no parser will help you. You either have to re-do the BLAST
with a different -m value that includes the information you desire, or
write code to convert your gene IDs into what you want.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University


From swapnatbhat at gmail.com  Wed Oct 31 23:49:45 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 20:49:45 -0700 (PDT)
Subject: [Bioperl-l] BLAST output parsing
In-Reply-To: <a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
References: <13519112.post@talk.nabble.com>
	<a79f6a4b0710311827m22365e5et8cfd2c9cca47f1ce@mail.gmail.com>
Message-ID: <13523150.post@talk.nabble.com>


which -m option do you think will be helpful.  

swapna

Torsten Seemann wrote:
> 
> Swapna,
> 
>> I am new to bioperl.  I did BLAST search of ~4000 genes and I need to
>> parse
>> it.  I did use -m 9 option to get a tabular information of the blast
>> data.
>> But it does not include the gene names or the names of the organisms of
>> each
>> hit.  Are there any parsers that can do this job ??
> 
> The -m 9 tabular output does not include gene descriptions and
> organisms. It only includes the "gene id" that was present immediately
> after the ">" sign in the FASTA file that was used to create the BLAST
> database you specified with the -d option when you ran BLAST.
> 
> Hence, no parser will help you. You either have to re-do the BLAST
> with a different -m value that includes the information you desire, or
> write code to convert your gene IDs into what you want.
> 
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Monash University
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13523150
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From alan at tll.org.sg  Mon Oct  1 01:53:07 2007
From: alan at tll.org.sg (alan)
Date: Mon, 1 Oct 2007 09:53:07 +0800
Subject: [Bioperl-l] exonerate
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
Message-ID: <29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>

Hi,


>> I am calling exonerate.pm within my script while attempting to  
>> align cDNA  to multiple genomic fragments. After processing about  
>> 120+ genomic fragments my code crashes with the following error:
>>
>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>> aborting...
>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF / 
>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/ 
>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>
>> The code in Exonerate.pm closes the tmpfile at the end of the  
>> routine yet I get the error message about "too many open files".
>> Any suggestions on how I should be closing these files?
>>
>>
>> Extract from my code that runs exonerate is listed below.
>>
>> foreach my $f(@files) {
>>   next unless (-f  "$dir/$f");
>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>   my $query_obj = $q_in->next_seq();
>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", - 
>> format=>"Fasta");
>>   my $target_obj = $target_in->next_seq();
>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>
>>   [code for parsing the data.......]
>>
>>   $exonerate_io->close; #tried this line out of desperation but it  
>> did not help :-)
>> }
>>
>> thanks
>> alan
>>
>>
>>
>> Alan Christoffels
>> Computational Biology Group
>> Temasek LifeSciences Laboratory
>> 1 Research Link
>> National University of Singapore
>> Singapore
>> 117604
>> Tel: +65 68744945
>> Fax: +65 68727007
>> Lab webpage: http://www.tll.org.sg/alan.asp
>>
>>
>



From outaleb at web.de  Mon Oct  1 11:46:08 2007
From: outaleb at web.de (issam outaleb)
Date: Mon, 01 Oct 2007 13:46:08 +0200
Subject: [Bioperl-l] help about Fasta file???
Message-ID: <2005673060@web.de>



hallo all,
i have a little problem,:

im using this programm,

i got some experiment and get some results--> IPI hits,(IPI Accnum)

what i want is how can i correlate this IPI ACC Numbers with the FASTA FILE (database fasta),so the programm

has to look where is the IPI Accnum in the db and copy this include description and Sequence to a new file;

all 



#!/usr/bin/perl#use warning;#use strict;use CGI qw(:all);open (IN,"C:/Documents and Settings/XXX/Desktop/Search_file") or die "Fehler beim oeffnen";open (FASTA_db,"C:/Documents and Settings/XXX/Desktop/FASTA1.fasta") or die "FASTA nicht m?glich zum ?ffnen!!" ;open (OUT,">C:/Documents and Settings/XXX/Desktop/reslut.txt") or die "Fehler beim Anlegen der neuen Datei";#print "\nDateien zum kopieren geoeffnet\n";while (<IN>){        $i = $_;        chomp $i;        if(/Hit\d">([^<\/A> ]*)/)#match string from htm datei,give me such result-->IOP123234(just IPIs)     {        #print OUT $1."\n"; #print this IPIs in this file.


 #what i thought was to push up this IPIs in the array than look at them in the fasta_db file and copy it to new file with the description


#and Sequence also. so generate a new fasta file include just my IPIs results.  how???    


		 $j = $1;                push(@array,$j);             }             }       while (defined($var=<suchdatei>)){


$var =~ /(>IPI:)([^| .]*)([^>]*)/   ;#    }} close (IN);close (FASTA_db);close (OUT);print "\nDateien  geschlossen, Kopiervorgang 


. 


	
Jetzt neu! Sch?tzen Sie Ihren PC mit McAfee und WEB.DE. 3 Monate 
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From shameer at ncbs.res.in  Mon Oct  1 16:57:15 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Mon, 1 Oct 2007 22:27:15 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>

Dear All,

Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
 My input file are in phylip  treefile format. Any Modules / codes in
Bio::Graphics / Phylogeny sections ?

Input file :
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);

-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 18:03:00 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:03:00 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
Message-ID: <1191261780.47013654cb81b@webmail.sas.upenn.edu>

I think you'll have better luck using some of already available programs to do
that, you'll get better looking trees. If you just have one tree to draw I
recommend you use:
http://itol.embl.de/

Lucia


Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear All,
>
> Is it possible to draw a phylogeny tree file in PNG format using Bioperl ?
>  My input file are in phylip  treefile format. Any Modules / codes in
> Bio::Graphics / Phylogeny sections ?
>
> Input file :
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:3.
> 
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__5
> 
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From shameer at ncbs.res.in  Mon Oct  1 18:39:05 2007
From: shameer at ncbs.res.in (Shameer Khadar)
Date: Tue, 2 Oct 2007 00:09:05 +0530 (IST)
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191263834.47013e5a6af93@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
Message-ID: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>

Dear Lucia,

Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
methods. Some how missed this excellent HOWTO :
http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
tried that and it worked very nicely. I have to work around to beautify
the tree and I am just going to do that.

Thanks & Cheers,
Shameer

> OK
>
> you can use the implementations in Bio::TreeIO
>
> you can basically read the tree in newick format and out as an svg graph
> something like this:
>
> my $in = new Bio::TreeIO(-file => 'input',
>                          -format => 'newick');
> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>                           -format => 'svggraph');
> while( my $tree = $in->next_tree ) {
>     $out->write_tree($tree);
> }
>
> you can also use Bio::Tree::Draw
>
> hope that helps
>
> Lucia
>
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Hi,
>>
>> Thanks for your mail. I have to create these trees as a part of a
>> webserver. i need to generate them dynamically using users input
>> sequence.
>> I think ITOL is not the stuff best suited for my purpose.
>>
>> > I think you'll have better luck using some of already available
>> programs
>> > to do
>> > that, you'll get better looking trees. If you just have one tree to
>> draw I
>> > recommend you use:
>> > http://itol.embl.de/
>> >
>> > Lucia
>> >
>> >
>> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
>> >
>> >> Dear All,
>> >>
>> >> Is it possible to draw a phylogeny tree file in PNG format using
>> Bioperl
>> >> ?
>> >>  My input file are in phylip  treefile format. Any Modules / codes in
>> >> Bio::Graphics / Phylogeny sections ?
>> >>
>> >> Input file :
>> >>
>> >
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
>>  3.
>> >>
>> >
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>  5
>> >>
>> >
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
>> >>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
>


-- 
Shameer Khadar
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
T - 91-080-23666001 EXT - 6251
W - http://www.ncbs.res.in



From luciap at sas.upenn.edu  Mon Oct  1 18:48:51 2007
From: luciap at sas.upenn.edu (Lucia Peixoto)
Date: Mon, 01 Oct 2007 14:48:51 -0400
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
Message-ID: <1191264531.47014113f2b54@webmail.sas.upenn.edu>

Yes,
that's the issue about those commands, trees are not pretty at all
that's why for a one tree only kind of thing I rather use ITOL
other thing to try is the tree drawer of the Mesquite package
glad I could help

Lucia

Quoting Shameer Khadar <shameer at ncbs.res.in>:

> Dear Lucia,
>
> Thanks for the mail. Now I got it. I didnt used this TreeIO / Tree::Draw
> methods. Some how missed this excellent HOWTO :
> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as well. I
> tried that and it worked very nicely. I have to work around to beautify
> the tree and I am just going to do that.
>
> Thanks & Cheers,
> Shameer
>
> > OK
> >
> > you can use the implementations in Bio::TreeIO
> >
> > you can basically read the tree in newick format and out as an svg graph
> > something like this:
> >
> > my $in = new Bio::TreeIO(-file => 'input',
> >                          -format => 'newick');
> > my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >                           -format => 'svggraph');
> > while( my $tree = $in->next_tree ) {
> >     $out->write_tree($tree);
> > }
> >
> > you can also use Bio::Tree::Draw
> >
> > hope that helps
> >
> > Lucia
> >
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Hi,
> >>
> >> Thanks for your mail. I have to create these trees as a part of a
> >> webserver. i need to generate them dynamically using users input
> >> sequence.
> >> I think ITOL is not the stuff best suited for my purpose.
> >>
> >> > I think you'll have better luck using some of already available
> >> programs
> >> > to do
> >> > that, you'll get better looking trees. If you just have one tree to
> >> draw I
> >> > recommend you use:
> >> > http://itol.embl.de/
> >> >
> >> > Lucia
> >> >
> >> >
> >> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >> >
> >> >> Dear All,
> >> >>
> >> >> Is it possible to draw a phylogeny tree file in PNG format using
> >> Bioperl
> >> >> ?
> >> >>  My input file are in phylip  treefile format. Any Modules / codes in
> >> >> Bio::Graphics / Phylogeny sections ?
> >> >>
> >> >> Input file :
> >> >>
> >> >
> >>
> >
>
((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461,(((((((_E_499_500:2.75000,_E_250_251:2.75000):0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381):1.51514,_H_255_263:6.20895):0.83877,(_L_246_249:4.30000,_H_244_245:4.30000):2.74772):0.92645,_H_520_534:7.97418):0.15279,(_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765):1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264,((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000):0.50000,_L_445_447:7.75000):0.50300):1.08808,(((((_E_381_382:2.65000,_E_377_378:2.65000):0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063):1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696):0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000):1.52226,_H_463_464:5.42226):0.94093,(_E_427_435:5.15000,_E_369_372:5.15000):1.21319):1.64489,_L_336_343:8.00808):0.88402,(((_H_355_365:6.20000,_L_349_354:6.20000):0.91541,(_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082,(((((_E_470_474:3.85000,_E_344_348:
> >>  3.
> >> >>
> >> >
> >>
> >
>
85000):0.89054,_L_475_478:4.74054):1.20107,(_E_329_335:3.85000,_E_315_317:3.85000):2.09161):0.71112,_L_513_519:6.65273):0.67204,((_L_296_304:5.00000,_H_292_295:5.00000):0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814):0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000):1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790,(_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784):4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000):1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266):1.08193,_H_229_243:7.93459):0.18730,(_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298,((((_H_159_171:7.00000,_L_156_158:7.00000):0.07448,_L_120_122:7.07448):1.59389,((((_L__90__91:2.65000,_E__88__89:2.65000):0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061):1.74719,_L_147_155:6.52780):2.14057):2.44189,((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544,(_L_172_178:3.95000,_L__77__79:3.95000):1.70544):0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>  5
> >> >>
> >> >
> >>
> >
>
8:6.53954):0.74619,_L_183_187:7.28573):0.73805,(_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197,((((_L_108_109:4.30000,_E_104_107:4.30000):1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044,(_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371,((_L__38__39:3.40000,_L__29__37:3.40000):3.64775,(((((_H___3___6:3.30000,_L___1___2:3.30000):0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856):0.88488,_E__40__48:5.79344):0.60814,(_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172):1.25080):0.17461):6.94325);
> >> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> >
>
>
> --
> Shameer Khadar
> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> National Centre for Biological Sciences (TIFR)
> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> T - 91-080-23666001 EXT - 6251
> W - http://www.ncbs.res.in
>


Lucia Peixoto
Department of Biology,SAS
University of Pennsylvania


From jason at bioperl.org  Mon Oct  1 19:32:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 1 Oct 2007 12:32:38 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
In-Reply-To: <1191264531.47014113f2b54@webmail.sas.upenn.edu>
References: <53150.192.168.1.1.1191257835.squirrel@mail.ncbs.res.in>
	<1191261780.47013654cb81b@webmail.sas.upenn.edu>
	<48581.192.168.1.1.1191262243.squirrel@mail.ncbs.res.in>
	<1191263834.47013e5a6af93@webmail.sas.upenn.edu>
	<58283.192.168.1.1.1191263945.squirrel@mail.ncbs.res.in>
	<1191264531.47014113f2b54@webmail.sas.upenn.edu>
Message-ID: <F9A7B451-C47F-40B9-AB19-4391BD373A94@bioperl.org>

I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
for prettier trees - you get postscript out but you can render this  
to png or jpg with unix tools.  If there is a better stand alone tree  
drawing engine we're happy to try and integrate it into bioperl - the  
modules here are native Perl only and you can use the bioperl-run  
modules that wrap DrawTree and DrawGram from EMBOSS to get other PS  
rendering output.

Mesquite, TreeView or other tools are usually much better but not  
always an option if you want to auto-render these images for a  
website, etc.

-jason


On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:

> Yes,
> that's the issue about those commands, trees are not pretty at all
> that's why for a one tree only kind of thing I rather use ITOL
> other thing to try is the tree drawer of the Mesquite package
> glad I could help
>
> Lucia
>
> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>
>> Dear Lucia,
>>
>> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
>> Tree::Draw
>> methods. Some how missed this excellent HOWTO :
>> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as  
>> well. I
>> tried that and it worked very nicely. I have to work around to  
>> beautify
>> the tree and I am just going to do that.
>>
>> Thanks & Cheers,
>> Shameer
>>
>>> OK
>>>
>>> you can use the implementations in Bio::TreeIO
>>>
>>> you can basically read the tree in newick format and out as an  
>>> svg graph
>>> something like this:
>>>
>>> my $in = new Bio::TreeIO(-file => 'input',
>>>                          -format => 'newick');
>>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
>>>                           -format => 'svggraph');
>>> while( my $tree = $in->next_tree ) {
>>>     $out->write_tree($tree);
>>> }
>>>
>>> you can also use Bio::Tree::Draw
>>>
>>> hope that helps
>>>
>>> Lucia
>>>
>>>
>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>
>>>> Hi,
>>>>
>>>> Thanks for your mail. I have to create these trees as a part of a
>>>> webserver. i need to generate them dynamically using users input
>>>> sequence.
>>>> I think ITOL is not the stuff best suited for my purpose.
>>>>
>>>>> I think you'll have better luck using some of already available
>>>> programs
>>>>> to do
>>>>> that, you'll get better looking trees. If you just have one  
>>>>> tree to
>>>> draw I
>>>>> recommend you use:
>>>>> http://itol.embl.de/
>>>>>
>>>>> Lucia
>>>>>
>>>>>
>>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> Is it possible to draw a phylogeny tree file in PNG format using
>>>> Bioperl
>>>>>> ?
>>>>>>  My input file are in phylip  treefile format. Any Modules /  
>>>>>> codes in
>>>>>> Bio::Graphics / Phylogeny sections ?
>>>>>>
>>>>>> Input file :
>>>>>>
>>>>>
>>>>
>>>
>>
> ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> 1.51514,_H_255_263:6.20895):0.83877, 
> (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> 0.92645,_H_520_534:7.97418):0.15279, 
> (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> 1.52226,_H_463_464:5.42226):0.94093, 
> (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> 1.64489,_L_336_343:8.00808):0.88402, 
> (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> (((((_E_470_474:3.85000,_E_344_348:
>>>>  3.
>>>>>>
>>>>>
>>>>
>>>
>>
> 85000):0.89054,_L_475_478:4.74054):1.20107, 
> (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> 0.71112,_L_513_519:6.65273):0.67204, 
> ((_L_296_304:5.00000,_H_292_295:5.00000): 
> 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> 1.08193,_H_229_243:7.93459):0.18730, 
> (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> 0.07448,_L_120_122:7.07448):1.59389, 
> ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> 0.42200,_E_138_146:6.07744):0.46209,_E__51__
>>>>  5
>>>>>>
>>>>>
>>>>
>>>
>>
> 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> 0.88488,_E__40__48:5.79344):0.60814, 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> 1.25080):0.17461):6.94325);
>>>>>>
>>>>
>>>> --
>>>> Shameer Khadar
>>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>>>> National Centre for Biological Sciences (TIFR)
>>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>>>> T - 91-080-23666001 EXT - 6251
>>>> W - http://www.ncbs.res.in
>>>>
>>>
>>>
>>> Lucia Peixoto
>>> Department of Biology,SAS
>>> University of Pennsylvania
>>>
>>
>>
>> --
>> Shameer Khadar
>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
>> National Centre for Biological Sciences (TIFR)
>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
>> T - 91-080-23666001 EXT - 6251
>> W - http://www.ncbs.res.in
>>
>
>
> Lucia Peixoto
> Department of Biology,SAS
> University of Pennsylvania
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From outaleb at web.de  Tue Oct  2 02:37:26 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 04:37:26 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
Message-ID: <4701AEE6.6070506@web.de>

Hi every body,
i have some AccNum in a file-> IPI67675
                                                 IPI98976.
                                                 ...

what i want is how can i look in the fasta file (db fasta) if there is 
some match
if yes then copy the entire entry into a new fasta file.
i tried with bioperl but cause i m noob:-(( i don t get it.
thx all



From ULNJUJERYDIX at spammotel.com  Tue Oct  2 06:21:31 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Tue, 2 Oct 2007 14:21:31 +0800
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
Message-ID: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>

Hi!
I am trying to annotate a 200kb sequence by doing blastx to find the protein
seq location
I need to split the sequence up so that I get the best hits for each region
(the top blast hits will mask the smaller proteins if i do it as a whole
sequence)
if i were to do it manually i can set the subsequence in the web gui for
ncbi's blast.
this way, the blast hits coords are based on the whole 200kb.

but I can't find this option in blast or a straightforward way to do it in
bioperl.

I found similar solutions like
http://www.bio.davidson.edu/projects/DAB/DAB.html
divide and blast (but I need to specify coords)

there also this from the bioperl archives
http://bioinformatics.org/pipermail/bioclusters/2002-August/000375.html

but isn't there an easier way like i can specify blast subsequence 200-900
of fasta file and it will return the blastx hits in coords in terms of the
whole 200kb?


From n.haigh at sheffield.ac.uk  Tue Oct  2 07:56:57 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 08:56:57 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701AEE6.6070506@web.de>
References: <4701AEE6.6070506@web.de>
Message-ID: <4701F9C9.4050808@sheffield.ac.uk>

outaleb Issame wrote:
> Hi every body,
> i have some AccNum in a file-> IPI67675
>                                                  IPI98976.
>                                                  ...
>
> what i want is how can i look in the fasta file (db fasta) if there is 
> some match
> if yes then copy the entire entry into a new fasta file.
> i tried with bioperl but cause i m noob:-(( i don t get it.
> thx all
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   

Can you state clearly, what is in the "AccNum" file exactly, some sample
text from the actual file would be good. Is the FASTA file containing
the sequences in raw FASTA format or has it been processed using
somthing like formatdb from the BLAST software?

A few more details will help people understand and in turn help you with
a swift solution.

Cheers
Nath


From outaleb at web.de  Tue Oct  2 09:22:17 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 11:22:17 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4701F9C9.4050808@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
Message-ID: <47020DC9.8040401@web.de>

hi,
with this file i mean, i picked out this Accession Number from IPI-Human 
Dbase,they come from a fasta file,
so they re under eachother like a i a table in separate file now.
what i want is how how can i check it in the fasta File (so in the 
IPI-Human FAsta File), i they re really there;
if yes please copy the entire entry of this Number (>....the sequence 
also)in new fasta file.so that i get at the end a new
FASTA file with jus this IPI Accession Number.
thx and hope was clearly.

Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>Hi every body,
>>i have some AccNum in a file-> IPI67675
>>                                                 IPI98976.
>>                                                 ...
>>
>>what i want is how can i look in the fasta file (db fasta) if there is 
>>some match
>>if yes then copy the entire entry into a new fasta file.
>>i tried with bioperl but cause i m noob:-(( i don t get it.
>>thx all
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>  
>>    
>>
>
>Can you state clearly, what is in the "AccNum" file exactly, some sample
>text from the actual file would be good. Is the FASTA file containing
>the sequences in raw FASTA format or has it been processed using
>somthing like formatdb from the BLAST software?
>
>A few more details will help people understand and in turn help you with
>a swift solution.
>
>Cheers
>Nath
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From n.haigh at sheffield.ac.uk  Tue Oct  2 09:56:49 2007
From: n.haigh at sheffield.ac.uk (Nathan S. Haigh)
Date: Tue, 02 Oct 2007 10:56:49 +0100
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47020DC9.8040401@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de>
Message-ID: <470215E1.4080901@sheffield.ac.uk>

outaleb Issame wrote:
> hi,
> with this file i mean, i picked out this Accession Number from
> IPI-Human Dbase,they come from a fasta file,
> so they re under eachother like a i a table in separate file now.
> what i want is how how can i check it in the fasta File (so in the
> IPI-Human FAsta File), i they re really there;
> if yes please copy the entire entry of this Number (>....the sequence
> also)in new fasta file.so that i get at the end a new
> FASTA file with jus this IPI Accession Number.
> thx and hope was clearly.

Ok, first of all, I'd read the contents of your Accession numbers into a
hash, something like the following (this could be written in a shorter
form, but since you're a newbie I'll leave it in a longer form so you
can follow easier).

-- start script --
use strict;
use Bio::SeqIO;

# change the following three lines to point to the relevant paths
# of your list of accessions file, your fasta file and your output
# fasta file
my $acc_file = "/path/to/your/file";
my $fasta_file_in = "/path/to/your/fasta/file";
my $fasta_file_out = "/path/to/your/fasta/output/file";

# Use a hash to keep a record of accessions we want to find
my %hash_of_req_acc;

# read all the required accessions from the file into the hash as keys
open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
while (<ACC_FILE>) {
  my $line = $_;
  chomp $line;
  $hash_of_req_acc{$_} = 1;
}
close ACC_FILE;

my $seqio_object_in = Bio::SeqIO->new(
  -file => $fasta_file_in,
  -format => 'fasta'
);
my $seqio_object_out = Bio::SeqIO->new(
  -file => $fasta_file_out,
  -format => 'fasta'
);

# loop through all the sequences in the fasta file
while (my $seq_object = $seqio_object_in->next_seq) {
  # get the sequence accession for easy matching
  my $seq_acc = $seq_object->accession_number;

  # write the sequence object to the output fasta file if we have a
matching accession
  $seqio_object_out->write_seq($seq_object) if exists
$hash_of_req_acc{$seq_acc};
}
-- end script --

I haven't tested this, but it should at least get you started. Also, the
fasta description line in the output file may not be exactly as it was
in the input fasta file - if this really matters, you may need to get
back to us. Also, if the input fasta file is huge (many thousands of
sequences) it may be wise to create an index of the fasta file in order
to speed up retrieval.

You may find this page helpful:
http://www.bioperl.org/wiki/HOWTO:SeqIO

Anyway, hope this helps to get you started.
Nath




From outaleb at web.de  Tue Oct  2 10:50:32 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 12:50:32 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <470215E1.4080901@sheffield.ac.uk>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk>
Message-ID: <47022278.7010700@web.de>

thx for the help, but i got a empty output file,
i think its problem with matching the acc number, my fasta file look like:

*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU...
 >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
DDHHHU..
 >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
MMMMM..*

and my i Accnum File look like:
*IPI00177321
IPI00453473

*i hopt it helps to understand.*
*.


Nathan S. Haigh wrote:

>outaleb Issame wrote:
>  
>
>>hi,
>>with this file i mean, i picked out this Accession Number from
>>IPI-Human Dbase,they come from a fasta file,
>>so they re under eachother like a i a table in separate file now.
>>what i want is how how can i check it in the fasta File (so in the
>>IPI-Human FAsta File), i they re really there;
>>if yes please copy the entire entry of this Number (>....the sequence
>>also)in new fasta file.so that i get at the end a new
>>FASTA file with jus this IPI Accession Number.
>>thx and hope was clearly.
>>    
>>
>
>Ok, first of all, I'd read the contents of your Accession numbers into a
>hash, something like the following (this could be written in a shorter
>form, but since you're a newbie I'll leave it in a longer form so you
>can follow easier).
>
>-- start script --
>use strict;
>use Bio::SeqIO;
>
># change the following three lines to point to the relevant paths
># of your list of accessions file, your fasta file and your output
># fasta file
>my $acc_file = "/path/to/your/file";
>my $fasta_file_in = "/path/to/your/fasta/file";
>my $fasta_file_out = "/path/to/your/fasta/output/file";
>
># Use a hash to keep a record of accessions we want to find
>my %hash_of_req_acc;
>
># read all the required accessions from the file into the hash as keys
>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>while (<ACC_FILE>) {
>  my $line = $_;
>  chomp $line;
>  $hash_of_req_acc{$_} = 1;
>}
>close ACC_FILE;
>
>my $seqio_object_in = Bio::SeqIO->new(
>  -file => $fasta_file_in,
>  -format => 'fasta'
>);
>my $seqio_object_out = Bio::SeqIO->new(
>  -file => $fasta_file_out,
>  -format => 'fasta'
>);
>
># loop through all the sequences in the fasta file
>while (my $seq_object = $seqio_object_in->next_seq) {
>  # get the sequence accession for easy matching
>  my $seq_acc = $seq_object->accession_number;
>
>  # write the sequence object to the output fasta file if we have a
>matching accession
>  $seqio_object_out->write_seq($seq_object) if exists
>$hash_of_req_acc{$seq_acc};
>}
>-- end script --
>
>I haven't tested this, but it should at least get you started. Also, the
>fasta description line in the output file may not be exactly as it was
>in the input fasta file - if this really matters, you may need to get
>back to us. Also, if the input fasta file is huge (many thousands of
>sequences) it may be wise to create an index of the fasta file in order
>to speed up retrieval.
>
>You may find this page helpful:
>http://www.bioperl.org/wiki/HOWTO:SeqIO
>
>Anyway, hope this helps to get you started.
>Nath
>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From cjfields at uiuc.edu  Tue Oct  2 13:00:57 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 08:00:57 -0500
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
Message-ID: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>

There is a script that comes with the bioperl core distribution,  
bp_split_seq.pl, which does this.  Here's the CVS location:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/ 
scripts/seq/?cvsroot=bioperl

chris

On Oct 2, 2007, at 1:21 AM, Kevin Lam wrote:

> Hi!
> I am trying to annotate a 200kb sequence by doing blastx to find  
> the protein
> seq location
> I need to split the sequence up so that I get the best hits for  
> each region
> (the top blast hits will mask the smaller proteins if i do it as a  
> whole
> sequence)
> if i were to do it manually i can set the subsequence in the web  
> gui for
> ncbi's blast.
> this way, the blast hits coords are based on the whole 200kb.
>
> but I can't find this option in blast or a straightforward way to  
> do it in
> bioperl.
>
> I found similar solutions like
> http://www.bio.davidson.edu/projects/DAB/DAB.html
> divide and blast (but I need to specify coords)
>
> there also this from the bioperl archives
> http://bioinformatics.org/pipermail/bioclusters/2002-August/ 
> 000375.html
>
> but isn't there an easier way like i can specify blast subsequence  
> 200-900
> of fasta file and it will return the blastx hits in coords in terms  
> of the
> whole 200kb?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From rrc22 at cam.ac.uk  Tue Oct  2 13:38:45 2007
From: rrc22 at cam.ac.uk (Roy Chaudhuri)
Date: Tue, 02 Oct 2007 14:38:45 +0100
Subject: [Bioperl-l] divide and blast blastunsplit blast subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <470249E5.6050206@cam.ac.uk>

> but isn't there an easier way like i can specify blast subsequence 200-900
> of fasta file and it will return the blastx hits in coords in terms of the
> whole 200kb?

Once you have split up your sequence (as Chris suggested), and run your 
BLAST, then you can add the hits to each subsequence as features. The 
subsequences can then be re-assembled using the cat method from 
Bio::SeqUtils, which will adjust the coordinates of the features 
appropriately.

Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.


From cjfields at uiuc.edu  Tue Oct  2 15:03:29 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 10:03:29 -0500
Subject: [Bioperl-l] exonerate
In-Reply-To: <29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
Message-ID: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>

One option is to try running $run->cleanup() after you finish  
parsing, which gets rid of the tempfiles on each run.

chris

On Sep 30, 2007, at 8:53 PM, alan wrote:

> Hi,
>
>
>>> I am calling exonerate.pm within my script while attempting to
>>> align cDNA  to multiple genomic fragments. After processing about
>>> 120+ genomic fragments my code crashes with the following error:
>>>
>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>> aborting...
>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>
>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>> routine yet I get the error message about "too many open files".
>>> Any suggestions on how I should be closing these files?
>>>
>>>
>>> Extract from my code that runs exonerate is listed below.
>>>
>>> foreach my $f(@files) {
>>>   next unless (-f  "$dir/$f");
>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>   my $query_obj = $q_in->next_seq();
>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>> format=>"Fasta");
>>>   my $target_obj = $target_in->next_seq();
>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>
>>>   [code for parsing the data.......]
>>>
>>>   $exonerate_io->close; #tried this line out of desperation but it
>>> did not help :-)
>>> }
>>>
>>> thanks
>>> alan




From outaleb at web.de  Tue Oct  2 14:51:05 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 16:51:05 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47022278.7010700@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de>
Message-ID: <47025AD9.1090105@web.de>

hi again,
i think i can resolve this problem with the method : id_parser();
how can i do that?
any suggestion .or experience??
ehx again



outaleb Issame wrote:

>thx for the help, but i got a empty output file,
>i think its problem with matching the acc number, my fasta file look like:
>
>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU...
> >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>DDHHHU..
> >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3 protein
>MMMMM..*
>
>and my i Accnum File look like:
>*IPI00177321
>IPI00453473
>
>*i hopt it helps to understand.*
>*.
>
>
>Nathan S. Haigh wrote:
>
>  
>
>>outaleb Issame wrote:
>> 
>>
>>    
>>
>>>hi,
>>>with this file i mean, i picked out this Accession Number from
>>>IPI-Human Dbase,they come from a fasta file,
>>>so they re under eachother like a i a table in separate file now.
>>>what i want is how how can i check it in the fasta File (so in the
>>>IPI-Human FAsta File), i they re really there;
>>>if yes please copy the entire entry of this Number (>....the sequence
>>>also)in new fasta file.so that i get at the end a new
>>>FASTA file with jus this IPI Accession Number.
>>>thx and hope was clearly.
>>>   
>>>
>>>      
>>>
>>Ok, first of all, I'd read the contents of your Accession numbers into a
>>hash, something like the following (this could be written in a shorter
>>form, but since you're a newbie I'll leave it in a longer form so you
>>can follow easier).
>>
>>-- start script --
>>use strict;
>>use Bio::SeqIO;
>>
>># change the following three lines to point to the relevant paths
>># of your list of accessions file, your fasta file and your output
>># fasta file
>>my $acc_file = "/path/to/your/file";
>>my $fasta_file_in = "/path/to/your/fasta/file";
>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>
>># Use a hash to keep a record of accessions we want to find
>>my %hash_of_req_acc;
>>
>># read all the required accessions from the file into the hash as keys
>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>while (<ACC_FILE>) {
>> my $line = $_;
>> chomp $line;
>> $hash_of_req_acc{$_} = 1;
>>}
>>close ACC_FILE;
>>
>>my $seqio_object_in = Bio::SeqIO->new(
>> -file => $fasta_file_in,
>> -format => 'fasta'
>>);
>>my $seqio_object_out = Bio::SeqIO->new(
>> -file => $fasta_file_out,
>> -format => 'fasta'
>>);
>>
>># loop through all the sequences in the fasta file
>>while (my $seq_object = $seqio_object_in->next_seq) {
>> # get the sequence accession for easy matching
>> my $seq_acc = $seq_object->accession_number;
>>
>> # write the sequence object to the output fasta file if we have a
>>matching accession
>> $seqio_object_out->write_seq($seq_object) if exists
>>$hash_of_req_acc{$seq_acc};
>>}
>>-- end script --
>>
>>I haven't tested this, but it should at least get you started. Also, the
>>fasta description line in the output file may not be exactly as it was
>>in the input fasta file - if this really matters, you may need to get
>>back to us. Also, if the input fasta file is huge (many thousands of
>>sequences) it may be wise to create an index of the fasta file in order
>>to speed up retrieval.
>>
>>You may find this page helpful:
>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>
>>Anyway, hope this helps to get you started.
>>Nath
>>
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> 
>>
>>    
>>
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>  
>



From rvos at interchange.ubc.ca  Tue Oct  2 17:00:36 2007
From: rvos at interchange.ubc.ca (rvos at interchange.ubc.ca)
Date: Tue, 02 Oct 2007 10:00:36 -0700
Subject: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?
Message-ID: <405453b66e.3b66e40545@interchange.ubc.ca>

An alternative is to explore the Bio::Phylo treedrawer:

http://search.cpan.org/~rvosa/Bio-Phylo-0.17_RC6/lib/Bio/Phylo/Treedrawer.pm

This is a separate install (in the interest of full disclosure: I'm the author).

Rutger

----- Original Message -----
From: Jason Stajich <jason at bioperl.org>
Date: Monday, October 1, 2007 12:32 pm
Subject: Re: [Bioperl-l] How to draw Phylogeny Tree using Bioperl ?

> I'd definitely recommend  Bio::Tree::Draw::Cladogram over svggraph  
> for prettier trees - you get postscript out but you can render this 
> 
> to png or jpg with unix tools.  If there is a better stand alone 
> tree  
> drawing engine we're happy to try and integrate it into bioperl - 
> the  
> modules here are native Perl only and you can use the bioperl-run  
> modules that wrap DrawTree and DrawGram from EMBOSS to get other PS 
> 
> rendering output.
> 
> Mesquite, TreeView or other tools are usually much better but not  
> always an option if you want to auto-render these images for a  
> website, etc.
> 
> -jason
> 
> 
> On Oct 1, 2007, at 11:48 AM, Lucia Peixoto wrote:
> 
> > Yes,
> > that's the issue about those commands, trees are not pretty at all
> > that's why for a one tree only kind of thing I rather use ITOL
> > other thing to try is the tree drawer of the Mesquite package
> > glad I could help
> >
> > Lucia
> >
> > Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >
> >> Dear Lucia,
> >>
> >> Thanks for the mail. Now I got it. I didnt used this TreeIO /  
> >> Tree::Draw
> >> methods. Some how missed this excellent HOWTO :
> >> http://www.bioperl.org/wiki/HOWTO:Trees. Thanks for that code as 
> 
> >> well. I
> >> tried that and it worked very nicely. I have to work around to  
> >> beautify
> >> the tree and I am just going to do that.
> >>
> >> Thanks & Cheers,
> >> Shameer
> >>
> >>> OK
> >>>
> >>> you can use the implementations in Bio::TreeIO
> >>>
> >>> you can basically read the tree in newick format and out as an  
> >>> svg graph
> >>> something like this:
> >>>
> >>> my $in = new Bio::TreeIO(-file => 'input',
> >>>                          -format => 'newick');
> >>> my $out = new Bio::TreeIO(-file => '>mytree.svg',
> >>>                           -format => 'svggraph');
> >>> while( my $tree = $in->next_tree ) {
> >>>     $out->write_tree($tree);
> >>> }
> >>>
> >>> you can also use Bio::Tree::Draw
> >>>
> >>> hope that helps
> >>>
> >>> Lucia
> >>>
> >>>
> >>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>
> >>>> Hi,
> >>>>
> >>>> Thanks for your mail. I have to create these trees as a part 
> of a
> >>>> webserver. i need to generate them dynamically using users input
> >>>> sequence.
> >>>> I think ITOL is not the stuff best suited for my purpose.
> >>>>
> >>>>> I think you'll have better luck using some of already available
> >>>> programs
> >>>>> to do
> >>>>> that, you'll get better looking trees. If you just have one  
> >>>>> tree to
> >>>> draw I
> >>>>> recommend you use:
> >>>>> http://itol.embl.de/
> >>>>>
> >>>>> Lucia
> >>>>>
> >>>>>
> >>>>> Quoting Shameer Khadar <shameer at ncbs.res.in>:
> >>>>>
> >>>>>> Dear All,
> >>>>>>
> >>>>>> Is it possible to draw a phylogeny tree file in PNG format 
> using>>>> Bioperl
> >>>>>> ?
> >>>>>>  My input file are in phylip  treefile format. Any Modules / 
> 
> >>>>>> codes in
> >>>>>> Bio::Graphics / Phylogeny sections ?
> >>>>>>
> >>>>>> Input file :
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > ((((((_L_537_539:3.70000,_H_535_536:3.70000):4.97461, 
> > (((((((_E_499_500:2.75000,_E_250_251:2.75000): 
> > 0.55805,_L_252_254:3.30805):1.38576,_H_494_497:4.69381): 
> > 1.51514,_H_255_263:6.20895):0.83877, 
> > (_L_246_249:4.30000,_H_244_245:4.30000):2.74772): 
> > 0.92645,_H_520_534:7.97418):0.15279, 
> > (_H_502_512:6.95000,_H_273_282:6.95000):1.17697):0.54765): 
> > 1.10967,_L_264_272:9.78428):0.53441,_L_283_291:10.31869):3.59264, 
> > ((((_H_479_493:8.25300,((_H_448_462:7.25000,_L_409_411:7.25000): 
> > 0.50000,_L_445_447:7.75000):0.50300):1.08808, 
> > (((((_E_381_382:2.65000,_E_377_378:2.65000): 
> > 0.26434,_L_379_380:2.91434):1.77630,_L_373_376:4.69063): 
> > 1.70029,_L_436_444:6.39093):0.93320,_L_383_391:7.32413):2.01696): 
> > 0.94916,(((((_L_465_469:3.90000,_L_366_368:3.90000): 
> > 1.52226,_H_463_464:5.42226):0.94093, 
> > (_E_427_435:5.15000,_E_369_372:5.15000):1.21319): 
> > 1.64489,_L_336_343:8.00808):0.88402, 
> > (((_H_355_365:6.20000,_L_349_354:6.20000):0.91541, 
> > (_L_327_328:3.40000,_L_318_326:3.40000):3.71541):0.59082, 
> > (((((_E_470_474:3.85000,_E_344_348:
> >>>>  3.
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 85000):0.89054,_L_475_478:4.74054):1.20107, 
> > (_E_329_335:3.85000,_E_315_317:3.85000):2.09161): 
> > 0.71112,_L_513_519:6.65273):0.67204, 
> > ((_L_296_304:5.00000,_H_292_295:5.00000): 
> > 0.71200,_L_305_314:5.71200):1.61276):0.38147):1.18587):1.39814): 
> > 0.37326,((((_L_397_398:3.55000,_E_394_396:3.55000): 
> > 1.36938,_L_392_393:4.91938):1.43993,_L_422_426:6.35931):1.00790, 
> > 
> (_E_412_421:5.95000,_E_399_408:5.95000):1.41721):3.29629):3.24784): 
> > 4.31679,((((((_L_206_210:3.80000,_H_203_205:3.80000): 
> > 1.75687,_L__49__50:5.55687):1.29579,_H_188_202:6.85266): 
> > 1.08193,_H_229_243:7.93459):0.18730, 
> > (_L_222_228:5.55000,_H_211_221:5.55000):2.57189):3.16298, 
> > ((((_H_159_171:7.00000,_L_156_158:7.00000): 
> > 0.07448,_L_120_122:7.07448):1.59389, 
> > ((((_L__90__91:2.65000,_E__88__89:2.65000): 
> > 0.18425,_E__92__93:2.83425):1.94636,_L__84__87:4.78061): 
> > 1.74719,_L_147_155:6.52780):2.14057):2.44189, 
> > ((((((((_E_179_182:3.50000,_E__80__83:3.50000):2.15544, 
> > (_L_172_178:3.95000,_L__77__79:3.95000):1.70544): 
> > 0.42200,_E_138_146:6.07744):0.46209,_E__51__
> >>>>  5
> >>>>>>
> >>>>>
> >>>>
> >>>
> >>
> > 8:6.53954):0.74619,_L_183_187:7.28573):0.73805, 
> > (_E_123_131:5.70000,_E_110_119:5.70000):2.32378):0.58197, 
> > ((((_L_108_109:4.30000,_E_104_107:4.30000): 
> > 1.34305,_H__66__76:5.64305):0.81535,_L_132_137:6.45840):1.22044, 
> > 
> (_L__94_103:6.55000,_L__59__65:6.55000):1.12884):0.92691):1.25371, 
> > ((_L__38__39:3.40000,_L__29__37:3.40000):3.64775, 
> > (((((_H___3___6:3.30000,_L___1___2:3.30000): 
> > 0.79885,_L__21__25:4.09885):0.80972,_E__26__28:4.90856): 
> > 0.88488,_E__40__48:5.79344):0.60814, 
> > 
> (_L__12__20:5.25000,_H___8__11:5.25000):1.15158):0.64616):2.81172): 
> > 1.25080):0.17461):6.94325);
> >>>>>>
> >>>>
> >>>> --
> >>>> Shameer Khadar
> >>>> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >>>> National Centre for Biological Sciences (TIFR)
> >>>> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >>>> T - 91-080-23666001 EXT - 6251
> >>>> W - http://www.ncbs.res.in
> >>>>
> >>>
> >>>
> >>> Lucia Peixoto
> >>> Department of Biology,SAS
> >>> University of Pennsylvania
> >>>
> >>
> >>
> >> --
> >> Shameer Khadar
> >> Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
> >> National Centre for Biological Sciences (TIFR)
> >> GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
> >> T - 91-080-23666001 EXT - 6251
> >> W - http://www.ncbs.res.in
> >>
> >
> >
> > Lucia Peixoto
> > Department of Biology,SAS
> > University of Pennsylvania
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From Russell.Smithies at agresearch.co.nz  Tue Oct  2 21:34:20 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 10:34:20 +1300
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>

I know this is the Bioperl list but how about just doing it with grep?

	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta



> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of outaleb Issame
> Sent: Wednesday, 3 October 2007 3:51 a.m.
> To: outaleb Issame
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> 
> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
> 
> 
> 
> outaleb Issame wrote:
> 
> >thx for the help, but i got a empty output file,
> >i think its problem with matching the acc number, my fasta file look
like:
> >
> >*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU...
> > >IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >DDHHHU..
> > >IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> protein
> >MMMMM..*
> >
> >and my i Accnum File look like:
> >*IPI00177321
> >IPI00453473
> >
> >*i hopt it helps to understand.*
> >*.
> >
> >
> >Nathan S. Haigh wrote:
> >
> >
> >
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>
> >>>hi,
> >>>with this file i mean, i picked out this Accession Number from
> >>>IPI-Human Dbase,they come from a fasta file,
> >>>so they re under eachother like a i a table in separate file now.
> >>>what i want is how how can i check it in the fasta File (so in the
> >>>IPI-Human FAsta File), i they re really there;
> >>>if yes please copy the entire entry of this Number (>....the
sequence
> >>>also)in new fasta file.so that i get at the end a new
> >>>FASTA file with jus this IPI Accession Number.
> >>>thx and hope was clearly.
> >>>
> >>>
> >>>
> >>>
> >>Ok, first of all, I'd read the contents of your Accession numbers
into a
> >>hash, something like the following (this could be written in a
shorter
> >>form, but since you're a newbie I'll leave it in a longer form so
you
> >>can follow easier).
> >>
> >>-- start script --
> >>use strict;
> >>use Bio::SeqIO;
> >>
> >># change the following three lines to point to the relevant paths
> >># of your list of accessions file, your fasta file and your output
> >># fasta file
> >>my $acc_file = "/path/to/your/file";
> >>my $fasta_file_in = "/path/to/your/fasta/file";
> >>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>
> >># Use a hash to keep a record of accessions we want to find
> >>my %hash_of_req_acc;
> >>
> >># read all the required accessions from the file into the hash as
keys
> >>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>while (<ACC_FILE>) {
> >> my $line = $_;
> >> chomp $line;
> >> $hash_of_req_acc{$_} = 1;
> >>}
> >>close ACC_FILE;
> >>
> >>my $seqio_object_in = Bio::SeqIO->new(
> >> -file => $fasta_file_in,
> >> -format => 'fasta'
> >>);
> >>my $seqio_object_out = Bio::SeqIO->new(
> >> -file => $fasta_file_out,
> >> -format => 'fasta'
> >>);
> >>
> >># loop through all the sequences in the fasta file
> >>while (my $seq_object = $seqio_object_in->next_seq) {
> >> # get the sequence accession for easy matching
> >> my $seq_acc = $seq_object->accession_number;
> >>
> >> # write the sequence object to the output fasta file if we have a
> >>matching accession
> >> $seqio_object_out->write_seq($seq_object) if exists
> >>$hash_of_req_acc{$seq_acc};
> >>}
> >>-- end script --
> >>
> >>I haven't tested this, but it should at least get you started. Also,
the
> >>fasta description line in the output file may not be exactly as it
was
> >>in the input fasta file - if this really matters, you may need to
get
> >>back to us. Also, if the input fasta file is huge (many thousands of
> >>sequences) it may be wise to create an index of the fasta file in
order
> >>to speed up retrieval.
> >>
> >>You may find this page helpful:
> >>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>
> >>Anyway, hope this helps to get you started.
> >>Nath
> >>
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >>
> >>
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



From thiago.venancio at gmail.com  Tue Oct  2 21:41:06 2007
From: thiago.venancio at gmail.com (Thiago Venancio)
Date: Tue, 2 Oct 2007 18:41:06 -0300
Subject: [Bioperl-l] frac_* methods
Message-ID: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>

Hi all,

This topic was discussed before, but I would like to put it on the list
again, maybe someone has an update.

The methods frac_identical, frac_conserved, frac_aligned_query and
frac_aligned_hit can also be used in the hit context, after HSP tilling. In
my point of view, it is better to use it just in HSPs individually, because
there are some rare/strange kinds of alignments. However, we frequently need
to get one measure of the whole alignment.

Any of the BioPerl masters has an update on this topic ? What is the best
current usage ?

Best.

Thiago

-- 
"Innovation distinguishes between a leader and a follower."
    Steve Jobs

========================
Thiago Motta Venancio, MSc
PhD student in Bioinformatics
University of Sao Paulo
========================


From outaleb at web.de  Tue Oct  2 21:47:07 2007
From: outaleb at web.de (outaleb Issame)
Date: Tue, 02 Oct 2007 23:47:07 +0200
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
Message-ID: <4702BC5B.7040407@web.de>

thx for this, but i want just create new fasta file with my accNumbers 
which i search in the FASTA file(localdbase).
so --> just search this Numbers in the FASTA file, if yes then copy the 
Header and Sequence to other new fasta file .
i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
i get crazy guys.
common some expert in this area??
 


Smithies, Russell wrote:

>I know this is the Bioperl list but how about just doing it with grep?
>
>	grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
>
>
>
>  
>
>>-----Original Message-----
>>From: bioperl-l-bounces at lists.open-bio.org
>>    
>>
>[mailto:bioperl-l-bounces at lists.open-
>  
>
>>bio.org] On Behalf Of outaleb Issame
>>Sent: Wednesday, 3 October 2007 3:51 a.m.
>>To: outaleb Issame
>>Cc: bioperl-l at lists.open-bio.org
>>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
>>
>>hi again,
>>i think i can resolve this problem with the method : id_parser();
>>how can i do that?
>>any suggestion .or experience??
>>ehx again
>>
>>
>>
>>outaleb Issame wrote:
>>
>>    
>>
>>>thx for the help, but i got a empty output file,
>>>i think its problem with matching the acc number, my fasta file look
>>>      
>>>
>like:
>  
>
>>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>      
>>>
>>protein
>>    
>>
>>>DDHHHU...
>>>      
>>>
>>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>DDHHHU..
>>>      
>>>
>>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
>>>>        
>>>>
>>protein
>>    
>>
>>>MMMMM..*
>>>
>>>and my i Accnum File look like:
>>>*IPI00177321
>>>IPI00453473
>>>
>>>*i hopt it helps to understand.*
>>>*.
>>>
>>>
>>>Nathan S. Haigh wrote:
>>>
>>>
>>>
>>>      
>>>
>>>>outaleb Issame wrote:
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>hi,
>>>>>with this file i mean, i picked out this Accession Number from
>>>>>IPI-Human Dbase,they come from a fasta file,
>>>>>so they re under eachother like a i a table in separate file now.
>>>>>what i want is how how can i check it in the fasta File (so in the
>>>>>IPI-Human FAsta File), i they re really there;
>>>>>if yes please copy the entire entry of this Number (>....the
>>>>>          
>>>>>
>sequence
>  
>
>>>>>also)in new fasta file.so that i get at the end a new
>>>>>FASTA file with jus this IPI Accession Number.
>>>>>thx and hope was clearly.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Ok, first of all, I'd read the contents of your Accession numbers
>>>>        
>>>>
>into a
>  
>
>>>>hash, something like the following (this could be written in a
>>>>        
>>>>
>shorter
>  
>
>>>>form, but since you're a newbie I'll leave it in a longer form so
>>>>        
>>>>
>you
>  
>
>>>>can follow easier).
>>>>
>>>>-- start script --
>>>>use strict;
>>>>use Bio::SeqIO;
>>>>
>>>># change the following three lines to point to the relevant paths
>>>># of your list of accessions file, your fasta file and your output
>>>># fasta file
>>>>my $acc_file = "/path/to/your/file";
>>>>my $fasta_file_in = "/path/to/your/fasta/file";
>>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>>
>>>># Use a hash to keep a record of accessions we want to find
>>>>my %hash_of_req_acc;
>>>>
>>>># read all the required accessions from the file into the hash as
>>>>        
>>>>
>keys
>  
>
>>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>>>while (<ACC_FILE>) {
>>>>my $line = $_;
>>>>chomp $line;
>>>>$hash_of_req_acc{$_} = 1;
>>>>}
>>>>close ACC_FILE;
>>>>
>>>>my $seqio_object_in = Bio::SeqIO->new(
>>>>-file => $fasta_file_in,
>>>>-format => 'fasta'
>>>>);
>>>>my $seqio_object_out = Bio::SeqIO->new(
>>>>-file => $fasta_file_out,
>>>>-format => 'fasta'
>>>>);
>>>>
>>>># loop through all the sequences in the fasta file
>>>>while (my $seq_object = $seqio_object_in->next_seq) {
>>>># get the sequence accession for easy matching
>>>>my $seq_acc = $seq_object->accession_number;
>>>>
>>>># write the sequence object to the output fasta file if we have a
>>>>matching accession
>>>>$seqio_object_out->write_seq($seq_object) if exists
>>>>$hash_of_req_acc{$seq_acc};
>>>>}
>>>>-- end script --
>>>>
>>>>I haven't tested this, but it should at least get you started. Also,
>>>>        
>>>>
>the
>  
>
>>>>fasta description line in the output file may not be exactly as it
>>>>        
>>>>
>was
>  
>
>>>>in the input fasta file - if this really matters, you may need to
>>>>        
>>>>
>get
>  
>
>>>>back to us. Also, if the input fasta file is huge (many thousands of
>>>>sequences) it may be wise to create an index of the fasta file in
>>>>        
>>>>
>order
>  
>
>>>>to speed up retrieval.
>>>>
>>>>You may find this page helpful:
>>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>>
>>>>Anyway, hope this helps to get you started.
>>>>Nath
>>>>
>>>>
>>>>_______________________________________________
>>>>Bioperl-l mailing list
>>>>Bioperl-l at lists.open-bio.org
>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>      
>>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>    
>>
>=======================================================================
>Attention: The information contained in this message and/or attachments
>from AgResearch Limited is intended only for the persons or entities
>to which it is addressed and may contain confidential and/or privileged
>material. Any review, retransmission, dissemination or other use of, or
>taking of any action in reliance upon, this information by persons or
>entities other than the intended recipients is prohibited by AgResearch
>Limited. If you have received this message in error, please notify the
>sender immediately.
>=======================================================================
>
>  
>



From jason at bioperl.org  Tue Oct  2 22:22:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 15:22:59 -0700
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>

I think my answer before was something to the tune of:

Use an alignment algorithm that finds a single best alignment like  
FASTA or Smith-Waterman (SW) if what you want is a single number that  
represents the alignment.  BLAST is great for fast searching but  
FASTA or SW/SSEARCH are going to be better at creating an alignment.   
Consider the -postsw option in WUBLAST as well as it will realign the  
HSPs with SW.

I personally never use the frac alignment summary stats for the Hit  
object for this reason unless I know I am going to have a single HSP.

-jason

On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago
>
> -- 
> "Innovation distinguishes between a leader and a follower."
>     Steve Jobs
>
> ========================
> Thiago Motta Venancio, MSc
> PhD student in Bioinformatics
> University of Sao Paulo
> ========================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct  2 22:32:30 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 2 Oct 2007 17:32:30 -0500
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
References: <44255ea80710021441v6ee2c5e0x57e91c66c0e07c3c@mail.gmail.com>
Message-ID: <B9E32251-2A8E-4079-B256-9665D9987B02@uiuc.edu>

I think their use is based on what you are trying to accomplish.  For  
instance I am currently running a lot of small BLASTN queries  
(limiting by normalized bit score), so I tend to look at the HSP data  
more.  However, in other circumstances I might want the overall  
frac_identical for all HSPs ($hit->frac_identical).  YMMV.

chris

On Oct 2, 2007, at 4:41 PM, Thiago Venancio wrote:

> Hi all,
>
> This topic was discussed before, but I would like to put it on the  
> list
> again, maybe someone has an update.
>
> The methods frac_identical, frac_conserved, frac_aligned_query and
> frac_aligned_hit can also be used in the hit context, after HSP  
> tilling. In
> my point of view, it is better to use it just in HSPs individually,  
> because
> there are some rare/strange kinds of alignments. However, we  
> frequently need
> to get one measure of the whole alignment.
>
> Any of the BioPerl masters has an update on this topic ? What is  
> the best
> current usage ?
>
> Best.
>
> Thiago




From razi.khaja at gmail.com  Tue Oct  2 23:46:12 2007
From: razi.khaja at gmail.com (Razi Khaja)
Date: Tue, 2 Oct 2007 19:46:12 -0400
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <4702BC5B.7040407@web.de>
References: <4701AEE6.6070506@web.de> <4701F9C9.4050808@sheffield.ac.uk>
	<47020DC9.8040401@web.de> <470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
	<D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz>
	<4702BC5B.7040407@web.de>
Message-ID: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>

Here is the easiest non-bioperl solution using executables provided
with ncbi's blast:

(1) format your multifasta file into a blast database

> /usr/local/ncbi/blast-2.2.16/bin/formatdb -i yourmultifastafile -t yourblastdb

(2) extract sequences from the newly created blast database with a
file containing a list of accession numbers (one on each line)

> /usr/local/ncib/blast-2.2.16/bin/fastacmd -d yourblastdb -i inputfilewithaccessionnumbers -o outputfile

Your outputfile should be a multifasta file of your list of accession numbers

blast executables are available from
http://www.ncbi.nlm.nih.gov/blast/download.shtml

Hope that helps.
Razi Khaja

On 10/2/07, outaleb Issame <outaleb at web.de> wrote:
> thx for this, but i want just create new fasta file with my accNumbers
> which i search in the FASTA file(localdbase).
> so --> just search this Numbers in the FASTA file, if yes then copy the
> Header and Sequence to other new fasta file .
> i m sitting in this 2 days now;  i dont think it s  difficult but howww?????
> i get crazy guys.
> common some expert in this area??
>
>
>
> Smithies, Russell wrote:
>
> >I know this is the Bioperl list but how about just doing it with grep?
> >
> >       grep -P '^>.*XM_001666470[\s^>]*' sequences.fasta
> >
> >
> >
> >
> >
> >>-----Original Message-----
> >>From: bioperl-l-bounces at lists.open-bio.org
> >>
> >>
> >[mailto:bioperl-l-bounces at lists.open-
> >
> >
> >>bio.org] On Behalf Of outaleb Issame
> >>Sent: Wednesday, 3 October 2007 3:51 a.m.
> >>To: outaleb Issame
> >>Cc: bioperl-l at lists.open-bio.org
> >>Subject: Re: [Bioperl-l] need help ??parse AcNum from fasta?
> >>
> >>hi again,
> >>i think i can resolve this problem with the method : id_parser();
> >>how can i do that?
> >>any suggestion .or experience??
> >>ehx again
> >>
> >>
> >>
> >>outaleb Issame wrote:
> >>
> >>
> >>
> >>>thx for the help, but i got a empty output file,
> >>>i think its problem with matching the acc number, my fasta file look
> >>>
> >>>
> >like:
> >
> >
> >>>*>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>
> >>>
> >>protein
> >>
> >>
> >>>DDHHHU...
> >>>
> >>>
> >>>>IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>DDHHHU..
> >>>
> >>>
> >>>>IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3
> >>>>
> >>>>
> >>protein
> >>
> >>
> >>>MMMMM..*
> >>>
> >>>and my i Accnum File look like:
> >>>*IPI00177321
> >>>IPI00453473
> >>>
> >>>*i hopt it helps to understand.*
> >>>*.
> >>>
> >>>
> >>>Nathan S. Haigh wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>outaleb Issame wrote:
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>>hi,
> >>>>>with this file i mean, i picked out this Accession Number from
> >>>>>IPI-Human Dbase,they come from a fasta file,
> >>>>>so they re under eachother like a i a table in separate file now.
> >>>>>what i want is how how can i check it in the fasta File (so in the
> >>>>>IPI-Human FAsta File), i they re really there;
> >>>>>if yes please copy the entire entry of this Number (>....the
> >>>>>
> >>>>>
> >sequence
> >
> >
> >>>>>also)in new fasta file.so that i get at the end a new
> >>>>>FASTA file with jus this IPI Accession Number.
> >>>>>thx and hope was clearly.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>Ok, first of all, I'd read the contents of your Accession numbers
> >>>>
> >>>>
> >into a
> >
> >
> >>>>hash, something like the following (this could be written in a
> >>>>
> >>>>
> >shorter
> >
> >
> >>>>form, but since you're a newbie I'll leave it in a longer form so
> >>>>
> >>>>
> >you
> >
> >
> >>>>can follow easier).
> >>>>
> >>>>-- start script --
> >>>>use strict;
> >>>>use Bio::SeqIO;
> >>>>
> >>>># change the following three lines to point to the relevant paths
> >>>># of your list of accessions file, your fasta file and your output
> >>>># fasta file
> >>>>my $acc_file = "/path/to/your/file";
> >>>>my $fasta_file_in = "/path/to/your/fasta/file";
> >>>>my $fasta_file_out = "/path/to/your/fasta/output/file";
> >>>>
> >>>># Use a hash to keep a record of accessions we want to find
> >>>>my %hash_of_req_acc;
> >>>>
> >>>># read all the required accessions from the file into the hash as
> >>>>
> >>>>
> >keys
> >
> >
> >>>>open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
> >>>>while (<ACC_FILE>) {
> >>>>my $line = $_;
> >>>>chomp $line;
> >>>>$hash_of_req_acc{$_} = 1;
> >>>>}
> >>>>close ACC_FILE;
> >>>>
> >>>>my $seqio_object_in = Bio::SeqIO->new(
> >>>>-file => $fasta_file_in,
> >>>>-format => 'fasta'
> >>>>);
> >>>>my $seqio_object_out = Bio::SeqIO->new(
> >>>>-file => $fasta_file_out,
> >>>>-format => 'fasta'
> >>>>);
> >>>>
> >>>># loop through all the sequences in the fasta file
> >>>>while (my $seq_object = $seqio_object_in->next_seq) {
> >>>># get the sequence accession for easy matching
> >>>>my $seq_acc = $seq_object->accession_number;
> >>>>
> >>>># write the sequence object to the output fasta file if we have a
> >>>>matching accession
> >>>>$seqio_object_out->write_seq($seq_object) if exists
> >>>>$hash_of_req_acc{$seq_acc};
> >>>>}
> >>>>-- end script --
> >>>>
> >>>>I haven't tested this, but it should at least get you started. Also,
> >>>>
> >>>>
> >the
> >
> >
> >>>>fasta description line in the output file may not be exactly as it
> >>>>
> >>>>
> >was
> >
> >
> >>>>in the input fasta file - if this really matters, you may need to
> >>>>
> >>>>
> >get
> >
> >
> >>>>back to us. Also, if the input fasta file is huge (many thousands of
> >>>>sequences) it may be wise to create an index of the fasta file in
> >>>>
> >>>>
> >order
> >
> >
> >>>>to speed up retrieval.
> >>>>
> >>>>You may find this page helpful:
> >>>>http://www.bioperl.org/wiki/HOWTO:SeqIO
> >>>>
> >>>>Anyway, hope this helps to get you started.
> >>>>Nath
> >>>>
> >>>>
> >>>>_______________________________________________
> >>>>Bioperl-l mailing list
> >>>>Bioperl-l at lists.open-bio.org
> >>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>_______________________________________________
> >>>Bioperl-l mailing list
> >>>Bioperl-l at lists.open-bio.org
> >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>>
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >=======================================================================
> >Attention: The information contained in this message and/or attachments
> >from AgResearch Limited is intended only for the persons or entities
> >to which it is addressed and may contain confidential and/or privileged
> >material. Any review, retransmission, dissemination or other use of, or
> >taking of any action in reliance upon, this information by persons or
> >entities other than the intended recipients is prohibited by AgResearch
> >Limited. If you have received this message in error, please notify the
> >sender immediately.
> >=======================================================================
> >
> >
> >
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From jason at bioperl.org  Wed Oct  3 00:50:37 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 2 Oct 2007 17:50:37 -0700
Subject: [Bioperl-l] need help ??parse AcNum from fasta?
In-Reply-To: <47025AD9.1090105@web.de>
References: <4701AEE6.6070506@web.de>	<4701F9C9.4050808@sheffield.ac.uk>	<47020DC9.8040401@web.de>	<470215E1.4080901@sheffield.ac.uk>
	<47022278.7010700@web.de> <47025AD9.1090105@web.de>
Message-ID: <CF48176B-CE5B-40EC-81DE-8C3114502ADE@bioperl.org>

http://bioperl.open-bio.org/wiki/ 
FAQ#How_do_I_use_Bio::Index::Fasta_and_index_on_different_ids.3F

On Oct 2, 2007, at 7:51 AM, outaleb Issame wrote:

> hi again,
> i think i can resolve this problem with the method : id_parser();
> how can i do that?
> any suggestion .or experience??
> ehx again
>
>
>
> outaleb Issame wrote:
>
>> thx for the help, but i got a empty output file,
>> i think its problem with matching the acc number, my fasta file  
>> look like:
>>
>> *>IPI:IPI00453473.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to  
>> NOD3 protein
>> DDHHHU...
>>> IPI:IPI00177321.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> DDHHHU..
>>> IPI:IPI00027547.1|REFSEQ_XP:XP_168060 Tax_Id=9606 similar to NOD3  
>>> protein
>> MMMMM..*
>>
>> and my i Accnum File look like:
>> *IPI00177321
>> IPI00453473
>>
>> *i hopt it helps to understand.*
>> *.
>>
>>
>> Nathan S. Haigh wrote:
>>
>>
>>
>>> outaleb Issame wrote:
>>>
>>>
>>>
>>>
>>>> hi,
>>>> with this file i mean, i picked out this Accession Number from
>>>> IPI-Human Dbase,they come from a fasta file,
>>>> so they re under eachother like a i a table in separate file now.
>>>> what i want is how how can i check it in the fasta File (so in the
>>>> IPI-Human FAsta File), i they re really there;
>>>> if yes please copy the entire entry of this Number (>....the  
>>>> sequence
>>>> also)in new fasta file.so that i get at the end a new
>>>> FASTA file with jus this IPI Accession Number.
>>>> thx and hope was clearly.
>>>>
>>>>
>>>>
>>>>
>>> Ok, first of all, I'd read the contents of your Accession numbers  
>>> into a
>>> hash, something like the following (this could be written in a  
>>> shorter
>>> form, but since you're a newbie I'll leave it in a longer form so  
>>> you
>>> can follow easier).
>>>
>>> -- start script --
>>> use strict;
>>> use Bio::SeqIO;
>>>
>>> # change the following three lines to point to the relevant paths
>>> # of your list of accessions file, your fasta file and your output
>>> # fasta file
>>> my $acc_file = "/path/to/your/file";
>>> my $fasta_file_in = "/path/to/your/fasta/file";
>>> my $fasta_file_out = "/path/to/your/fasta/output/file";
>>>
>>> # Use a hash to keep a record of accessions we want to find
>>> my %hash_of_req_acc;
>>>
>>> # read all the required accessions from the file into the hash as  
>>> keys
>>> open (ACC_FILE, $acc_file) or die "Couldn't open file: $!\n";
>>> while (<ACC_FILE>) {
>>> my $line = $_;
>>> chomp $line;
>>> $hash_of_req_acc{$_} = 1;
>>> }
>>> close ACC_FILE;
>>>
>>> my $seqio_object_in = Bio::SeqIO->new(
>>> -file => $fasta_file_in,
>>> -format => 'fasta'
>>> );
>>> my $seqio_object_out = Bio::SeqIO->new(
>>> -file => $fasta_file_out,
>>> -format => 'fasta'
>>> );
>>>
>>> # loop through all the sequences in the fasta file
>>> while (my $seq_object = $seqio_object_in->next_seq) {
>>> # get the sequence accession for easy matching
>>> my $seq_acc = $seq_object->accession_number;
>>>
>>> # write the sequence object to the output fasta file if we have a
>>> matching accession
>>> $seqio_object_out->write_seq($seq_object) if exists
>>> $hash_of_req_acc{$seq_acc};
>>> }
>>> -- end script --
>>>
>>> I haven't tested this, but it should at least get you started.  
>>> Also, the
>>> fasta description line in the output file may not be exactly as  
>>> it was
>>> in the input fasta file - if this really matters, you may need to  
>>> get
>>> back to us. Also, if the input fasta file is huge (many thousands of
>>> sequences) it may be wise to create an index of the fasta file in  
>>> order
>>> to speed up retrieval.
>>>
>>> You may find this page helpful:
>>> http://www.bioperl.org/wiki/HOWTO:SeqIO
>>>
>>> Anyway, hope this helps to get you started.
>>> Nath
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From Russell.Smithies at agresearch.co.nz  Wed Oct  3 01:05:25 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Wed, 3 Oct 2007 14:05:25 +1300
Subject: [Bioperl-l] coloring of HSPs in blast panel
In-Reply-To: <62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
References: <4701AEE6.6070506@web.de>
	<4701F9C9.4050808@sheffield.ac.uk><47020DC9.8040401@web.de>
	<470215E1.4080901@sheffield.ac.uk><47022278.7010700@web.de>
	<47025AD9.1090105@web.de><D5DBA313349A4B458528BE63B387F36C05DCDB97@imail.agresearch.co.nz><4702BC5B.7040407@web.de>
	<62e9dabc0710021646h479d3104wca106ebc99a38b0e@mail.gmail.com>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05DCDC73@imail.agresearch.co.nz>

Hi all,
I'm using a modified version of Lincoln's tutorial
(http://www.bioperl.org/wiki/HOWTO:Graphics#Parsing_Real_BLAST_Output)
and I'm colouring the HSPs by setting the -bgcolor by score with a sub
to give a similar image to that from NCBI but for some reason, my
colours are coming out wrong (see attached example)
They seem to be off by one but I can't see why.

Any ideas?

I can't be certain but I think it's only started doing this since our
BLAST upgrade to 2.2.17 a few weeks ago.

Here's the colouring code:
------------------------------------------------------------------------
-------
my $track = $panel->add_track(
                              -glyph       => 'segments',
                              -label       => 1,
                              -connector   => 'dashed',
                              -bgcolor     => sub {
                                my $feature = shift;
                                my $score = $feature->score;
			return 'red'       if $score >= 200;
                                    return 'fuchsia' if $score >= 80;
                                    return 'lime'      if $score >= 50;
			return 'blue'      if $score >= 40;
                                    return 'black';
                               },
                              -font2color  => 'gray',
                              -sort_order  => 'high_score',
                              -description => sub {
                                my $feature = shift;
                                return unless
$feature->has_tag('description');
                                my ($description) =
$feature->each_tag_value('description');
                                my $score = $feature->score;
                                "$description, score=$score";
                               },
                             );
------------------------------------------------------------------------
---------


Thanx,

Russell Smithies




=======================================================================
Attention: The information contained in this message and/or attachments
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to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
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From aaron.j.mackey at gsk.com  Wed Oct  3 01:40:14 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Tue, 2 Oct 2007 21:40:14 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
Message-ID: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>

Let me second Jason's comment that while BLAST is a great search program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with the 
FASTA package) is now vector-parallelized on most i386 architectures, it 
is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run 
BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 14:50:47 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 10:50:47 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
References: <3DC00A97-EF7E-41B4-854F-B088715AB901@bioperl.org>
	<OF84BBED54.6B63F93A-ON85257369.00082331-85257369.00093614@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>

I agree that BLAST is not a very good alignment algorithm but believe
there are plenty of reasons to run BLAST, especially when placing a
contig /BAC/PAC to a genome. In those cases, fully implementation of SW
requires an unpractical matrix of n X m.   

Currently we are developing an algorithm which will run global alignment
after BLAST. Hopefully a Perl wrapper will become available next year.


Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Tuesday, October 02, 2007 9:40 PM
To: Jason Stajich
Cc: bioperl-l list; Thiago Venancio
Subject: Re: [Bioperl-l] frac_* methods

Let me second Jason's comment that while BLAST is a great search
program, 
it is not a very good alignment algorithm.  In this day and age with so 
many good pairwise alignment algorithms out there (customized for the 
context in which the alignment is performed), BLAST-based alignments 
should frankly be ignored.  See: exonerate, pairagon, etc.

Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
the 
FASTA package) is now vector-parallelized on most i386 architectures, it

is only about 10 times slower than BLAST for complete database searches 
(with superior sensitivity/specificity); add PVM or MPI-based CPU 
parallelization on top of that, and there's almost no reason to even run

BLAST anymore ...

-Aaron

bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:

> I think my answer before was something to the tune of:
> 
> Use an alignment algorithm that finds a single best alignment like 
> FASTA or Smith-Waterman (SW) if what you want is a single number that 
> represents the alignment.  BLAST is great for fast searching but 
> FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> Consider the -postsw option in WUBLAST as well as it will realign the 
> HSPs with SW.
> 
> I personally never use the frac alignment summary stats for the Hit 
> object for this reason unless I know I am going to have a single HSP.
> 
> -jason
> 
> On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> 
> > Hi all,
> >
> > This topic was discussed before, but I would like to put it on the 
> > list
> > again, maybe someone has an update.
> >
> > The methods frac_identical, frac_conserved, frac_aligned_query and
> > frac_aligned_hit can also be used in the hit context, after HSP 
> > tilling. In
> > my point of view, it is better to use it just in HSPs individually, 
> > because
> > there are some rare/strange kinds of alignments. However, we 
> > frequently need
> > to get one measure of the whole alignment.
> >
> > Any of the BioPerl masters has an update on this topic ? What is 
> > the best
> > current usage ?
> >
> > Best.
> >
> > Thiago
> >
> > -- 
> > "Innovation distinguishes between a leader and a follower."
> >     Steve Jobs
> >
> > ========================
> > Thiago Motta Venancio, MSc
> > PhD student in Bioinformatics
> > University of Sao Paulo
> > ========================
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> jason at bioperl.org
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 


_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l



From aaron.j.mackey at gsk.com  Wed Oct  3 15:53:12 2007
From: aaron.j.mackey at gsk.com (aaron.j.mackey at gsk.com)
Date: Wed, 3 Oct 2007 11:53:12 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
Message-ID: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are expected 
to occur naturally (i.e. are not an artifact of the experiment that in an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very 
good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical significance)

Please don't get me wrong, I think BLAST is an invaluable tool that fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures, it
> 
> is only about 10 times slower than BLAST for complete database searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment. 
> > Consider the -postsw option in WUBLAST as well as it will realign the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the 
> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From vebaev at gmail.com  Wed Oct  3 16:44:35 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 19:44:35 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
Message-ID: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>

Hi,
What methods should I use to draw a CG plot of a sequence (with
bio::graphics)?

Thanks

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com

-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From cuiw at ncbi.nlm.nih.gov  Wed Oct  3 17:37:51 2007
From: cuiw at ncbi.nlm.nih.gov (Cui, Wenwu (NIH/NLM/NCBI) [C])
Date: Wed, 3 Oct 2007 13:37:51 -0400
Subject: [Bioperl-l] frac_* methods
In-Reply-To: <OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
References: <18C407FD4FFB424292D769FBD68C198701B18C35@NIHCESMLBX8.nih.gov>
	<OFC17CB146.3CECA88E-ON85257369.0055F4E1-85257369.00574D87@gsk.com>
Message-ID: <18C407FD4FFB424292D769FBD68C198701B18C36@NIHCESMLBX8.nih.gov>

I agree what you said. 

One of the reasons that we introduce 'BLAST-guided-global alignment
(NW)' is that a significant amount of clones are either of low quality,
partially sequenced, erroneously assembled, or come from non reference
strain.   

Wenwu Cui, PhD

-----Original Message-----
From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
Sent: Wednesday, October 03, 2007 11:53 AM
To: Cui, Wenwu (NIH/NLM/NCBI) [C]
Cc: bioperl-l list; Jason Stajich; Thiago Venancio
Subject: RE: [Bioperl-l] frac_* methods

I think Wenwu makes a nice distinction here between alignment and 
placement.  BLAST is great at finding things and (thus) placing things.

String matching has a long and rich history in computer science, and we 
tend to confuse the terms "alignment" with "matching".  The "align a 
BAC/PAC to a genome" problem is one of string matching (with allowance
for 
errors due to sequencing artifacts and possible SNPs); if there were no 
errors, we wouldn't use BLAST at all (and, in fact, I personally think 
programs such as MUMMER, or the various genome assembly tiling
algorithms, 
are better for this particular problem).  The problem of pairwise 
alignment can also be called matching, but the distinction (at least to 
me) is that the "errors" are true evolutionary mutations, and are
expected 
to occur naturally (i.e. are not an artifact of the experiment that in
an 
optimal world would not occur).  BLAST is good at finding matches whose 
"errors" fit scoring-matrix-based evolutionary models, but it isn't very

good at teasing out the actual evolutionary events that lead to those 
"errors" (this is not really a criticism of BLAST - it's job is not to 
generate evolutionarily-accurate, and -complete alignments, but to 
identify evolutionarily-conserved regions having statistical
significance)

Please don't get me wrong, I think BLAST is an invaluable tool that
fully 
deserves its top-most place in the bioinformatics hall of fame.  But I 
also don't believe that bioinformatics begins and ends with running a 
BLAST search and poring over the report details.

-Aaron

"Cui, Wenwu (NIH/NLM/NCBI) [C]" <cuiw at ncbi.nlm.nih.gov> wrote on 
10/03/2007 10:50:47 AM:

> I agree that BLAST is not a very good alignment algorithm but believe
> there are plenty of reasons to run BLAST, especially when placing a
> contig /BAC/PAC to a genome. In those cases, fully implementation of
SW
> requires an unpractical matrix of n X m. 
> 
> Currently we are developing an algorithm which will run global
alignment
> after BLAST. Hopefully a Perl wrapper will become available next year.
> 
> 
> Wenwu Cui, PhD
> 
> -----Original Message-----
> From: aaron.j.mackey at gsk.com [mailto:aaron.j.mackey at gsk.com] 
> Sent: Tuesday, October 02, 2007 9:40 PM
> To: Jason Stajich
> Cc: bioperl-l list; Thiago Venancio
> Subject: Re: [Bioperl-l] frac_* methods
> 
> Let me second Jason's comment that while BLAST is a great search
> program, 
> it is not a very good alignment algorithm.  In this day and age with
so 
> many good pairwise alignment algorithms out there (customized for the 
> context in which the alignment is performed), BLAST-based alignments 
> should frankly be ignored.  See: exonerate, pairagon, etc.
> 
> Oh, and since ssearch35 (the Smith-Waterman algorithm that comes with
> the 
> FASTA package) is now vector-parallelized on most i386 architectures,
it
> 
> is only about 10 times slower than BLAST for complete database
searches 
> (with superior sensitivity/specificity); add PVM or MPI-based CPU 
> parallelization on top of that, and there's almost no reason to even
run
> 
> BLAST anymore ...
> 
> -Aaron
> 
> bioperl-l-bounces at lists.open-bio.org wrote on 10/02/2007 06:22:59 PM:
> 
> > I think my answer before was something to the tune of:
> > 
> > Use an alignment algorithm that finds a single best alignment like 
> > FASTA or Smith-Waterman (SW) if what you want is a single number
that 
> > represents the alignment.  BLAST is great for fast searching but 
> > FASTA or SW/SSEARCH are going to be better at creating an alignment.

> > Consider the -postsw option in WUBLAST as well as it will realign
the 
> > HSPs with SW.
> > 
> > I personally never use the frac alignment summary stats for the Hit 
> > object for this reason unless I know I am going to have a single
HSP.
> > 
> > -jason
> > 
> > On Oct 2, 2007, at 2:41 PM, Thiago Venancio wrote:
> > 
> > > Hi all,
> > >
> > > This topic was discussed before, but I would like to put it on the

> > > list
> > > again, maybe someone has an update.
> > >
> > > The methods frac_identical, frac_conserved, frac_aligned_query and
> > > frac_aligned_hit can also be used in the hit context, after HSP 
> > > tilling. In
> > > my point of view, it is better to use it just in HSPs
individually, 
> > > because
> > > there are some rare/strange kinds of alignments. However, we 
> > > frequently need
> > > to get one measure of the whole alignment.
> > >
> > > Any of the BioPerl masters has an update on this topic ? What is 
> > > the best
> > > current usage ?
> > >
> > > Best.
> > >
> > > Thiago
> > >
> > > -- 
> > > "Innovation distinguishes between a leader and a follower."
> > >     Steve Jobs
> > >
> > > ========================
> > > Thiago Motta Venancio, MSc
> > > PhD student in Bioinformatics
> > > University of Sao Paulo
> > > ========================
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> > --
> > Jason Stajich
> > jason at bioperl.org
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 




From cjfields at uiuc.edu  Wed Oct  3 18:19:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 13:19:43 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
Message-ID: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>

You should look at Bio::Graphics::Glyph::dna.  From the POD:

---------------------------

This glyph draws DNA sequences.  At high magnifications, this glyph
will draw the actual base pairs of the sequence (both strands).  At
low magnifications, the glyph will plot the GC content.  By default,
the GC calculation will use non-overlapping bins, but this can be
changed by specifying the gc_window option, in which case, a
sliding window calculation will be used.

For this glyph to work, the feature must return a DNA sequence string
in response to the dna() method. For example, you can use a
Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
like this:
     my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
     my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end  
=> 800 );
     $feature->attach_seq($dna);
     $panel->add_track( $feature, -glyph => 'dna' );

A Bio::Graphics::Feature object may also be used.

---------------------------

chris

On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:

> Hi,
> What methods should I use to draw a CG plot of a sequence (with
> bio::graphics)?
>
> Thanks
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
>
> -- 
> ------------------------------------------------
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology
> Bioinformatics Group
> Tzar Assen 24
> Plovdiv 4000, BULGARIA
> 032/ 261 (534)
> 089/ 57-444-67
> Skype: vesselin_baev
> vebaev at gmail.com
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From vebaev at gmail.com  Wed Oct  3 18:31:49 2007
From: vebaev at gmail.com (Vesselin Baev)
Date: Wed, 3 Oct 2007 21:31:49 +0300
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
Message-ID: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>

Thanks,
I will use Bio::Graphics::Glyph::dna for the classical CG%
(this type is for C+G % or CpG)?


and if I want to draw a similar plot but for example for a % of dinucleotide
(NpN) occurrances in a sliding windiw, what should I use?


Thanks!




2007/10/3, Chris Fields <cjfields at uiuc.edu>:
>
> You should look at Bio::Graphics::Glyph::dna.  From the POD:
>
> ---------------------------
>
> This glyph draws DNA sequences.  At high magnifications, this glyph
> will draw the actual base pairs of the sequence (both strands).  At
> low magnifications, the glyph will plot the GC content.  By default,
> the GC calculation will use non-overlapping bins, but this can be
> changed by specifying the gc_window option, in which case, a
> sliding window calculation will be used.
>
> For this glyph to work, the feature must return a DNA sequence string
> in response to the dna() method. For example, you can use a
> Bio::SeqFeature::Generic object with an attached Bio::PrimarySeq
> like this:
>      my $dna = Bio::PrimarySeq->new( -seq => 'A' x 1000 );
>      my $feature = Bio::SeqFeature::Generic->new( -start => 1, -end
> => 800 );
>      $feature->attach_seq($dna);
>      $panel->add_track( $feature, -glyph => 'dna' );
>
> A Bio::Graphics::Feature object may also be used.
>
> ---------------------------
>
> chris
>
> On Oct 3, 2007, at 11:44 AM, Vesselin Baev wrote:
>
> > Hi,
> > What methods should I use to draw a CG plot of a sequence (with
> > bio::graphics)?
> >
> > Thanks
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> >
> > --
> > ------------------------------------------------
> > University of Plovdiv
> > Faculty of Biology
> > Dept. Molecular Biology
> > Bioinformatics Group
> > Tzar Assen 24
> > Plovdiv 4000, BULGARIA
> > 032/ 261 (534)
> > 089/ 57-444-67
> > Skype: vesselin_baev
> > vebaev at gmail.com
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
------------------------------------------------
University of Plovdiv
Faculty of Biology
Dept. Molecular Biology
Bioinformatics Group
Tzar Assen 24
Plovdiv 4000, BULGARIA
032/ 261 (534)
089/ 57-444-67
Skype: vesselin_baev
vebaev at gmail.com


From dave at davemessina.com  Wed Oct  3 18:22:23 2007
From: dave at davemessina.com (Dave Messina)
Date: Wed, 3 Oct 2007 20:22:23 +0200
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <37574C6D-98BA-47A5-875E-9255377133B8@sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the  
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Graphics/Panel.html

I think the example code will help you to do what you want.


Dave



From cjfields at uiuc.edu  Wed Oct  3 19:10:46 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 3 Oct 2007 14:10:46 -0500
Subject: [Bioperl-l] CG content plot of sequence
In-Reply-To: <a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
References: <a71127900710030940s6c1f19d9mddaf7339569467cc@mail.gmail.com>
	<a71127900710030944k270aa5e4v7bf8496f9dd9558a@mail.gmail.com>
	<3427C150-D571-4C7B-99FC-F6FE77C9A344@uiuc.edu>
	<a71127900710031131n363bc80v18311b58db7026f0@mail.gmail.com>
Message-ID: <7B62B534-2A8C-4EAE-B956-F0FADB726195@uiuc.edu>

On Oct 3, 2007, at 1:31 PM, Vesselin Baev wrote:

> Thanks,
> I will use Bio::Graphics::Glyph::dna for the classical CG%
> (this type is for C+G % or CpG)?
>
>
> and if I want to draw a similar plot but for example for a % of  
> dinucleotide
> (NpN) occurrances in a sliding windiw, what should I use?
>
>
> Thanks!

It would be GC content, not CpG.  Not sure what you would use for  
dinucleotide content; you could look at the Bio::Graphics::Glyph::dna  
code and either subclass it for your needs (probably the best option)  
or add an extra parameter and 'rewire' the appropriate methods to do  
what you want.

chris


From dmessina at sbc.su.se  Wed Oct  3 18:55:10 2007
From: dmessina at sbc.su.se (dmessina at sbc.su.se)
Date: Wed, 3 Oct 2007 20:55:10 +0200 (CEST)
Subject: [Bioperl-l] CG content plot of sequence
Message-ID: <61118.217.213.158.117.1191437710.squirrel@mail.sbc.su.se>

Hi Vesselin,

I believe what you want to use is Bio::Graphics::Panel with the
Bio::Graphics::Glyph::dna glyph.

See

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Glyph/dna.html

and

http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Graphics/Panel.html

I think the example code will help you to do what you want.


Dave




From lzhtom at hotmail.com  Wed Oct  3 22:30:43 2007
From: lzhtom at hotmail.com (zhihuali)
Date: Wed, 3 Oct 2007 22:30:43 +0000
Subject: [Bioperl-l] Loading Blast Report in a minimal way
Message-ID: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>


Hi netters,

I'm using SearchIO to parse my blast reports. They are extremely huge, and not surprisingly, it's extremely slow and sometimes the system crashed due to memmory problem. As I can handle small reports quickly, it seems like a problem related to the way SearchIO works: it slurps the whole report into the memory and builds millions of objects.

I've checked old posts and some people used FastHitEventBuilder to build hit objects without any hsp objects. And some people suggested using tabular output of blast. But in my case I need to go to each of the hsps of each hit, parse the alignment, and gather the information needed if that hsp fits certain criteria, and then move on to the next hsp/or jump over to the next hit/ or exit the processing, according to the information I have already got. An ideal way would be to read one hsp at a time from the report to the memory.  Is there some way to modify SearchIO (or build another Search Event) to do this?

Thanks a lot!


Zhihua Li
_________________________________________________________________
? Live Search ???????
http://www.live.com/?searchOnly=true


From budd at embl-heidelberg.de  Thu Oct  4 13:43:57 2007
From: budd at embl-heidelberg.de (Aidan Budd)
Date: Thu, 4 Oct 2007 15:43:57 +0200 (CEST)
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
Message-ID: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>

Hi bioperlers,

I've been trying to add info to a feature in a RichSeq object so that when 
the Seq is written in swissprot format I can put information in the final
field of the feature

FT   DOMAIN      208    392       Helicase ATP-binding.

i.e. where it says "Helicase ATP-binding."

I can control what goes in the primary field, and set the location, but 
haven't been able to work out how to add info to go in this final field.

Thanks,

Aidan

-- 
----------------------------------------------------------------------
Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
Meyerhofstr. 1, 69117 Heidelberg, Germany

URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html



From cjfields at uiuc.edu  Thu Oct  4 14:32:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 09:32:43 -0500
Subject: [Bioperl-l] Adding info to Features to view in SwissProt
In-Reply-To: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
References: <Pine.LNX.4.44.0710041540540.20949-100000@bibo.EMBL-Heidelberg.DE>
Message-ID: <84A6CB47-6890-476B-A375-6FCF37655330@uiuc.edu>

Try adding it as a tag value with the name 'description','note', or  
'product' (the first two are probably the best to use for most  
purposes).  There is a quick explanation here:

http://www.bioperl.org/wiki/HOWTO:Feature- 
Annotation#Building_Your_Own_Sequences

You can also do something like:

$sf->add_tag_value('description', 'Helicase ATP-binding');

See Bio::SeqFeature::Generic POD for more.

chris

On Oct 4, 2007, at 8:43 AM, Aidan Budd wrote:

> Hi bioperlers,
>
> I've been trying to add info to a feature in a RichSeq object so  
> that when
> the Seq is written in swissprot format I can put information in the  
> final
> field of the feature
>
> FT   DOMAIN      208    392       Helicase ATP-binding.
>
> i.e. where it says "Helicase ATP-binding."
>
> I can control what goes in the primary field, and set the location,  
> but
> haven't been able to work out how to add info to go in this final  
> field.
>
> Thanks,
>
> Aidan
>
> -- 
> ----------------------------------------------------------------------
> Aidan Budd, PhD                               tel:+49 (0)6221 387 8530
> EMBL - European Molecular Biology Laboratory  fax:+49 (0)6221 387 8517
> Meyerhofstr. 1, 69117 Heidelberg, Germany
>
> URL: http://www-db.embl.de/jss/EmblGroupsHD/per_1807.html
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cain.cshl at gmail.com  Thu Oct  4 15:08:52 2007
From: cain.cshl at gmail.com (Scott Cain)
Date: Thu, 04 Oct 2007 11:08:52 -0400
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
Message-ID: <1191510532.2787.16.camel@localhost.localdomain>

Hi Chris,

I think adding the type=MYISAM is the right thing to do; please go ahead
and commit it.

Scott



On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
> Just thought I would forward this on to the GBrowse list as well in  
> case anyone has run into the same problem.  The issue pops up when  
> using bioperl from CVS and appears to be related to a fix Lincoln  
> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using  
> FULLTEXT, which only works for MyISAM currently.
> 
> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE  
> queries does work when InnoDB is set to the default.  Should I go  
> ahead and commit?
> 
> chris
> 
> Begin forwarded message:
> 
> > I'm getting the following error on my local MySQL (v 5.0.41) with
> > bp_seqfeature_load:
> >
> > -------------------- EXCEPTION --------------------
> > MSG: The used table type doesn't support FULLTEXT indexes
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /Library/
> > Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
> > STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
> > Bio/DB/SeqFeature/Store.pm:382
> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
> > 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
> > STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
> > SeqFeature/Store.pm:345
> > STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
> > -------------------------------------------
> >
> > The default setting for storage is InnoDB; switching to MyISAM fixes
> > the issue.  Should we specify TYPE = MyISAM with the various CREATE
> > TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
> > safe side?
> >
> > chris
> 
> 
> 
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2005.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory



From cjfields at uiuc.edu  Thu Oct  4 15:14:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 10:14:37 -0500
Subject: [Bioperl-l] [Gmod-gbrowse] Fwd:  DB::SeqFeature::Store error
In-Reply-To: <1191510532.2787.16.camel@localhost.localdomain>
References: <A56E6D20-EF3E-4B5D-B3F2-9F2B7D0178EF@uiuc.edu>
	<D102CDC9-00FD-478F-8100-9DD39D58AD32@uiuc.edu>
	<1191510532.2787.16.camel@localhost.localdomain>
Message-ID: <9DEFB5C1-6F79-465B-8FB4-68305C53E427@uiuc.edu>

Done.  If we run into issues and need to roll back let me know.

chris

On Oct 4, 2007, at 10:08 AM, Scott Cain wrote:

> Hi Chris,
>
> I think adding the type=MYISAM is the right thing to do; please go  
> ahead
> and commit it.
>
> Scott
>
>
>
> On Mon, 2007-10-01 at 10:14 -0500, Chris Fields wrote:
>> Just thought I would forward this on to the GBrowse list as well in
>> case anyone has run into the same problem.  The issue pops up when
>> using bioperl from CVS and appears to be related to a fix Lincoln
>> added recently in Bio::DB::SeqFeature::Store::DBI::mysql using
>> FULLTEXT, which only works for MyISAM currently.
>>
>> Making the suggested changes (adding TYPE=MYISAM) to the CREATE TABLE
>> queries does work when InnoDB is set to the default.  Should I go
>> ahead and commit?
>>
>> chris
>>
>> Begin forwarded message:
>>
>>> I'm getting the following error on my local MySQL (v 5.0.41) with
>>> bp_seqfeature_load:
>>>
>>> -------------------- EXCEPTION --------------------
>>> MSG: The used table type doesn't support FULLTEXT indexes
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database / 
>>> Library/
>>> Perl/5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:414
>>> STACK Bio::DB::SeqFeature::Store::init_database /Library/Perl/5.8.6/
>>> Bio/DB/SeqFeature/Store.pm:382
>>> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /Library/Perl/
>>> 5.8.6/Bio/DB/SeqFeature/Store/DBI/mysql.pm:218
>>> STACK Bio::DB::SeqFeature::Store::new /Library/Perl/5.8.6/Bio/DB/
>>> SeqFeature/Store.pm:345
>>> STACK toplevel /usr/local/bin/bp_seqfeature_load.pl:57
>>> -------------------------------------------
>>>
>>> The default setting for storage is InnoDB; switching to MyISAM fixes
>>> the issue.  Should we specify TYPE = MyISAM with the various CREATE
>>> TABLE queries in Bio::DB::SeqFeature::Store::DBI::mysql to be on the
>>> safe side?
>>>
>>> chris
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ----
>> This SF.net email is sponsored by: Microsoft
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>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
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>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> -- 
> ---------------------------------------------------------------------- 
> --
> Scott Cain, Ph. D.                                          
> cain at cshl.edu
> GMOD Coordinator (http://www.gmod.org/)                      
> 216-392-3087
> Cold Spring Harbor Laboratory
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Thu Oct  4 19:30:48 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 14:30:48 -0500
Subject: [Bioperl-l] blastxml oddity
Message-ID: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>

Just noticed an oddity from BLASTXML output from the NCBI server; I'm  
cc'ing this to NCBI so maybe they can explain.  BTW, the following  
doesn't occur via URLAPI.

When running a standard BLAST query using the NCBI web page, if  
requesting XML output after the run I get the entire query seq masked  
out and no midline.  This occurs with all default settings except  
output type (set to XML).  Can anyone replicate this?

Here's a sample:

<Hit_hsps>
             <Hsp>
               <Hsp_num>1</Hsp_num>
               <Hsp_bit-score>320.472</Hsp_bit-score>
               <Hsp_score>820</Hsp_score>
               <Hsp_evalue>2.17708e-86</Hsp_evalue>
               <Hsp_query-from>1</Hsp_query-from>
               <Hsp_query-to>181</Hsp_query-to>
               <Hsp_hit-from>1</Hsp_hit-from>
               <Hsp_hit-to>181</Hsp_hit-to>
               <Hsp_query-frame>0</Hsp_query-frame>
               <Hsp_hit-frame>0</Hsp_hit-frame>
               <Hsp_identity>0</Hsp_identity>
               <Hsp_positive>0</Hsp_positive>
               <Hsp_gaps>0</Hsp_gaps>
               <Hsp_align-len>181</Hsp_align-len>
                
<Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
                
<Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPV 
TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAV 
LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
                
<Hsp_midline>                                                            
                                                                         
                                                    </Hsp_midline>
             </Hsp>
           </Hit_hsps>



<notblast>chris</notblast>


From cjfields at uiuc.edu  Thu Oct  4 20:36:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 4 Oct 2007 15:36:25 -0500
Subject: [Bioperl-l] blastxml oddity
In-Reply-To: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
References: <23DE7F77-3FB4-4E00-86CA-43B55A6A7311@uiuc.edu>
Message-ID: <86D7D694-1ACF-4D91-9FEC-0FEA21C1B689@uiuc.edu>

NCBI's BLAST team is working on this; it occurs only if you use an GI/ 
accession instead of a full sequence, and only for XML.

chris

On Oct 4, 2007, at 2:30 PM, Chris Fields wrote:

> Just noticed an oddity from BLASTXML output from the NCBI server; I'm
> cc'ing this to NCBI so maybe they can explain.  BTW, the following
> doesn't occur via URLAPI.
>
> When running a standard BLAST query using the NCBI web page, if
> requesting XML output after the run I get the entire query seq masked
> out and no midline.  This occurs with all default settings except
> output type (set to XML).  Can anyone replicate this?
>
> Here's a sample:
>
> <Hit_hsps>
>              <Hsp>
>                <Hsp_num>1</Hsp_num>
>                <Hsp_bit-score>320.472</Hsp_bit-score>
>                <Hsp_score>820</Hsp_score>
>                <Hsp_evalue>2.17708e-86</Hsp_evalue>
>                <Hsp_query-from>1</Hsp_query-from>
>                <Hsp_query-to>181</Hsp_query-to>
>                <Hsp_hit-from>1</Hsp_hit-from>
>                <Hsp_hit-to>181</Hsp_hit-to>
>                <Hsp_query-frame>0</Hsp_query-frame>
>                <Hsp_hit-frame>0</Hsp_hit-frame>
>                <Hsp_identity>0</Hsp_identity>
>                <Hsp_positive>0</Hsp_positive>
>                <Hsp_gaps>0</Hsp_gaps>
>                <Hsp_align-len>181</Hsp_align-len>
>
> <Hsp_qseq>XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 
> XX
> XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</Hsp_qseq>
>
> <Hsp_hseq>MNQKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGN 
> PV
> TVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQL 
> AV
> LVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYENE</Hsp_hseq>
>
> <Hsp_midline>
>
>                                                     </Hsp_midline>
>              </Hsp>
>            </Hit_hsps>
>
>
>
> <notblast>chris</notblast>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 19:35:25 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 14:35:25 -0500
Subject: [Bioperl-l] bp_search2gff.pl
Message-ID: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>

Hello,

I have been playing with the bp_search2gff.pl script (on HEAD of
bioperl-live).    There are a couple of issues I was wondering about.

One is the ID that gets generated for a match feature when the --match
option is set.   The ID is  set to the ID of the query sequence.  This
can be problematic if you are representing the query sequence and the
blast hit in the same gff file.  When using the resultant gff file for
loading into Chado, it also creates a problem if you have more than
one hit for a given query sequence, for example if you ran two
different analyses that each had a hit for a given query.  Would it be
possible to have an option to create a unique ID for match features.
One suggestion could be to create an ID based on the ID of the query +
the id of the hit + the source

As long as two different analyses were loaded as different sources,
this would ensure unique IDs for the match features.


Also, is there a reason for writing the Target string as

Target=Sequence:SOME_ID

as opposed to

Target=SOME_ID


The latter seems a little more in line with the gff3 spec and plays a
little nicer with the GMOD tools.

Thanks for looking into this.

Eric


From cjfields at uiuc.edu  Fri Oct  5 19:51:20 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 5 Oct 2007 14:51:20 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
Message-ID: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>

We might want to file this as a bug so we can track it.

The core devs have been mulling over the state of GFF/GFF3 in  
BioPerl; proper handling of any SearchIO data is certainly included  
in that.  I believe some road forward is to be planned soon (after  
Genome Informatics).

chris

On Oct 5, 2007, at 2:35 PM, Eric Just wrote:

> Hello,
>
> I have been playing with the bp_search2gff.pl script (on HEAD of
> bioperl-live).    There are a couple of issues I was wondering about.
>
> One is the ID that gets generated for a match feature when the --match
> option is set.   The ID is  set to the ID of the query sequence.  This
> can be problematic if you are representing the query sequence and the
> blast hit in the same gff file.  When using the resultant gff file for
> loading into Chado, it also creates a problem if you have more than
> one hit for a given query sequence, for example if you ran two
> different analyses that each had a hit for a given query.  Would it be
> possible to have an option to create a unique ID for match features.
> One suggestion could be to create an ID based on the ID of the query +
> the id of the hit + the source
>
> As long as two different analyses were loaded as different sources,
> this would ensure unique IDs for the match features.
>
>
> Also, is there a reason for writing the Target string as
>
> Target=Sequence:SOME_ID
>
> as opposed to
>
> Target=SOME_ID
>
>
> The latter seems a little more in line with the gff3 spec and plays a
> little nicer with the GMOD tools.
>
> Thanks for looking into this.
>
> Eric
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From e-just at northwestern.edu  Fri Oct  5 20:06:48 2007
From: e-just at northwestern.edu (Eric Just)
Date: Fri, 5 Oct 2007 15:06:48 -0500
Subject: [Bioperl-l] bp_search2gff.pl
In-Reply-To: <54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
References: <fa1fe35c0710051235x3d12caamfda81bb8ba23443b@mail.gmail.com>
	<54632965-D21E-4B0B-B2D6-254D9CB88F3B@uiuc.edu>
Message-ID: <fa1fe35c0710051306v1636d6er6f02133f4ecef91c@mail.gmail.com>

Thanks Chris, I'll enter it as a bug.  I'd also be glad to help on the
solution if there is an executive decision made at some point.



On 10/5/07, Chris Fields <cjfields at uiuc.edu> wrote:
> We might want to file this as a bug so we can track it.
>
> The core devs have been mulling over the state of GFF/GFF3 in
> BioPerl; proper handling of any SearchIO data is certainly included
> in that.  I believe some road forward is to be planned soon (after
> Genome Informatics).
>
> chris
>
> On Oct 5, 2007, at 2:35 PM, Eric Just wrote:
>
> > Hello,
> >
> > I have been playing with the bp_search2gff.pl script (on HEAD of
> > bioperl-live).    There are a couple of issues I was wondering about.
> >
> > One is the ID that gets generated for a match feature when the --match
> > option is set.   The ID is  set to the ID of the query sequence.  This
> > can be problematic if you are representing the query sequence and the
> > blast hit in the same gff file.  When using the resultant gff file for
> > loading into Chado, it also creates a problem if you have more than
> > one hit for a given query sequence, for example if you ran two
> > different analyses that each had a hit for a given query.  Would it be
> > possible to have an option to create a unique ID for match features.
> > One suggestion could be to create an ID based on the ID of the query +
> > the id of the hit + the source
> >
> > As long as two different analyses were loaded as different sources,
> > this would ensure unique IDs for the match features.
> >
> >
> > Also, is there a reason for writing the Target string as
> >
> > Target=Sequence:SOME_ID
> >
> > as opposed to
> >
> > Target=SOME_ID
> >
> >
> > The latter seems a little more in line with the gff3 spec and plays a
> > little nicer with the GMOD tools.
> >
> > Thanks for looking into this.
> >
> > Eric
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


From bix at sendu.me.uk  Sun Oct  7 12:40:44 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sun, 07 Oct 2007 13:40:44 +0100
Subject: [Bioperl-l] Bio::FeatureIO::gff bug?
In-Reply-To: <5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
References: <46F784EB.9050507@sendu.me.uk>	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>	<46F7B9A1.9080206@sendu.me.uk>	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>	<46F8DC34.6020908@sendu.me.uk>	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
Message-ID: <4708D3CC.60909@sendu.me.uk>

Hilmar Lapp wrote:
> On Sep 28, 2007, at 5:34 PM, Chris Fields wrote:
> 
>> The section writing the gff header info in _initialize() checks the  
>> file specifically for '>' prior to output; I think Sendu planned on  
>> changing that to use mode() instead.
> 
> What if we pass in a file handle?

mode() is supposed to work in that instance as well: it sees if the file 
handle is writable.


From er at xs4all.nl  Sun Oct  7 14:13:45 2007
From: er at xs4all.nl (Erik)
Date: Sun, 7 Oct 2007 16:13:45 +0200 (CEST)
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <4708D3CC.60909@sendu.me.uk>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
Message-ID: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>


http://bioperl.org/
http://www.bioperl.org/wiki/Main_Page

seems to be having problems - I only receive an empty
screen...

regards,
Erik






From cjfields at uiuc.edu  Sun Oct  7 21:16:02 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sun, 7 Oct 2007 16:16:02 -0500
Subject: [Bioperl-l] bioperl.org
In-Reply-To: <12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
References: <46F784EB.9050507@sendu.me.uk>
	<7C7D7FB3-86B9-43CF-B506-E66FA8264CFC@uiuc.edu>
	<46F7B9A1.9080206@sendu.me.uk>
	<EEC9B51B-8245-48FA-9C04-D778789107E9@uiuc.edu>
	<234C109D-85FE-4161-8CBA-8E24BE34C5B5@gmx.net>
	<46F8DC34.6020908@sendu.me.uk>
	<8283EF43-2AF0-4B3B-8A00-4DE615186EC7@gmx.net>
	<5298B700-EFDE-45E4-A8F3-674FA673A0C7@uiuc.edu>
	<41A20518-63BC-4D01-8FFC-01C903ADD423@gmx.net>
	<530A0322-A3BC-471D-AE91-17AD8F0EB237@uiuc.edu>
	<5FC8F92C-42DD-4DAF-8008-0F8C545065B5@gmx.net>
	<4708D3CC.60909@sendu.me.uk>
	<12957.156.83.1.146.1191766425.squirrel@webmail.xs4all.nl>
Message-ID: <EBD33439-22B4-44FC-A60C-D3EC653EC363@uiuc.edu>

Should be back up.  Jason was running some wiki updates.

chris

On Oct 7, 2007, at 9:13 AM, Erik wrote:

>
> http://bioperl.org/
> http://www.bioperl.org/wiki/Main_Page
>
> seems to be having problems - I only receive an empty
> screen...
>
> regards,
> Erik




From alan at tll.org.sg  Mon Oct  8 05:02:45 2007
From: alan at tll.org.sg (alan)
Date: Mon, 8 Oct 2007 13:02:45 +0800
Subject: [Bioperl-l] exonerate
In-Reply-To: <73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
References: <034FB11C-B4E9-4E4E-B213-D4AC6A397B1B@tll.org.sg>
	<29C4D729-6715-4C19-9872-3B1AF90EAFA3@tll.org.sg>
	<73B4E193-69D0-409D-9F89-20FB677F45C9@uiuc.edu>
Message-ID: <F5563806-FCAE-46C6-8EE3-3C55FCDD906C@tll.org.sg>

Hi Chris,

On 02 Oct 2007, at 11:03 PM, Chris Fields wrote:

> One option is to try running $run->cleanup() after you finish  
> parsing, which gets rid of the tempfiles on each run.
>

I tried this option in the past but it did not change anything.

I found a temporary solution: I am using tcsh and the ulimit for open  
files (descriptors) was set to 256. I changed this limit to 2000 and  
I got my code to run to completion. This imply that I am  
circumventing the real problem of open files. I will continue to look  
at the file closing step in bioperl but the ulimit or limit option  
allows me to get a quick work around for now.

for bash shell (ulimit -n [number])

for tcsh shell (limit descriptors [number])

alan




> chris
>
> On Sep 30, 2007, at 8:53 PM, alan wrote:
>
>> Hi,
>>
>>
>>>> I am calling exonerate.pm within my script while attempting to
>>>> align cDNA  to multiple genomic fragments. After processing about
>>>> 120+ genomic fragments my code crashes with the following error:
>>>>
>>>> ** ERROR **: Could not open [/tmp/tlInatbOED] : Too many open files
>>>> aborting...
>>>> MSG: Exonerate call (/usr/local/bin/exonerate   /tmp/8X9jQuHUGF /
>>>> tmp/tlInatbOED  > /tmp/EolF5qCNLZ/cIf0HfIRf5) crashed: 34304
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::_run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:214
>>>> STACK Bio::Tools::Run::Alignment::Exonerate::run /nfs1/alan/
>>>> cvs_src/bioperl-run/Bio/Tools/Run/Alignment/Exonerate.pm:174
>>>>
>>>> The code in Exonerate.pm closes the tmpfile at the end of the
>>>> routine yet I get the error message about "too many open files".
>>>> Any suggestions on how I should be closing these files?
>>>>
>>>>
>>>> Extract from my code that runs exonerate is listed below.
>>>>
>>>> foreach my $f(@files) {
>>>>   next unless (-f  "$dir/$f");
>>>>   my $q_in = Bio::SeqIO->new(-file=>$query, -format=>"Fasta");
>>>>   my $query_obj = $q_in->next_seq();
>>>>   my $target_in = Bio::SeqIO->new(-file=>"$dir/$f", -
>>>> format=>"Fasta");
>>>>   my $target_obj = $target_in->next_seq();
>>>>   my $run = Bio::Tools::Run::Alignment::Exonerate->new();
>>>>   my $exonerate_io = $run->run($query_obj, $target_obj);
>>>>
>>>>   [code for parsing the data.......]
>>>>
>>>>   $exonerate_io->close; #tried this line out of desperation but it
>>>> did not help :-)
>>>> }
>>>>
>>>> thanks
>>>> alan
>
>



From bix at sendu.me.uk  Mon Oct  8 09:54:15 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Mon, 08 Oct 2007 10:54:15 +0100
Subject: [Bioperl-l] Loading Blast Report in a minimal way
In-Reply-To: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
References: <BAY110-W1530D153D698DCFF7AEEA2C7AF0@phx.gbl>
Message-ID: <4709FE47.3040103@sendu.me.uk>

zhihuali wrote:
> Hi netters,
> 
> I'm using SearchIO to parse my blast reports. They are extremely 
> huge, and not surprisingly, it's extremely slow and sometimes the 
> system crashed due to memmory problem. As I can handle small reports 
> quickly, it seems like a problem related to the way SearchIO works: 
> it slurps the whole report into the memory and builds millions of 
> objects.
> 
> I've checked old posts and some people used FastHitEventBuilder to 
> build hit objects without any hsp objects. And some people suggested 
> using tabular output of blast. But in my case I need to go to each of
>  the hsps of each hit, parse the alignment, and gather the
> information needed if that hsp fits certain criteria, and then move
> on to the next hsp/or jump over to the next hit/ or exit the
> processing, according to the information I have already got. An ideal
> way would be to read one hsp at a time from the report to the memory.
> Is there some way to modify SearchIO (or build another Search Event)
> to do this?

Use Bio::SearchIO::blast_pull

(ie.
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'blast_pull',
                                             -file =>
't/data/new_blastn.txt');
)

It doesn't yet support all kinds of Blast report, however. Let me know
how you get on.

Cheers,
Sendu.


From bix at sendu.me.uk  Wed Oct 10 14:09:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 15:09:24 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
Message-ID: <470CDD14.4000005@sendu.me.uk>

Once I store a feature like so:

$db = Bio::DB::SeqFeature::Store->new( # mysql );
$db->new_feature(-primary_tag  => 'X',
                  -seq_id       => 'Y',
                  #...
		 -source       => 'Z');

How do I search for it again? I could have sworn that in the past the 
source somehow became one of the feature's attributes so that I could do:

@feats = $db->features(-attributes => {source => 'Z'});

(Or does/did some other feature-related module store source as an 
attribute, and in the past I stored those features in my db?)

The obvious isn't implemented:

@feats = $db->features(-source => 'Z');

Looking at the code I see I can do type and source at the same time:

@feats = $db->features(-type => 'X:Z');

which works, but how do I just search for all Z, regardless of type?


From lstein at cshl.edu  Wed Oct 10 14:20:33 2007
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed, 10 Oct 2007 10:20:33 -0400
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <470CDD14.4000005@sendu.me.uk>
References: <470CDD14.4000005@sendu.me.uk>
Message-ID: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>

Hi Sendu,

This may be a glaring omission on my part. Try searching for:

 @feats = $db->get_features_by_type(":$source");

Remove the colon in front of $source.

This might not work, but give it a try.

Lincoln

On 10/10/07, Sendu Bala <bix at sendu.me.uk> wrote:
>
> Once I store a feature like so:
>
> $db = Bio::DB::SeqFeature::Store->new( # mysql );
> $db->new_feature(-primary_tag  => 'X',
>                   -seq_id       => 'Y',
>                   #...
>                  -source       => 'Z');
>
> How do I search for it again? I could have sworn that in the past the
> source somehow became one of the feature's attributes so that I could do:
>
> @feats = $db->features(-attributes => {source => 'Z'});
>
> (Or does/did some other feature-related module store source as an
> attribute, and in the past I stored those features in my db?)
>
> The obvious isn't implemented:
>
> @feats = $db->features(-source => 'Z');
>
> Looking at the code I see I can do type and source at the same time:
>
> @feats = $db->features(-type => 'X:Z');
>
> which works, but how do I just search for all Z, regardless of type?
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


From bix at sendu.me.uk  Wed Oct 10 15:10:45 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 10 Oct 2007 16:10:45 +0100
Subject: [Bioperl-l] Searching by source in Bio::DB::SeqFeature::Store?
In-Reply-To: <6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
References: <470CDD14.4000005@sendu.me.uk>
	<6dce9a0b0710100720p4fc5d0c1w7b1c4bfc786dd5e3@mail.gmail.com>
Message-ID: <470CEB75.7050804@sendu.me.uk>

Lincoln Stein wrote:
> Hi Sendu,
> 
> This may be a glaring omission on my part. Try searching for:
> 
>  @feats = $db->get_features_by_type(":$source");
> 
> Remove the colon in front of $source.

It doesn't, unfortunately, colon or not. get_features_by_type is 
implemented using _features(-type => ), just like features(). In any 
case, I'm searching for multiple things at the same time so need to use 
the features() method.


The following patch seems to do the job in my hands, allowing:

@feats = $db->features(-source => 'Z');
to work as expected.

Also, we now have:
@feats = $db->features(-type => 'X', -source => 'Z');
as a nicer (ie. matching the syntax the user used to create the feature 
in the first place) alternative to:
@feats = $db->features(-type => 'X:Y');

Of course, this patch is specific to the mysql implementation. You may 
want to check it over to see if it is sane, see if there is a cleaner 
way to do it, or see if there's a more general way to apply it to all 
implementations.


RCS file: 
/home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/DBI/mysql.pm,v
retrieving revision 1.33
diff -r1.33 mysql.pm
724c724,725
<       $iterator
---
 >       $iterator,
 >       $sources
731a733
 >             ['SOURCE','SOURCES']
760c762,785
<
---
 >
 >   if (defined($sources)) {
 >     my @sources = ref($sources) eq 'ARRAY' ? @{$sources} : ($sources);
 >     if (defined($types)) {
 >         my @types = ref($types) eq 'ARRAY' ? @{$types} : ($types);
 >         my @final_types;
 >         foreach my $type (@types) {
 >             # *** not sure what to do if user supplies both -source
 >             #     and -type where the type includes a source!
 >             if ($type =~ /:/) {
 >                 push(@final_types, $type);
 >             }
 >             else {
 >                 foreach my $source (@sources) {
 >                     push(@final_types, $type.':'.$source);
 >                 }
 >             }
 >         }
 >         $types = \@final_types;
 >     }
 >     else {
 >         $types = [map { ':'.$_ } @sources];
 >     }
 >   }
939,940c964,971
<       push @matches,"tl.tag=?";
<       push @args,"$primary_tag:$source_tag";
---
 >       if (length($primary_tag)) {
 >         push @matches,"tl.tag=?";
 >         push @args,"$primary_tag:$source_tag";
 >       }
 >       else {
 >         push @matches,"tl.tag LIKE ?";
 >         push @args,"%:$source_tag";
 >       }


From bix at sendu.me.uk  Thu Oct 11 10:40:24 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Thu, 11 Oct 2007 11:40:24 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
Message-ID: <470DFD98.4030603@sendu.me.uk>

Following Chris's changes to SF::Annotated et al., lots of existing user 
code breaks. Also, at least some Bioperl code breaks, notably 
Bio::DB::SeqFeature::Store, which in mysql mode calls 
_get_location_and_bin() which calls $feature->seq_id which ends up 
storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
the database, instead of an actual sequence id (which completely breaks 
searching by seq_id).

I propose its API be changed to be more consistent with 
Bio::SeqFeatureI, eg. instead of:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : a Bio::Annotation::SimpleValue object representing the
            seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

we have:

seq_id()
  Usage   : $obj->seq_id($newval)
  Function: holds a string corresponding to the unique
            seq_id of the sequence underlying the feature
            (e.g. database accession or primary key).
  Returns : string representing the seq_id.
  Args    : on set, some string or a Bio::Annotation::SimpleValue object.

This would apply to seq_id(), name(), type(), source(), phase() and 
frame(). Internally the implementation could store the string value in a 
SimpleValue object.


However, I'm obviously missing something, because I have no idea what 
the justification for returning SimpleValue objects was in the first 
place (what other module needs them?), nor even what the point of 
SimpleValue objects is in the first place.


From ULNJUJERYDIX at spammotel.com  Thu Oct 11 11:32:33 2007
From: ULNJUJERYDIX at spammotel.com (Kevin Lam)
Date: Thu, 11 Oct 2007 19:32:33 +0800
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
Message-ID: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>

wow thanks for the replies!
I have gotten the answer from the blast help

Subsequence range can be specified by the ?L parameter. Please refer
to this web document for more information:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/blastall_node60.html



Other end-user oriented standalone blast documents are at:

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/


but will try this method as well to see which works better.

cheers!
kevin

There is a script that comes with the bioperl core distribution,

> bp_split_seq.pl, which does this.  Here's the CVS location:
>
> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
> scripts/seq/?cvsroot=bioperl
>
> chris
>



From cjfields at uiuc.edu  Thu Oct 11 13:49:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 08:49:59 -0500
Subject: [Bioperl-l] **Fwd: Re: divide and blast blastunsplit blast
	subsequence
In-Reply-To: <5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
References: <5b6410e0710012321h4320d804p6c6262860eff2463@mail.gmail.com>
	<C157AA2F-A6F2-44F4-999A-4605C047BBFC@uiuc.edu>
	<5b6410e0710110432mb4a652emc7bb6be1fb378770@mail.gmail.com>
Message-ID: <F866A1FE-EBC7-4722-A3E6-2F4A10FD0373@uiuc.edu>

Yep, started using this myself for mapping old predicted CDS onto new  
assemblies using BLASTX.  Works very well, particularly since it  
retains the seq position on hits, where using bp_slit_seq would  
require mapping to the correct coordinates.

chris

On Oct 11, 2007, at 6:32 AM, Kevin Lam wrote:

> wow thanks for the replies!
> I have gotten the answer from the blast help
>
> Subsequence range can be specified by the ?L parameter. Please refer
> to this web document for more information:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/blastall/ 
> blastall_node60.html
>
>
>
> Other end-user oriented standalone blast documents are at:
>
> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/
>
>
> but will try this method as well to see which works better.
>
> cheers!
> kevin
>
> There is a script that comes with the bioperl core distribution,
>
>> bp_split_seq.pl, which does this.  Here's the CVS location:
>>
>> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/
>> scripts/seq/?cvsroot=bioperl
>>
>> chris
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From cjfields at uiuc.edu  Thu Oct 11 14:19:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 09:19:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>


On Oct 11, 2007, at 5:40 AM, Sendu Bala wrote:

> Following Chris's changes to SF::Annotated et al., lots of existing  
> user
> code breaks. Also, at least some Bioperl code breaks, notably
> Bio::DB::SeqFeature::Store, which in mysql mode calls
> _get_location_and_bin() which calls $feature->seq_id which ends up
> storing something like 'Bio::Annotation::SimpleValue=HASH 
> (0x1f435d0)' in
> the database, instead of an actual sequence id (which completely  
> breaks
> searching by seq_id).
>
> I propose its API be changed to be more consistent with
> Bio::SeqFeatureI, eg. instead of:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> we have:
>
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue  
> object.
>
> This would apply to seq_id(), name(), type(), source(), phase() and
> frame(). Internally the implementation could store the string value  
> in a
> SimpleValue object.

Agreed.  It would be easy to change over but we need to also make  
sure FeatureIO fixes are in place.  In reality all FeatureIO methods  
should be changed over to recognize any SeqFeatureI or (if we retain  
it) the stricter TypedSeqFeatureI.  Using only Bio::SF::Annotated  
limits other more lightweight implementations.  I simply haven't had  
time to work on it yet due to $job; if you want to make the necessary  
changes you are more than welcome; the few tests I found I moved into  
SeqFeatAnnotated.t, which likely expects the wrong behavior.

> However, I'm obviously missing something, because I have no idea what
> the justification for returning SimpleValue objects was in the first
> place (what other module needs them?), nor even what the point of
> SimpleValue objects is in the first place.

I believe it was to ensure any data stored or retrieved was strongly  
typed (i.e. scalars in SimpleValue, dbxrefs in DBLink, comments in  
Comment, etc).  Since B::SF::Generic is also AnnotatableI, it can  
store a mix of scalars in methods as well as Bio::Annotation data;  
this class attempts to lump them all together as Bio::Annotation in a  
Collection in a strongly typed, uniform way.  Hilmar's  
Bio::SF::AnnotationAdaptor frankly does a better job of describing  
the reasoning behind this and is more flexible; I use that now for  
typing via feature(), though I just realized it should be changed to  
be a singleton instance per class (oops!).

B::SF::A violated the SeqFeatureI interface from the get-go by  
returning objects.  To trick it's way around the issue it used  
overloading so that calling it in some contexts (print, comparison)  
returned a string or value; removing the overloads unmasked that  
behavior.  To me an object returned (regardless of overloading) is  
still an object and not a scalar, and still violates the interface  
methods where scalars are expected.  I can't fault the authors  
involved completely since the idea was to radically change the way  
SFs/Annotation worked together, but the implementation was never  
completed so I rolled it back and limited typing to B::SF::A until  
something else can be worked out.

Personally I think it's too 'heavy' and other options should be  
explored, such as abstracting out the type checking into a separate  
utility class which FeatureIO can use on any SeqFeatureI (TypeMapper  
does something like this for the primary_tag()).

chris


From jaudall at gmail.com  Fri Oct 12 00:51:50 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 18:51:50 -0600
Subject: [Bioperl-l] Hsp_hit-from
Message-ID: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>

Bioperl -

I'm parsing an XML blast output using SearchIO and the usual fields seem to
work fine.

print $result->query_name . "\t" . $hit->name . "\n";

However, I'm curious as to the 5' position distribution of my hits.  So I'd
like to access this data field <Hsp_query-from> in the xml output file.  I
searched both the mailing lists and the Search docs including
*Bio::Search::Hit::HitI,
*but I can't seem to find an example of someone accessing this data field.
Perhaps, I missed it, but do any of you have any suggestions as to how I
might get at the <Hsp_query-from> for each hit?  Thanks.

Josh


From cjfields at uiuc.edu  Fri Oct 12 02:14:21 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 11 Oct 2007 21:14:21 -0500
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
Message-ID: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>


On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:

> Bioperl -
>
> I'm parsing an XML blast output using SearchIO and the usual fields  
> seem to
> work fine.
>
> print $result->query_name . "\t" . $hit->name . "\n";
>
> However, I'm curious as to the 5' position distribution of my  
> hits.  So I'd
> like to access this data field <Hsp_query-from> in the xml output  
> file.  I
> searched both the mailing lists and the Search docs including
> *Bio::Search::Hit::HitI,
> *but I can't seem to find an example of someone accessing this data  
> field.
> Perhaps, I missed it, but do any of you have any suggestions as to  
> how I
> might get at the <Hsp_query-from> for each hit?  Thanks.
>
> Josh

That tag (as well as related tags) are mapped to start(), end(), and  
strand() in the HSP objects.  To access the relevant data pass  
'query' or 'hit' to the method, so for the query use: $hsp->start 
('query') or $hsp->end('query').

Note: in BioPerl all location starts are less than the end (strand  
determines the orientation for DNA).

chris


From hlapp at gmx.net  Fri Oct 12 03:25:22 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu, 11 Oct 2007 23:25:22 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>


On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:

> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.

type() and source() should be ontology-typed in a TypedSeqFeatureI  
(and therefore be instances of Bio::Annotation::OntologyTerm, not  
Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't  
understand what the benefit of typing seq_id() any stronger than a  
string would be.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From jaudall at gmail.com  Fri Oct 12 03:34:18 2007
From: jaudall at gmail.com (Joshua Udall)
Date: Thu, 11 Oct 2007 20:34:18 -0700
Subject: [Bioperl-l] Hsp_hit-from
In-Reply-To: <162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
References: <52cea20c0710111751n31a6c96ai309ff3b3714358cc@mail.gmail.com>
	<162E9AF9-92FC-41A1-ABEB-9AF7113CC6FD@uiuc.edu>
Message-ID: <52cea20c0710112034k60f14241k8884a07d26939e86@mail.gmail.com>

Thanks!  For some reason I was stuck on the idea that it would be different
with an xml file.  I'm glad it's not ...

On 10/11/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 11, 2007, at 7:51 PM, Joshua Udall wrote:
>
> > Bioperl -
> >
> > I'm parsing an XML blast output using SearchIO and the usual fields
> > seem to
> > work fine.
> >
> > print $result->query_name . "\t" . $hit->name . "\n";
> >
> > However, I'm curious as to the 5' position distribution of my
> > hits.  So I'd
> > like to access this data field <Hsp_query-from> in the xml output
> > file.  I
> > searched both the mailing lists and the Search docs including
> > *Bio::Search::Hit::HitI,
> > *but I can't seem to find an example of someone accessing this data
> > field.
> > Perhaps, I missed it, but do any of you have any suggestions as to
> > how I
> > might get at the <Hsp_query-from> for each hit?  Thanks.
> >
> > Josh
>
> That tag (as well as related tags) are mapped to start(), end(), and
> strand() in the HSP objects.  To access the relevant data pass
> 'query' or 'hit' to the method, so for the query use: $hsp->start
> ('query') or $hsp->end('query').
>
> Note: in BioPerl all location starts are less than the end (strand
> determines the orientation for DNA).
>
> chris
>


From pellet at cervi-lyon.inserm.fr  Fri Oct 12 08:48:06 2007
From: pellet at cervi-lyon.inserm.fr (Johann PELLET)
Date: Fri, 12 Oct 2007 10:48:06 +0200
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
Message-ID: <470F34C6.9050800@cervi-lyon.inserm.fr>

Hi,
I have two questions:
First, I have problems for example with this genbank entry: NC_008210. 
Indeed, for one CDS, the location is : 
join(161990..162784,complement(88222..88806),complement(86666..87448))

When I parse a genbank file with this entry.

my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
                               -file => $input_file);

while( my $seq = $seq_in->next_seq() ) {
    my @features = $seq->get_SeqFeatures();
    for ( my $i =0; $i < scalar @features; $i++ ){
        my $feat = @features[$i];
         if ( $feat->primary_tag eq 'CDS' ){


             my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
             my $seq_CDS=$seq_CDS_obj->seq;


I have this error:
Can't call method "isa" without a package or object reference at ....

Secondly, When location is like: 
join(complement(AY421753.1:1..6),complement(3813..5699)) I know that we 
must use spliced_seq with the argument db, but it's not working.
      my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
How can we valid a Bio::DB::RandomAccessI?

Thanks

-- 
Johann Pellet
phone (work): +33(0)4 37282352
E-mail:    pellet at cervi-lyon.inserm.fr
Centre d'Etudes et de Recherche en Virologie et Immunologie
INSERM U503
21, Avenue Tony Garnier
69365 Lyon cedex 07 France 



From bix at sendu.me.uk  Fri Oct 12 13:04:25 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 14:04:25 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
Message-ID: <470F70D9.6030108@sendu.me.uk>

Chris Fields wrote:
> B::SF::A violated the SeqFeatureI interface from the get-go by returning 
> objects.

On that note, the other major change I'd propose is to make B::SF::A 
inherit from B::SeqFeatureI. I really need this for RangeI methods.

Or, heck, since it's such a mess, do we just want to drop Annotated 
entirely and recommend using AnnotationAdaptor with Generic? What does 
Annotated bring to the table?

(Since its one of the modules added in 1.5 I think it's fair to drop it 
from the 1.6 release: stuff that doesn't work can and should be moved 
out of the path of stable branches.)


From hlapp at gmx.net  Fri Oct 12 14:46:19 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 10:46:19 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>


On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

My recollection may be wrong since it's been quite a while, but I  
believe one of the main motivations was to reflect the ontology- 
typing of feature type and other annotation that GFF3 requires.

The motivation of AnnotationAdaptor was primarily to provide a view  
onto a SeqFeatureI that makes tag/value annotation transparently  
appear as B:AnnotatableI and B:AnnotationCollectionI compliant, mixed  
in with the annotation collection that B:S:Generic may hold already.

Although sometimes confused, these are not the same motivations.  
AnnotationAdaptor provides a view - you use it when that's the view  
you need on a SeqFeatureI object you have in hand. For example,  
bioperl-db uses it so it doesn't have to bother about how to de/ 
serialize tag/value pairs, when it knows how to de/serialize  
annotation collections already from sequence objects.  
AnnotationAdaptor doesn't care whether the primary_tag, or any other  
tag, is from an ontology.

>
> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
>> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

I agree with that unless someone steps up and makes it work.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From cjfields at uiuc.edu  Fri Oct 12 14:49:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 09:49:25 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F70D9.6030108@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
Message-ID: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>


On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> B::SF::A violated the SeqFeatureI interface from the get-go by  
>> returning
>> objects.
>
> On that note, the other major change I'd propose is to make B::SF::A
> inherit from B::SeqFeatureI. I really need this for RangeI methods.

It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,  
which itself is-a SeqFeatureI.  We might want to run the tests on  
that but a quick inheritance tree check on my ends seems to confirm  
that.  If the Range methods don't work there may be an issue within  
B::SF::A (which wouldn't surprise me).

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

I agree about getting rid of B::SF::A, but if we do we will need a  
reasonable replacement for SFs in FeatureIO, as it relies directly on  
B::SF::A.  As for AnnotationAdaptor, it runs a simple type check on  
the data within a SF but I don't think it checks the primary_tag  
against the current SO or other ontologies for GFF3.

My inclination is to hold back FeatureIO from 1.6 and retool it to  
use any SeqFeatureI, then find a way to optionally type a  
SeqFeatureI.  This is so we don't have to completely retool every  
Bio::Tools* class.  For instance:

# a SF::Generic with a few type-related methods added to SeqFeatureI
$sf->type(); # undef, not checked
$sf->ontology_term; # undef, not checked

# call proper methods to type check
# or use a utility class dedicated to this function

$sf->validate_sf_type(); # or...
$util->validate_sf_type($sf);

$sf->type(); # returns string
$sf->ontology_term; # returns Bio::Ontology::TermI

My feeling is that FeatureIO needs the ability to validate SFs and  
maybe have it turned on by default, but it should be optional.  The  
TermI would be a Bio::Annotation::OntologyTerm if we insist on using  
AnnotationAdaptor for richly typed SFs, which may not be necessary  
(Hilmar?).  As not all SeqFeatureI are also AnnotatableI that should  
probably be optional anyway.

> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

Agreed.  If anyone wants to use experimental stuff they can always  
use bioperl-live.

chris


From cjfields at uiuc.edu  Fri Oct 12 15:02:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 10:02:03 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
Message-ID: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>


On Oct 12, 2007, at 9:46 AM, Hilmar Lapp wrote:

>
> On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:
>
>> Or, heck, since it's such a mess, do we just want to drop Annotated
>> entirely and recommend using AnnotationAdaptor with Generic? What  
>> does
>> Annotated bring to the table?
>
> My recollection may be wrong since it's been quite a while, but I  
> believe one of the main motivations was to reflect the ontology- 
> typing of feature type and other annotation that GFF3 requires.
>
> The motivation of AnnotationAdaptor was primarily to provide a view  
> onto a SeqFeatureI that makes tag/value annotation transparently  
> appear as B:AnnotatableI and B:AnnotationCollectionI compliant,  
> mixed in with the annotation collection that B:S:Generic may hold  
> already.
>
> Although sometimes confused, these are not the same motivations.  
> AnnotationAdaptor provides a view - you use it when that's the view  
> you need on a SeqFeatureI object you have in hand. For example,  
> bioperl-db uses it so it doesn't have to bother about how to de/ 
> serialize tag/value pairs, when it knows how to de/serialize  
> annotation collections already from sequence objects.  
> AnnotationAdaptor doesn't care whether the primary_tag, or any  
> other tag, is from an ontology.

Ah, forgot it returns a Collection.  It doesn't modify the SF I assume?

>> (Since its one of the modules added in 1.5 I think it's fair to  
>> drop it
>>> from the 1.6 release: stuff that doesn't work can and should be  
>>> moved
>> out of the path of stable branches.)
>
> I agree with that unless someone steps up and makes it work.
>
> 	-hilmar

Making it work may be more trouble than it's worth.  Sincerest  
apologies to the authors of the module but we should probably  
deprecate it in favor of something more flexible when we can.  It's  
obvious anything reliant on it would also have to be dropped.

The GMOD meeting is a few weeks away, where I assume some things will  
be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth  
saving; maybe retooling it would be in our best interests, but it  
needs a decent roadmap to move forward.

chris


From bix at sendu.me.uk  Fri Oct 12 15:06:30 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 12 Oct 2007 16:06:30 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
Message-ID: <470F8D76.8080101@sendu.me.uk>

Chris Fields wrote:
> 
> On Oct 12, 2007, at 8:04 AM, Sendu Bala wrote:
> 
>> Chris Fields wrote:
>>> B::SF::A violated the SeqFeatureI interface from the get-go by
>>> returning objects.
>> 
>> On that note, the other major change I'd propose is to make
>> B::SF::A inherit from B::SeqFeatureI. I really need this for RangeI
>> methods.
> 
> It should already be SeqFeatureI; B::SF::A is-a TypedSeqFeatureI,
> which itself is-a SeqFeatureI.  We might want to run the tests on
> that but a quick inheritance tree check on my ends seems to confirm
> that.  If the Range methods don't work there may be an issue within
> B::SF::A (which wouldn't surprise me).

Sorry, I was looking at the docs on the website and for whatever reason
its failing to display all the inherited modules. If RangeI methods
don't work I'll post back, but for now assume they do (I'm not in a
position to test right now).


> My inclination is [snip]

I still don't really understand what the deal is with all these modules,
so I'll leave it your hands to make further recommendations and take action.

 From my limited understanding what you said seems reasonable, except for
excluding FeatureIO completely. At least, I'd really like to see it in
1.6; it would be a shame to miss it just because of Annotated. Worst
case, isn't Generic 'good enough' as a replacement?


> The GMOD meeting is a few weeks away, where I assume some things will
> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
> saving; maybe retooling it would be in our best interests, but it
> needs a decent roadmap to move forward.

Agreed. I guess we'll wait for the results of that meeting? Is anyone 
going planning to discuss this issue?


From cjfields at uiuc.edu  Fri Oct 12 16:15:51 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 12 Oct 2007 11:15:51 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <470F8D76.8080101@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<DE520E11-9C63-4331-8866-CC780968ED63@uiuc.edu>
	<470F8D76.8080101@sendu.me.uk>
Message-ID: <EAD0DE5B-3E55-453B-A57B-C478F2BB9AE4@uiuc.edu>


On Oct 12, 2007, at 10:06 AM, Sendu Bala wrote:
...

>
> I still don't really understand what the deal is with all these  
> modules,
> so I'll leave it your hands to make further recommendations and  
> take action.
>
> From my limited understanding what you said seems reasonable,  
> except for
> excluding FeatureIO completely. At least, I'd really like to see it in
> 1.6; it would be a shame to miss it just because of Annotated. Worst
> case, isn't Generic 'good enough' as a replacement?

It probably could work, but type checking, ontology_term(), and SF  
data validation wouldn't be implemented immediately as it would  
require additional code.  I'll try looking into it this weekend to  
see what needs to be done and work from there.

>> The GMOD meeting is a few weeks away, where I assume some things will
>> be hammered out re: GFF3 and BioPerl.  The idea of FeatureIO is worth
>> saving; maybe retooling it would be in our best interests, but it
>> needs a decent roadmap to move forward.
>
> Agreed. I guess we'll wait for the results of that meeting? Is  
> anyone going planning to discuss this issue?

Jason is going to be there and intends to bring it up as it affects  
GBrowse/GMOD/Chado.

chris



From jason at bioperl.org  Fri Oct 12 16:18:15 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 12 Oct 2007 09:18:15 -0700
Subject: [Bioperl-l] Get nucleic CDS sequence from Genbank files using
	spliced_seq
In-Reply-To: <470F34C6.9050800@cervi-lyon.inserm.fr>
References: <470F34C6.9050800@cervi-lyon.inserm.fr>
Message-ID: <90E849A1-C5AB-40B3-9AB1-2DC79EBF5C4C@bioperl.org>

1.

Always 'use strict;' in your code - you'll see the bug more clearly  
that you should use $feat not $cds in the if stmt.


2.
You should pass in an actual Bio::DB::GenBank object to the -db  
argument.

my $db = Bio::DB::GenBank->new;
my $cds = $seq->spliced_seq(-db => $db);

-jason
On Oct 12, 2007, at 1:48 AM, Johann PELLET wrote:

> Hi,
> I have two questions:
> First, I have problems for example with this genbank entry: NC_008210.
> Indeed, for one CDS, the location is :
> join(161990..162784,complement(88222..88806),complement(86666..87448))
>
> When I parse a genbank file with this entry.
>
> my $seq_in  = Bio::SeqIO->new( -format => 'genbank',
>                                -file => $input_file);
>
> while( my $seq = $seq_in->next_seq() ) {
>     my @features = $seq->get_SeqFeatures();
>     for ( my $i =0; $i < scalar @features; $i++ ){
>         my $feat = @features[$i];
>          if ( $feat->primary_tag eq 'CDS' ){
>
>
>              my $seq_CDS_obj=$cds->spliced_seq( -nosort => 0);
>              my $seq_CDS=$seq_CDS_obj->seq;
>


>
> I have this error:
> Can't call method "isa" without a package or object reference at ....
>
> Secondly, When location is like:
> join(complement(AY421753.1:1..6),complement(3813..5699)) I know  
> that we
> must use spliced_seq with the argument db, but it's not working.
>       my $seq_CDS_obj=$cds->spliced_seq( -db => "genbank");
> How can we valid a Bio::DB::RandomAccessI?
>
> Thanks
>
> -- 
> Johann Pellet
> phone (work): +33(0)4 37282352
> E-mail:    pellet at cervi-lyon.inserm.fr
> Centre d'Etudes et de Recherche en Virologie et Immunologie
> INSERM U503
> 21, Avenue Tony Garnier
> 69365 Lyon cedex 07 France
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From hlapp at gmx.net  Fri Oct 12 17:22:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 12 Oct 2007 13:22:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<D12D3CB7-DE9F-47DF-980E-DDA56879C5D5@uiuc.edu>
	<470F70D9.6030108@sendu.me.uk>
	<81888A43-B6D5-44ED-B445-56520A142AC2@gmx.net>
	<D04D78DC-17A9-4AA7-9E24-93CBCB71B5CB@uiuc.edu>
Message-ID: <9762F1F9-68C8-42E2-8488-6656C76D36B8@gmx.net>


On Oct 12, 2007, at 11:02 AM, Chris Fields wrote:

>> Although sometimes confused, these are not the same motivations.  
>> AnnotationAdaptor provides a view - you use it when that's the  
>> view you need on a SeqFeatureI object you have in hand. For  
>> example, bioperl-db uses it so it doesn't have to bother about how  
>> to de/serialize tag/value pairs, when it knows how to de/serialize  
>> annotation collections already from sequence objects.  
>> AnnotationAdaptor doesn't care whether the primary_tag, or any  
>> other tag, is from an ontology.
>
> Ah, forgot it returns a Collection.  It doesn't modify the SF I  
> assume?

No, not if you only use getters. It does support adding annotation  
too, though.

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From smwilson at hpc.unm.edu  Fri Oct 12 17:45:41 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Fri, 12 Oct 2007 11:45:41 -0600
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
	against latest Homo_sapiens.ags file
Message-ID: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>

Hi,

I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
memory.  I get a simple "Out of memory" output even with the  
following code:

#!/usr/bin/perl
use strict;
use Bio::ASN1::EntrezGene;
   my $parser = Bio::ASN1::EntrezGene->new('file' =>  
"Homo_sapiens.xml");
   while(my $result = $parser->next_seq)
   {
   }



Thanks.
Susan





From arareko at campus.iztacala.unam.mx  Fri Oct 12 18:10:44 2007
From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra)
Date: Fri, 12 Oct 2007 14:10:44 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FB8A4.2050601@campus.iztacala.unam.mx>

Hi Susan,

Bio::ASN1::EntrezGene is not part of the BioPerl distribution, even 
though it shares the same namespace and is used by BP. Maybe you'd want 
to contact Mingyi Liu who is the author of the module. for more info 
take a look here:

http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene/

Regards,
Mauricio.

Susan Wilson wrote:
> Hi,
> 
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
> 
> 
> 
> Thanks.
> Susan
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Gen?tica
Unidad de Morfofisiolog?a y Funci?n
Facultad de Estudios Superiores Iztacala, UNAM



From Kevin.M.Brown at asu.edu  Fri Oct 12 18:19:48 2007
From: Kevin.M.Brown at asu.edu (Kevin Brown)
Date: Fri, 12 Oct 2007 11:19:48 -0700
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>

> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> machine with 256GB of memory.  I get a simple "Out of memory" 
> output even with the following code:
> 
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }

I think most systems have a per process memory limit (either hardcoded
in the OS or configured depending on the OS) and IIRC most of the IO
handlers for BioPerl load entire file contents into memory to process
them.  Some of the IO parsers have been changed recently (a new one
added for blast) so that it only pulls into memory as much as it needs
to process the next result rather than the whole file in one shebang.



From stefan.kirov at bms.com  Fri Oct 12 18:34:49 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:34:49 -0400
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <470FBE49.7010703@bms.com>

Kevin Brown wrote:
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
>> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
>> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
>> machine with 256GB of memory.  I get a simple "Out of memory" 
>> output even with the following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>     
>
> I think most systems have a per process memory limit (either hardcoded
> in the OS or configured depending on the OS) and IIRC most of the IO
> handlers for BioPerl load entire file contents into memory to process
> them.  Some of the IO parsers have been changed recently (a new one
> added for blast) so that it only pulls into memory as much as it needs
> to process the next result rather than the whole file in one shebang.
>   
The file is approx. 6GB, so on a 256GB machine this is not going to
create any problem. I think this might be deep not well controlled
recursion problem.
Stefan
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From mingyi.liu at gpc-biotech.com  Fri Oct 12 19:06:25 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 15:06:25 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <470FC5B1.3090606@gpc-biotech.com>

BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi


From j_martin at lbl.gov  Fri Oct 12 18:58:41 2007
From: j_martin at lbl.gov (Joel Martin)
Date: Fri, 12 Oct 2007 11:58:41 -0700
Subject: [Bioperl-l] Out of memory errors
	running	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FBE49.7010703@bms.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
	<470FBE49.7010703@bms.com>
Message-ID: <20071012185841.GE13838@eniac.jgi-psf.org>

Hello,
    Just a suggestion, is /usr/bin/perl a 64 bit perl?
Even on our sun machines with 72+ GB memory, for some reason they're
distributed with a 32 bit perl which can handle large files but would
probably have out of memory errrors if trying to read one into memory.

% file /usr/bin/perl 
/usr/bin/perl:  ELF 32-bit MSB executable SPARC Version 1, dynamically
linked, stripped

Joel

On Fri, Oct 12, 2007 at 02:34:49PM -0400, Stefan Kirov wrote:
> Kevin Brown wrote:
> >> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
> >> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on 
> >> it to generate Homo_sapiens.xml which is 5821420628 bytes.  I 
> >> cannot parse this file with Bio::ASN1::EntrezGene, even on a 
> >> machine with 256GB of memory.  I get a simple "Out of memory" 
> >> output even with the following code:
> >>
> >> #!/usr/bin/perl
> >> use strict;
> >> use Bio::ASN1::EntrezGene;
> >>    my $parser = Bio::ASN1::EntrezGene->new('file' => 
> >> "Homo_sapiens.xml");
> >>    while(my $result = $parser->next_seq)
> >>    {
> >>    }
> >>     
> >
> > I think most systems have a per process memory limit (either hardcoded
> > in the OS or configured depending on the OS) and IIRC most of the IO
> > handlers for BioPerl load entire file contents into memory to process
> > them.  Some of the IO parsers have been changed recently (a new one
> > added for blast) so that it only pulls into memory as much as it needs
> > to process the next result rather than the whole file in one shebang.
> >   
> The file is approx. 6GB, so on a 256GB machine this is not going to
> create any problem. I think this might be deep not well controlled
> recursion problem.
> Stefan
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >   
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


From stefan.kirov at bms.com  Fri Oct 12 18:20:38 2007
From: stefan.kirov at bms.com (Stefan Kirov)
Date: Fri, 12 Oct 2007 14:20:38 -0400
Subject: [Bioperl-l] Out of memory errors running Bio::ASN1::EntrezGene
 against latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FBAF6.1050509@bms.com>

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   
Susan,
Are you running the latest version of Bio::ASN1::EntrezGene? You may
have a better chance of getting a fast (and useful) answer if you
contact Mingyi Liu (see on CPAN) directly- the module is not part of
Bioperl. Just to mention- I have also seen similar problems and there
seems to be particular problematic records. I think NCBI made some
changes/additions to their format (might have to do something with the
number/structure of contigs). I will have to run my pipeline soon again
and if I run into the same problem I will probably create bug report for
Mingyi. I hope you do it before me- it is boring and long process.
Stefan



From mingyi.liu at gpc-biotech.com  Fri Oct 12 18:50:08 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Fri, 12 Oct 2007 14:50:08 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
Message-ID: <470FC1E0.4070708@gpc-biotech.com>

Hi, Susan,

Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, it's better to directly contact me.  I actually deleted a few messages of this discussion before one caught my eye. Nowadays I'm working in some other areas and not tracking bioperl mailing list closely, a direct email to me would usually work out better.

As for the problem you mentioned, there could be two reasons: 1. It 
seems that you converted the file to XML file instead of ASN file. My 
parser is designed for ASN file, so please use gene2xml to convert the 
downloaded file to ASN file instead of XML file.  It is likely the wrong 
syntax of the file caused my parser to attempt to read the entire file 
as a string (because it couldn't find the start/end).  However, there's 
another minor possibility (which you might have taken care of already): 
2. Perl 5.8 added 64 bit support, but I don't know if you have perl 5.8 
64 bit installed on your system to support the 256 GB system memory you 
have?  If not, your >5 GB file is over the 4 GB 32 bit Perl limit.

Let me know if my suggestions work out for you.

Best,

Mingyi

Susan Wilson wrote:
> Hi,
>
> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB of  
> memory.  I get a simple "Out of memory" output even with the  
> following code:
>
> #!/usr/bin/perl
> use strict;
> use Bio::ASN1::EntrezGene;
>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
> "Homo_sapiens.xml");
>    while(my $result = $parser->next_seq)
>    {
>    }
>
>
>
> Thanks.
> Susan
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>   



From gyang at plantbio.uga.edu  Fri Oct 12 20:52:06 2007
From: gyang at plantbio.uga.edu (Guojun Yang)
Date: Fri, 12 Oct 2007 16:52:06 -0400
Subject: [Bioperl-l] hide XML display on web
In-Reply-To: 41A08079-6EEC-4B62-8104-C41E70C03083@uiuc.edu
Message-ID: <20071012205206.9105fd09@dogwood.plantbio.uga.edu>

Hi, All,  
I have a cgi script that uses remoteblast (xml output). Every time, before and after the blast is finished, a lot of information is displayed on the client's screen, it's a nuisance but I am wondering if anyone knows how to rid of these. See below for examples:  
   
Thanks  
Guojun Yang  
_______________________example_____________________  
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>NCBI Blast:</title>
<link rel="stylesheet" type="text/css" href="css/main.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/blastRes.css" media="screen" />
<link rel="stylesheet" type="text/css" href="css/print.css" media="print" />
<!--[if lte IE 6]>
<link rel="stylesheet" type="text/css" href="css/ie6_or_less.css" />
<![endif]-->
<script type="text/javascript" src="js/utils.js"></script>
<script type="text/javascript" src="js/results.js"></script>
</head>

<body id="type-a" class="noToggleCheck" >
<div id="wrap">
   <div id="header">
  <div id="site-name"><a id="logolink" href="http://www.ncbi.nlm.nih.gov" title="NCBI Home Page"><img src="css/images/helix.gif" alt="NCBI Logo" title="Link to NCBI Home Page" /></a>BLAST <span class="desc"> Basic Local Alignment Search Tool</span>
  </div>
  <div id="search">
  <div><script language="JavaScript" type="text/javascript"><!--
    var myncbi_xo = 0;
    var myncbi_x = MyNCBI_find();
    var myncbi_cu = unescape('http%3A%2F%2Fwww%2Encbi%2Enlm%2Enih%2Egov%2Fblast%2FBlast%2Ecgi%3F');
    function MyNCBI_find()
    {
        var cs = document.cookie.split('; ');
        for(var i = 0; i < cs.length; i++) {
            // a name/value pair (a crumb) is separated by an equal sign
            var c = cs[i].split('=');
            if(c[0] == 'WebCubbyUser') { return c[1]; }
        }
        return '';
    }
.........


From hlapp at gmx.net  Sat Oct 13 21:49:49 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Sat, 13 Oct 2007 17:49:49 -0400
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<1A4207F8295607498283FE9E93B775B403D39379@EX02.asurite.ad.asu.edu>
Message-ID: <F2EFD76D-AA02-4FF7-8CAA-86AAC58E2D2E@gmx.net>


On Oct 12, 2007, at 2:19 PM, Kevin Brown wrote:

> IIRC most of the IO handlers for BioPerl load entire file contents  
> into memory to process them

As was determined already this most likely isn't the issue here, but  
I'm still confused by your statement. Most BioPerl Bio::SeqIO,  
Bio::ClusterIO, and Bio::OntologyIO parsers read an input file line  
by line, or at least by chunk.

Did you possibly mean something else?

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From mingyi.liu at gpc-biotech.com  Sun Oct 14 03:28:09 2007
From: mingyi.liu at gpc-biotech.com (Mingyi Liu)
Date: Sat, 13 Oct 2007 23:28:09 -0400
Subject: [Bioperl-l] Out of memory errors running
 Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC1E0.4070708@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
Message-ID: <47118CC9.8090807@gpc-biotech.com>

Hi, Susan,

Let us know how my suggestions worked for you.  I replied to both you 
and the bioperl mailing list last Friday in the hope that my answer 
could be helpful for the list discussion, but it seems that the mailing 
list server had serious problems and dropped both of my emails.  I'm 
therefore replying again and combined the content of my 2 emails 
together below. Hopefully the email gets sent out to the mailing list.  
If not, would one of you please forward it out?  Thanks.

Mingyi Liu wrote:
> Hi, Susan,
>
> Mauricio is right. When there's a problem with Bio::ASN1::EntrezGene, 
> it's better to directly contact me.  I actually deleted a few messages 
> of this discussion before one caught my eye. Nowadays I'm working in 
> some other areas and not tracking bioperl mailing list closely, a 
> direct email to me would usually work out better.
>
> As for the problem you mentioned, there could be two reasons: 1. It 
> seems that you converted the file to XML file instead of ASN file. My 
> parser is designed for ASN file, so please use gene2xml to convert the 
> downloaded file to ASN file instead of XML file.  It is likely the 
> wrong syntax of the file caused my parser to attempt to read the 
> entire file as a string (because it couldn't find the start/end).  
> However, there's another minor possibility (which you might have taken 
> care of already): 2. Perl 5.8 added 64 bit support, but I don't know 
> if you have perl 5.8 64 bit installed on your system to support the 
> 256 GB system memory you have?  If not, your >5 GB file is over the 4 
> GB 32 bit Perl limit.
>
> Let me know if my suggestions work out for you.
>
> Best,
>
> Mingyi
>
BTW, here's the syntax in one of my messages last year about how to 
convert the compressed binary ASN format NCBI provides to the text ASN 
format my module (or Stefan's SeqIO::entrezgene) expects (the -x switch 
does the trick, overwriting the default option to produce XML output):

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped 
binary file directly downloaded from NCBI

Same syntax should be used when you're using SeqIO (thus 
SeqIO::entrezgene).

BTW, text ASN is both smaller and faster to parse than XML format.

Best,

Mingyi

> Susan Wilson wrote:
>> Hi,
>>
>> I downloaded the latest ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ 
>> ASN_BINARY/Mammalia/Homo_sapiens.ags.gz and ran gene2xml on it to  
>> generate Homo_sapiens.xml which is 5821420628 bytes.  I cannot parse  
>> this file with Bio::ASN1::EntrezGene, even on a machine with 256GB 
>> of  memory.  I get a simple "Out of memory" output even with the  
>> following code:
>>
>> #!/usr/bin/perl
>> use strict;
>> use Bio::ASN1::EntrezGene;
>>    my $parser = Bio::ASN1::EntrezGene->new('file' =>  
>> "Homo_sapiens.xml");
>>    while(my $result = $parser->next_seq)
>>    {
>>    }
>>
>>
>>
>> Thanks.
>> Susan
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>   
>
>



From smwilson at hpc.unm.edu  Mon Oct 15 15:08:55 2007
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 15 Oct 2007 09:08:55 -0600
Subject: [Bioperl-l] Out of memory errors running
	Bio::ASN1::EntrezGeneagainst latest Homo_sapiens.ags file
In-Reply-To: <470FC5B1.3090606@gpc-biotech.com>
References: <7F4D241A-A3EF-44BA-9DAE-CE51E7449F5C@hpc.unm.edu>
	<470FC1E0.4070708@gpc-biotech.com>
	<470FC5B1.3090606@gpc-biotech.com>
Message-ID: <72C50125-E169-448C-8F25-AB13A8AD308D@hpc.unm.edu>

Mingyi,

Thank you very much for your advice.  The text ASN file 1/4 the size  
of the (evil, evil) XML file and parsing it ran just fine.  We are  
still pursuing a 64-bit perl on our 256GB server and I will let you  
know how it works.

Thanks.
Susan



On Oct 12, 2007, at 1:06 PM, Mingyi Liu wrote:

> BTW, here's the syntax in one of my messages last year about how to  
> convert the compressed binary ASN format NCBI provides to the text  
> ASN format my module (or Stefan's SeqIO::entrezgene) expects (the - 
> x switch does the trick, overwriting the default option to produce  
> XML output):
>
> my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i  
> Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the  
> gzipped binary file directly downloaded from NCBI
>
> Same syntax should be used when you're using SeqIO (thus  
> SeqIO::entrezgene).
>
> BTW, text ASN is both smaller and faster to parse than XML format.
>
> Best,
>
> Mingyi



From wgallin at ualberta.ca  Mon Oct 15 22:25:14 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 15 Oct 2007 16:25:14 -0600
Subject: [Bioperl-l] Capturing Joined Sequence from two records
Message-ID: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>

I have encountered a case of a protein sequence record for which the  
coding sequence is a join with ranges from two nucleotide sequence  
records:

gi # is 7648673

Relevant annotation is:

   CDS             1..630
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"


Is there any way using Bio::Seq objects to seamlessly get the CDS  
nucleic acid sequence, or do I need to just treat it as an oddity and  
cobble together something manually?

Warren Gallin


From esnyder at vbi.vt.edu  Mon Oct 15 20:38:06 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 16:38:06 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713CFAE.7020007@vbi.vt.edu>

Hello Again,

I think I've discovered the problem.  Apparently I've got an old version 
of BioPerl which expected an array of arguments rather than a named 
list.  When I cut-and-pasted the new code for translate() into my 
distribution, the problem went away.

So, the next question is: how can I be sure that I have the most 
up-to-date distribution available (or at least the one that matches the 
BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within 
the last year but I don't know where it actually came from.

Thanks,
eesnyder

-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"




From jason at bioperl.org  Mon Oct 15 22:54:38 2007
From: jason at bioperl.org (Jason Stajich)
Date: Mon, 15 Oct 2007 15:54:38 -0700
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
Message-ID: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>

pass in a db handle to spliced_seq. There was a question about this  
on the list a few days ago.
http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html

  - does anyone want to add this solution in more example to FAQ?

-jason

On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:

> I have encountered a case of a protein sequence record for which the
> coding sequence is a join with ranges from two nucleotide sequence
> records:
>
> gi # is 7648673
>
> Relevant annotation is:
>
>    CDS             1..630
>                       /gene="KCND2"
>                       /coded_by="join
> (AF166007.1:430..1544,AF166008.1:345..507,
>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>                        
> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>
>
> Is there any way using Bio::Seq objects to seamlessly get the CDS
> nucleic acid sequence, or do I need to just treat it as an oddity and
> cobble together something manually?
>
> Warren Gallin
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org

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From torsten.seemann at infotech.monash.edu.au  Tue Oct 16 00:49:16 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Tue, 16 Oct 2007 10:49:16 +1000
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <a79f6a4b0710151749o240a5e72j697a1cff6bf39baf@mail.gmail.com>

>  pass in a db handle to spliced_seq. There was a question about this on the
> list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?

Done.

http://www.bioperl.org/wiki/FAQ#How_do_I_get_the_complete_spliced_sequence_when_the_coordinates_refer_to_Genbank_identifiers.3F

If anyone spots any errors or wants to improve it, please do so.

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From cjfields at uiuc.edu  Tue Oct 16 01:02:25 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:02:25 -0500
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
In-Reply-To: <4713CFAE.7020007@vbi.vt.edu>
References: <4713CFAE.7020007@vbi.vt.edu>
Message-ID: <67EBC789-C27F-4918-941C-46E62ACFE934@uiuc.edu>

http://www.bioperl.org/wiki/ 
FAQ#How_can_I_tell_what_version_of_BioPerl_is_installed.3F

If you installed BioPerl via CPAN you more than likely have 1.4.  The  
most recent dev release is 1.5.2.

chris

On Oct 15, 2007, at 3:38 PM, Eric E. Snyder wrote:

> Hello Again,
>
> I think I've discovered the problem.  Apparently I've got an old  
> version
> of BioPerl which expected an array of arguments rather than a named
> list.  When I cut-and-pasted the new code for translate() into my
> distribution, the problem went away.
>
> So, the next question is: how can I be sure that I have the most
> up-to-date distribution available (or at least the one that matches  
> the
> BioPerl docs on bioperl.org)?  I downloaded BioPerl using CPAN within
> the last year but I don't know where it actually came from.
>
> Thanks,
> eesnyder
>
> -- 
> Eric E. Snyder, Ph.D.
> Virginia Bioinformatics Institute
> Virginia Polytechnic Institute and State University
> Blacksburg, VA 24061-0447
> USA
>
> Office:    (540) 231-5428
> Mobile:    (540) 230-5225
> Fax:    (540) 231-2606
> Email:    eesnyder at vbi.vt.edu
> JDAM:    N 37 12'01.6", W 80 24'26.9"
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Tue Oct 16 01:39:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 15 Oct 2007 20:39:37 -0500
Subject: [Bioperl-l] Capturing Joined Sequence from two records
In-Reply-To: <EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca>
	<EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
Message-ID: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>

Would spliced_seq() work with a protein sequence this way?  The  
location string is in a tag 'coded_by', which would require a little  
more work to get the sequence.

chris

On Oct 15, 2007, at 5:54 PM, Jason Stajich wrote:

> pass in a db handle to spliced_seq. There was a question about this  
> on the list a few days ago.
> http://lists.open-bio.org/pipermail/bioperl-l/2007-October/026631.html
>
>  - does anyone want to add this solution in more example to FAQ?
>
> -jason
>
> On Oct 15, 2007, at 3:25 PM, Warren Gallin wrote:
>
>> I have encountered a case of a protein sequence record for which the
>> coding sequence is a join with ranges from two nucleotide sequence
>> records:
>>
>> gi # is 7648673
>>
>> Relevant annotation is:
>>
>>    CDS             1..630
>>                       /gene="KCND2"
>>                       /coded_by="join
>> (AF166007.1:430..1544,AF166008.1:345..507,
>>                       AF166008.1:8976..9071,AF166008.1:9952..10044,
>>                        
>> AF166008.1:13222..13469,AF166008.1:15123..15300)"
>>
>>
>> Is there any way using Bio::Seq objects to seamlessly get the CDS
>> nucleic acid sequence, or do I need to just treat it as an oddity and
>> cobble together something manually?
>>
>> Warren Gallin
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason at bioperl.org
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From Russell.Smithies at agresearch.co.nz  Tue Oct 16 03:51:40 2007
From: Russell.Smithies at agresearch.co.nz (Smithies, Russell)
Date: Tue, 16 Oct 2007 16:51:40 +1300
Subject: [Bioperl-l] Parsing EMBL records
In-Reply-To: <50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
References: <700D5DE8-8B8E-49EC-9148-C76D72417945@ualberta.ca><EE672777-E573-43BA-B32C-D75ED31F18B9@bioperl.org>
	<50E792DF-5259-4896-ABFE-155AC771C543@uiuc.edu>
Message-ID: <D5DBA313349A4B458528BE63B387F36C05EFC097@imail.agresearch.co.nz>

I've got some output from "newcpgreport" that looks like embl format but
I'm having trouble parsing it.
One of the reasons might be because of this warning but I'm not sure.
	-------------------- WARNING ---------------------
	MSG: Got a sequence with no letters in it cannot guess alphabet
[]
	---------------------------------------------------

I need to get it into gff or tabbed format and don't want to have to
resort to Perl regexes to do it.
Has anyone got some example code for parsing embl or swiss output I
could borrow?

The "newcpgreport " output looks like this:
-----------------------------------------------------
ID   BTA28  46084206 BP.
XX
DE   CpG Island report.
XX
CC   Obs/Exp ratio > 0.60.
CC   % C + % G > 50.00.
CC   Length > 200.
XX
FH   Key              Location/Qualifiers
FT   CpG island       181953..182223
FT                    /size=271
FT                    /Sum C+G=162
FT                    /Percent CG=59.78
FT                    /ObsExp=0.75
FT   CpG island       222609..223040
FT                    /size=432
FT                    /Sum C+G=290
FT                    /Percent CG=67.13
FT                    /ObsExp=0.97
FT   CpG island       288537..288741
FT                    /size=205
FT                    /Sum C+G=112
FT                    /Percent CG=54.63
FT                    /ObsExp=0.85 
------------------------------------------------------


Any help greatly appreciated  :-)

Russell Smithies

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From esnyder at vbi.vt.edu  Mon Oct 15 18:50:54 2007
From: esnyder at vbi.vt.edu (Eric E. Snyder)
Date: Mon, 15 Oct 2007 14:50:54 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
	parameters
Message-ID: <4713B68E.2040804@vbi.vt.edu>

Hello,

I am having trouble with translate() when supplying parameters such as 
-frame, -codontable_id, etc.  I am working straight out of the tutorial 
with a very simple program-- which has me stumped!

use Bio::SeqIO;
foreach my $file ( @ARGV ){
     my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
                                     -format =>  "fasta" );
     my $seq_obj = $seqio_obj->next_seq;

     print "loaded one sequence:\n\tdisplay_id\t" .
	   $seq_obj->display_id() . "\n" .
     	   "\tdescription\t" . $seq_obj->description() . "\n";

     foreach my $frame ( 0 .. 2){
         $prot_obj = $seq_obj->translate( '-frame' => $frame );
         print "translation = " . $prot_obj->seq . "\n";
     }
}

Everything works as expected until calling translate.  The output I get 
is the translation of my FASTA sequence (in frame zero, repeated three 
times) in which every "stop" is replaced with "-frame" (!!).  However, 
with no parameters, translate works as advertised.

This is getting me down because by using the full complement of 
translate options, including specifying frame, genetic code, alternative 
start codons, etc., BioPerl will save me a huge amount of time... but 
only if I can figure out how to use it properly!

Any assistance would be greatly appreciated!!!

Sincerely,
eesnyder


-- 
Eric E. Snyder, Ph.D.
Virginia Bioinformatics Institute
Virginia Polytechnic Institute and State University
Blacksburg, VA 24061-0447
USA

Office:    (540) 231-5428
Mobile:    (540) 230-5225
Fax:    (540) 231-2606
Email:    eesnyder at vbi.vt.edu
JDAM:    N 37 12'01.6", W 80 24'26.9"



From bosborne11 at verizon.net  Tue Oct 16 12:57:46 2007
From: bosborne11 at verizon.net (Brian Osborne)
Date: Tue, 16 Oct 2007 08:57:46 -0400
Subject: [Bioperl-l] Problem with $seqobj->translate() when supplying
 parameters
In-Reply-To: <4713B68E.2040804@vbi.vt.edu>
Message-ID: <C33A2D8A.FF00%bosborne11@verizon.net>

Eric,

I took your code, unmodified, and ran it using a file in the distribution.
The output looks OK, different frames are used and I don't see "-frame" in
the output sequence (see below). This is using the latest bioperl-live -
what version Bioperl are you using?

Brian O.


269 ~/bioperl-live>./test.pl t/data/HUMBETGLOA.fa
loaded one sequence:
        display_id      HUMBETGLOA
        description     Human haplotype C4 beta-globin gene, complete cds.
translation = 
TSYLTPLITPLIVTLWVVSDFLFICIFDCIKRSLVFYLLFPKT**VTNAQSTLICIYSIFRHNLLACMSKLRKTTT
NECIYMYMYVCTYTHIYIYIFFLFLPEGFNPNKEKICLELR*SFHPFCPVSILHILETQEEIHLHIPKLNYGRQNS
STFSASTSYLCNKKIGKTIFNMLTKL*FQILRKYTCKGGCF**QFVLMVWGQEIYLRGRAEGLKSNS*ASARRAKD
RYGCHHLDLTLWSHTLGLANLLPGAGRAGARAGHKSQGRAIYCLHLLLTQLCSLATSNRHHGASDS*GEVCRYCPV
GQGERG*SWW*GPGQVGIKVTRQV*GDQ*KLGMWRQRRLLGF**ALTLSAYWSIFPPLGCWWSTLGPRGSLSPLGI
CPLLMLLWATLR*RLMARKCSVPLVMAWLTWTTSRAPLPH*VSCTVTSCTWILRTSG*VYGTLDVFFPLLFYG*VH
VIGRG*VTGYSLEWETDE*LHQCGSLRIVLVSFICCS*QLFSFV*FLLSFFFFSAIFTIILNALTLCITKGNISEI
H*VT*KKTLHSLPSTLLFGIYVCLFAYS*SPYFIFFYF*LIHNHYTYLWVKV*CFNMCTHIDQIRVILHL*F*KML
SSFNILFCLSYF*YFP*SLSFRAIMIQCIMPLCTILKNNSDNFWVKAIAISLHINISAYKL*LM*EVSYC**QLQS
SYHSAFILWLG*GWIILSPS*ALLLIMFIPLIFLPQLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHK
YH*ARFLAVQFLLKVPLFPKSNY*TGGYYEGP*ASGFCLIKNIYFHCNDVFKLFLNILLKRECGRSVHLKHKEMKS
*FKPWENTLYLKLHERR*GCKQLMHIGNSPDAYALFIPQKRIQVEA*FGG*SFAMLYFTLLIVLAVLMNVFSLPIC
LSCISQP*LHSVLLLRDTTFPLKCSFHVLRRDGFSSPGHSALVVSVVL*RST*RRKNRGHGLTVL*ALLPCLPHSQ
*PGICSASLPELS
translation = 
PPI*HH*LPH**SHFGL*VTFYLFVFLTALRGL*FFTSCFPKPNK*LMHRAH*FVFILFLDIIY*HA*AN*EKQQQ
MNAYICICMCVHIHIYIYIYFFFSYQKVLIQIRRRYA*N*GRVFIHSVL*VFCIFWRRRKRSIYISQS*IMVDKTL
PLLVHQLLICVIRKLGKRSSICLPSCDSKYYVNTLAKEDVFSSNLY*WYGAKRYILEGGLRV*SPTPKPVPEEPRT
GTAVIT*TSPCGATP*GWPIYSQEQGGQEPGLGIKVRAEPSIAYICF*HNCVH*QPQTDTMVHLTPEEKSAVTALW
GKVNVDEVGGEALGRLVSRLQDRFKETNRNWACGDREDSWVSDRH*LSLPIGLFSHP*AAGGLPLDPEVL*VLWGS
VHS*CCYGQP*GEGSWQESARCL**WPGSPGQPQGHLCHTE*AAL*QAARGS*ELQGESMGPLMFSFPFFSMVKFM
S*EGDK*QGTV*NGKQTNDCISVEVSGSF*FLLFAVHNNCFLLFNSCFLFFSSPQFLLLYLMP*HCV*QKEISLRY
IK*LKKKLYTVCLVHYYLEYMCAYLHIHNLPTLFSFIFN*YIIIIHIYGLKCNVLICVHILTKSG*FCICNFKKCF
LLLIYFFVYLISNTFPNLFLSGQ**YNVSCLFAPF*RITVIISGLRQ*QYLCI*IFLHINCN*CKRFHIANSSYNP
ATILLLFYGWDKAGLF*VQARPFC*SCSYLLSSSHSSWATCWSVCWPITLAKNSPHQCRLPIRKWWLVWLMPWPTS
ITKLAFLLSNFY*RFLCSLSPTTKLGDIMKGLEHLDSA**KTFIFIAMMYLNYF*IFY*KGNVGGQCI*NIKK*RA
SSNLGKIHYILNSMKEGEAANS*CTLATALMHMPYSSLRKGFK*RLDLEVKVLLCCILHYLLF*LSS*MSFHYPFA
YPASLSLDSTQFSCLEIPPFP*SVPSMFYGEMVSPRLATQP*LSLLSYRGLLEEGKTGVMV*LSCEPFFPASPTHS
DPESAVLVSRNY
translation = 
LLFDTTDYPIDSHTLGCK*LFIYLYF*LH*EVSSFLPLVSQNLISN*CTEHIDLYLFYF*T*FISMHEQIKKNNNK
*MHIYVYVCVYIYTYIYIYIFSFLTRRF*SK*GEDMLRTEVEFSSILSCKYFAYSGDAGRDPSTYPKAELW*TKLF
HF*CINFLFV**ENWENDLQYAYQAVIPNIT*IHLQRRMFLVAICTDGMGPRDIS*REG*GFEVQLLSQCQKSQGQ
VRLSSLRPHPVEPHPRVGQSTPRSREGRSQGWA*KSGQSHLLLTFASDTTVFTSNLKQTPWCI*LLRRSLPLLPCG
AR*TWMKLVVRPWAGWYQGYKTGLRRPIETGHVETEKTLGFLIGTDSLCLLVYFPTLRLLVVYPWTQRFFESFGDL
STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRVSLWDP*CFLSPSFLWLSSC
HRKGISNRVQFRMGNRRMIASVWKSQDRFSFFYLLFITIVFFCLILAFFFFLLRNFYYYT*CLNIVYNKRKYL*DT
LSNLKKNFTQSA*YITIWNICVLICIFIISLLYFLLFLIDT*SLYIFMG*SVMF*YVYTY*PNQGNFAFVILKNAF
FF*YTFLFILFLILSLISFFQGNNDTMYHASLHHSKE*Q**FLG*GNSNISAYKYFCI*IVTDVRGFILLIAATIQ
LPFCFYFMVGIRLDYSESKLGPFANHVHTSYLPPTAPGQRAGLCAGPSLWQRIHPTSAGCLSESGGWCG*CPGPQV
SLSSLSCCPISIKGSFVP*VQLLNWGIL*RALSIWILPNKKHLFSLQ*CI*IISEYFTKKGMWEVSAFKT*RNEEL
VQTLGKYTIS*TP*KKVRLQTANAHWQQP*CICLIHPSEKDSSRGLIWRLKFCYAVFYITYCFSCPHECLFTTHLL
ILHLSALTPLSSLA*RYHLSPEVFLPCFTARWFLLAWPLSLSCLCCLIEVYLKKEKQGSWFDCPVSPSSLPPPLTV
TRNLQC*SPGTI



On 10/15/07 2:50 PM, "Eric E. Snyder" <esnyder at vbi.vt.edu> wrote:

> Hello,
> 
> I am having trouble with translate() when supplying parameters such as
> -frame, -codontable_id, etc.  I am working straight out of the tutorial
> with a very simple program-- which has me stumped!
> 
> use Bio::SeqIO;
> foreach my $file ( @ARGV ){
>      my $seqio_obj = Bio::SeqIO->new(-file   =>  "<$file",
>                                      -format =>  "fasta" );
>      my $seq_obj = $seqio_obj->next_seq;
> 
>      print "loaded one sequence:\n\tdisplay_id\t" .
>   $seq_obj->display_id() . "\n" .
>   "\tdescription\t" . $seq_obj->description() . "\n";
> 
>      foreach my $frame ( 0 .. 2){
>          $prot_obj = $seq_obj->translate( '-frame' => $frame );
>          print "translation = " . $prot_obj->seq . "\n";
>      }
> }
> 
> Everything works as expected until calling translate.  The output I get
> is the translation of my FASTA sequence (in frame zero, repeated three
> times) in which every "stop" is replaced with "-frame" (!!).  However,
> with no parameters, translate works as advertised.
> 
> This is getting me down because by using the full complement of
> translate options, including specifying frame, genetic code, alternative
> start codons, etc., BioPerl will save me a huge amount of time... but
> only if I can figure out how to use it properly!
> 
> Any assistance would be greatly appreciated!!!
> 
> Sincerely,
> eesnyder
> 




From sheris at berkeley.edu  Tue Oct 16 23:15:43 2007
From: sheris at berkeley.edu (Sheri Simmons)
Date: Tue, 16 Oct 2007 16:15:43 -0700
Subject: [Bioperl-l] what are the key features of genbank file recognized by
	SeqIO?
Message-ID: <200710161615.43420.sheris@berkeley.edu>

I'm hoping someone can help me with figuring out how to generate genbank files 
from scratch that can be interpreted with SeqIO. The problem is that genbank 
files generated via the artemis program are not recognized by SeqIO, so I am 
attempting to generate SeqIO-compatible genbank files so they can be 
converted to other formats later. 
I produced a file which looks by eye exactly like standard genbank files, but 
which is not recognized by SeqIO. Could anyone tell me or refer me to a 
source that explains the exact format that SeqIO::genbank requires? 
FYI here's a snippet of the file generated by my program:

########
LOCUS   Contig2406              66712 bp        dna     linear  UNK
FEATURES             Location/Qualifiers
     CDS                 83..1222
                            /gene="org_2406_0001"
     CDS                1259..1576
                           /gene="org_2406_0002"
     CDS                complement(1830..3284)
                           /gene="org_2406_0003c"
(more CDS)
BASE COUNT      14091 a         19796 c         18841 g         13747 t
ORIGIN
        1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta acatacacaa
      61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg ccgatatcaa
(more sequence)
###########

Thanks,
Sheri

-- 
Sheri Simmons
Department of Earth and Planetary Sciences
University of California, Berkeley
Berkeley, CA 94720-4767
http://webfiles.berkeley.edu/~sheris


From barry.moore at genetics.utah.edu  Tue Oct 16 23:47:56 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 16 Oct 2007 17:47:56 -0600
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>

Hi Sheri,

You would need to look at the source code for Bio::SeqIO::genbank.pm  
specifically the next_seq method.  If you let us know what kind of  
errors you're getting, or what data is missing in your seq object  
perhaps we could help you narrow it down.  You could also send one of  
your GenBank style files that isn't working and someone might be  
willing to take a stab at running it.

Barry

On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:

> I'm hoping someone can help me with figuring out how to generate  
> genbank files
> from scratch that can be interpreted with SeqIO. The problem is  
> that genbank
> files generated via the artemis program are not recognized by  
> SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank  
> files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me  
> to a
> source that explains the exact format that SeqIO::genbank requires?
> FYI here's a snippet of the file generated by my program:
>
> ########
> LOCUS   Contig2406              66712 bp        dna     linear  UNK
> FEATURES             Location/Qualifiers
>      CDS                 83..1222
>                             /gene="org_2406_0001"
>      CDS                1259..1576
>                            /gene="org_2406_0002"
>      CDS                complement(1830..3284)
>                            /gene="org_2406_0003c"
> (more CDS)
> BASE COUNT      14091 a         19796 c         18841 g          
> 13747 t
> ORIGIN
>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta  
> acatacacaa
>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg  
> ccgatatcaa
> (more sequence)
> ###########
>
> Thanks,
> Sheri
>
> --
> Sheri Simmons
> Department of Earth and Planetary Sciences
> University of California, Berkeley
> Berkeley, CA 94720-4767
> http://webfiles.berkeley.edu/~sheris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From jason at bioperl.org  Tue Oct 16 23:58:46 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 16 Oct 2007 16:58:46 -0700
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
References: <200710161615.43420.sheris@berkeley.edu>
	<020311F9-7F3F-4CA2-A23B-439795943E9B@genetics.utah.edu>
Message-ID: <74393EF9-C4B9-4F3B-8150-E22BECE81587@bioperl.org>

I am sure we should also let the Artemis developers know what is  
going on so they can help fix the bug on their end as well.

Have you also tried dumping EMBL from Artemis, a format I assume they  
are more likely to use, and seeing if that parses fine in BioPerl?

-jason
On Oct 16, 2007, at 4:47 PM, Barry Moore wrote:

> Hi Sheri,
>
> You would need to look at the source code for Bio::SeqIO::genbank.pm
> specifically the next_seq method.  If you let us know what kind of
> errors you're getting, or what data is missing in your seq object
> perhaps we could help you narrow it down.  You could also send one of
> your GenBank style files that isn't working and someone might be
> willing to take a stab at running it.
>
> Barry
>
> On Oct 16, 2007, at 5:15 PM, Sheri Simmons wrote:
>
>> I'm hoping someone can help me with figuring out how to generate
>> genbank files
>> from scratch that can be interpreted with SeqIO. The problem is
>> that genbank
>> files generated via the artemis program are not recognized by
>> SeqIO, so I am
>> attempting to generate SeqIO-compatible genbank files so they can be
>> converted to other formats later.
>> I produced a file which looks by eye exactly like standard genbank
>> files, but
>> which is not recognized by SeqIO. Could anyone tell me or refer me
>> to a
>> source that explains the exact format that SeqIO::genbank requires?
>> FYI here's a snippet of the file generated by my program:
>>
>> ########
>> LOCUS   Contig2406              66712 bp        dna     linear  UNK
>> FEATURES             Location/Qualifiers
>>      CDS                 83..1222
>>                             /gene="org_2406_0001"
>>      CDS                1259..1576
>>                            /gene="org_2406_0002"
>>      CDS                complement(1830..3284)
>>                            /gene="org_2406_0003c"
>> (more CDS)
>> BASE COUNT      14091 a         19796 c         18841 g
>> 13747 t
>> ORIGIN
>>         1 gtcgactctg aggatcccct ccttctgaat agaccaacca tttgaagcta
>> acatacacaa
>>       61 taagaattct attgcacttg agatgcttcg tctagtagat gcattgcctg
>> ccgatatcaa
>> (more sequence)
>> ###########
>>
>> Thanks,
>> Sheri
>>
>> --
>> Sheri Simmons
>> Department of Earth and Planetary Sciences
>> University of California, Berkeley
>> Berkeley, CA 94720-4767
>> http://webfiles.berkeley.edu/~sheris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From torsten.seemann at infotech.monash.edu.au  Wed Oct 17 01:31:03 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Wed, 17 Oct 2007 11:31:03 +1000
Subject: [Bioperl-l] what are the key features of genbank file
	recognized by SeqIO?
In-Reply-To: <200710161615.43420.sheris@berkeley.edu>
References: <200710161615.43420.sheris@berkeley.edu>
Message-ID: <a79f6a4b0710161831x30efa062oacc64844706e8a96@mail.gmail.com>

On 17/10/2007, Sheri Simmons <sheris at berkeley.edu> wrote:
> I'm hoping someone can help me with figuring out how to generate genbank files
> from scratch that can be interpreted with SeqIO. The problem is that genbank
> files generated via the artemis program are not recognized by SeqIO, so I am
> attempting to generate SeqIO-compatible genbank files so they can be
> converted to other formats later.
> I produced a file which looks by eye exactly like standard genbank files, but
> which is not recognized by SeqIO. Could anyone tell me or refer me to a
> source that explains the exact format that SeqIO::genbank requires?

Here is NCBI's documentation on the feature table format.
http://www.ncbi.nlm.nih.gov/collab/FT/

Regarding Artemis: if you load an EMBL file, then save as EMBL, it
seems to keep the header. If you save it as Genbank though, it
discards the header and only outputs the feature table and sequence.
Also, Artemis for many of its Save options only saves the feature
table. Both of these last two can't be read by BioPerl. At one stage I
had some code to whack in a fake header and empty sequence at the end
to get it to load.

Now, regarding your example output. I'm never sure if the first line
is LOCUS or ID, I guess one is deprecated. You also don't have a Date
at the end of the first line, but maybe it is optional. You are also
missing the "//" on the final line. Finally, Genbank is strict on
correct spacing etc, but I'm sure the Bioperl parser is written
relatively defensively here, so that might not be the problem.

Hope this helps,

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From wgallin at ualberta.ca  Thu Oct 18 01:42:54 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Wed, 17 Oct 2007 19:42:54 -0600
Subject: [Bioperl-l] Still trouble with remote joined records
Message-ID: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>

I must be missing something, but I can not get the procedure outlined  
in FAQ 5.5 to do what I think it should (maybe my expectations are  
incorrect.

I think I have an up-to-date release:

GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print  
$Bio::Root::Version::VERSION,"\n"'
1.005002102


If I run the following script (not that gi7648673 is a protein record):
___________________________________________________________
#! /usr/bin/perl

#071017 - Small script to test the method for getting the ORF sequence
#using dbh passing into the sequence method.


use strict;
use warnings;
use LWP::Simple;
use Bio::DB::GenPept;
use Bio::DB::GenBank;
use Bio::Seq;

#Create handles to GenBank and GenPept

my $gbh = Bio::DB::GenBank -> new;
my $gph = Bio::DB::GenPept -> new;

#This is the gi number of the entry being tested

my $test_gi = 7648673;

#Get the protein sequence file from GENBANK

my $test_na_record = $gph -> get_Seq_by_gi ($test_gi);

#Go through the features - when the CDS feature is found splice  
together the sequence and translate.


   for my $feat ( $test_na_record->get_SeqFeatures ) {
     if ( $feat->primary_tag eq 'CDS' ) {
        my $cds = $feat->spliced_seq(-db => $gbh, -nosort => 1);
        print $cds->translate->seq, "\n";
     }
   }


exit;
_______________________________________________________________________
I get an error that a protein sequence can not be translated.  I  
thought that by feeding the handle to GenBank into the spliced_seq  
method that it would retrieve the necessary nucleic acid sequence  
records and splice together the specified ranges.

So I tried using the corresponding nucleic acid record, gi7648671,  
which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).

That yielded the correct amino acid sequence for the first half the  
protein, encoded by the sequence in the record itself, but it did not  
retrieve the other nucleic acid record that is specified to contain  
the 3' end of the sequence.

So, as far as I can see, passing the DB handle isn't causing the  
spliced_seq method to go elsewhere for the nucleic acid sequence data.

I thought that was the purpose.

Can anyone enlighten me, or is this a bug?

Warren Gallin



From cjfields at uiuc.edu  Thu Oct 18 02:49:37 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 21:49:37 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
Message-ID: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>

On Oct 17, 2007, at 8:42 PM, Warren Gallin wrote:

> I must be missing something, but I can not get the procedure outlined
> in FAQ 5.5 to do what I think it should (maybe my expectations are
> incorrect.
>
> I think I have an up-to-date release:
>
> GallinPowerbook:~ wgallin$ perl -MBio::Root::Version -e 'print
> $Bio::Root::Version::VERSION,"\n"'
> 1.005002102
> ...
> I get an error that a protein sequence can not be translated.  I
> thought that by feeding the handle to GenBank into the spliced_seq
> method that it would retrieve the necessary nucleic acid sequence
> records and splice together the specified ranges.

No, the error is expected:

MSG: Can't translate an amino acid sequence.

The record in question is a protein record, so you are retrieving a  
protein sequence, which can't be translated (the exception is valid,  
in other words).  Note that the 'CDS' feature in this case has a  
specified location of 1..630 (indicated by arrow):

      CDS             1..630   <---------
                      /gene="KCND2"
                      /coded_by="join 
(AF166007.1:430..1544,AF166008.1:345..507,
                      AF166008.1:8976..9071,AF166008.1:9952..10044,
                      AF166008.1:13222..13469,AF166008.1:15123..15300)"

The tag name 'coded_by' has the data you want; however it is stored  
as a string only.

> So I tried using the corresponding nucleic acid record, gi7648671,
> which holds the 5' end of the CDS ( I used $gbh on the get_Seq step).
>
> That yielded the correct amino acid sequence for the first half the
> protein, encoded by the sequence in the record itself, but it did not
> retrieve the other nucleic acid record that is specified to contain
> the 3' end of the sequence.
> ...
> So, as far as I can see, passing the DB handle isn't causing the
> spliced_seq method to go elsewhere for the nucleic acid sequence data.
>
> I thought that was the purpose.
>
> Can anyone enlighten me, or is this a bug?
>
> Warren Gallin

This appears to be a bug.  The remote sequence is designated in the  
feature:

      CDS             join 
(430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
                      AF166008.1:9952..10044,AF166008.1:13222..13469,
                      AF166008.1:15123..15300)
                      /gene="KCND2"
                      /codon_start=1
                      /product="voltage-gated potassium channel Kv4.2"
                      /protein_id="AAF65618.1"
                      /db_xref="GI:7648673"

but the location is truncated when passed through SeqIO to genbank  
output, which explains the spliced_seq() problem:

      CDS             430..1544
                      /db_xref="GI:7648673"
                      /codon_start=1
                      /protein_id="AAF65618.1"
                      /gene="KCND2"

I'll try looking into this; if I can't get to it immediately I'll  
file a bug report.  Thanks!

chris


From cjfields at uiuc.edu  Thu Oct 18 03:45:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 17 Oct 2007 22:45:55 -0500
Subject: [Bioperl-l] Still trouble with remote joined records
In-Reply-To: <8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
References: <8C39416A-1CA6-498B-983F-CEC35AB9E7CA@ualberta.ca>
	<8893B607-1EF3-44E5-AF42-F0967F98EC33@uiuc.edu>
Message-ID: <872F9A22-AC32-4381-B7FE-4554943C8D75@uiuc.edu>


On Oct 17, 2007, at 9:49 PM, Chris Fields wrote:

> ...
>> So, as far as I can see, passing the DB handle isn't causing the
>> spliced_seq method to go elsewhere for the nucleic acid sequence  
>> data.
>>
>> I thought that was the purpose.
>>
>> Can anyone enlighten me, or is this a bug?
>>
>> Warren Gallin
>
> This appears to be a bug.  The remote sequence is designated in the
> feature:
>
>       CDS             join
> (430..1544,AF166008.1:345..507,AF166008.1:8976..9071,
>                       AF166008.1:9952..10044,AF166008.1:13222..13469,
>                       AF166008.1:15123..15300)
>                       /gene="KCND2"
>                       /codon_start=1
>                       /product="voltage-gated potassium channel Kv4.2"
>                       /protein_id="AAF65618.1"
>                       /db_xref="GI:7648673"
>
> but the location is truncated when passed through SeqIO to genbank
> output, which explains the spliced_seq() problem:
>
>       CDS             430..1544
>                       /db_xref="GI:7648673"
>                       /codon_start=1
>                       /protein_id="AAF65618.1"
>                       /gene="KCND2"
>
> I'll try looking into this; if I can't get to it immediately I'll
> file a bug report.  Thanks!
>
> chris

Looked into it and there isn't a problem with BioPerl, but there  
appears to be an error on NCBI's end with some full GenBank seqs and  
remote locations.  The default return type for records using  
Bio::DB::GenBank is 'gbwithparts' (which retrieves full records for  
everything), but this particular record version has a truncated  
location.  You can see the truncated version here via eutils:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
db=nucleotide&retmode=text&id=7648671&rettype=gbwithparts

You can get around this in your script by changing the requested  
format to 'gb', which has the correct location string and returns the  
full protein seq:

my $gbh = Bio::DB::GenBank->new(-format => 'gb');

chris


From smei_26 at yahoo.com  Fri Oct 19 03:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From smei_26 at yahoo.com  Fri Oct 19 03:11:47 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Thu, 18 Oct 2007 20:11:47 -0700 (PDT)
Subject: [Bioperl-l] Bioperl DB RefSeq
Message-ID: <534058.73546.qm@web38804.mail.mud.yahoo.com>

Hi, 

I have a list of refseq accession  numbers and  wish  to get  their sequences. I used Bio::DB:: RefSeq module 

However, if the $acc is bad (such as deleted accession), an exception  would  printed out  and the script stops execution.   


---------------EXCEPTION-------------------
MSG: id does not exist
...
----------------------------------------------------

my $seq = $seq_refseq->get_Seq_by_id("$acc");


What I wish to happen is the script would handle the next accession (bypass the bad accession) and continue until all the accessions have been processed. 

Anyone have idea how to handle this issue? Thanks 

-- Mike



__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From cjfields at uiuc.edu  Fri Oct 19 04:47:12 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 18 Oct 2007 23:47:12 -0500
Subject: [Bioperl-l] Bioperl DB RefSeq
In-Reply-To: <534058.73546.qm@web38804.mail.mud.yahoo.com>
References: <534058.73546.qm@web38804.mail.mud.yahoo.com>
Message-ID: <744D3248-EA8E-4832-847D-4434DFF258E6@uiuc.edu>

Use an eval {} block, described here:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Error_Handling

my $seq;
eval {
   $seq =  $seq = $seq_refseq->get_Seq_by_id("$acc");
};

print "ID does not exist!\n" if $@;

chris

On Oct 18, 2007, at 10:11 PM, Steven Mei wrote:

> Hi,
>
> I have a list of refseq accession  numbers and  wish  to get  their  
> sequences. I used Bio::DB:: RefSeq module
>
> However, if the $acc is bad (such as deleted accession), an  
> exception  would  printed out  and the script stops execution.
>
>
> ---------------EXCEPTION-------------------
> MSG: id does not exist
> ...
> ----------------------------------------------------
>
> my $seq = $seq_refseq->get_Seq_by_id("$acc");
>
>
> What I wish to happen is the script would handle the next accession  
> (bypass the bad accession) and continue until all the accessions  
> have been processed.
>
> Anyone have idea how to handle this issue? Thanks
>
> -- Mike



From j.s.soares at gmail.com  Fri Oct 19 12:45:25 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 05:45:25 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of the gene. This is the thing where the script goes weird. It doesn't
reset the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need to know how
many repetitions of the pattern there are in each gene, as above, it does
not reset the counting of repetitions and istead gives me the repitions in
the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;

#print "What is the pattern you're looking for?";
#chomp (my $pat = <>);# Taking the pattern input from the user and cuting
the new line character in the end

#print "How many letters in the pattern?";
#chomp (my $patlen = <>);# Taking the length of the pattern input from the
user and cuting the new line character in the end

print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";# Taking the file to analyse
input from the user and cuting the new line character in the end

print "Where do you want to store the rough file?";
chomp (my $rough = <>);# Taking the rough file input from the user and
cuting the new line character in the end

print "Where do you want to store the final file?";
chomp (my $final = <>);# Taking the clean file input from the user and
cuting the new line character in the end

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0,
0);#Initialization of the variables common to the whole script:
#$count_of_pat3 is used to count how many times the pattern appears in a DNA
sequence.
#$position states the location in number of bases from the start of the
sequence to the first base of the pattern. 
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');#A
BioPerl module was used here (Bio::Tools::SeqPattern in order to give the
program a better direction telling it what exactly the pattern is about. If
it's DNA, RNA or Protein. In this case it's DNA.

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {#Using
BioPerl module Bio::SeqIO to open the file that contains the sequences to be
analysed
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
#Using Perl's simple default function open to create the rough file and make
it writable

        while (my $seq_obj = $in->next_seq) {
#This while loop uses BioPerl objects: $seq_obj and next_seq. It basically
states that for each sequence in the Sequences file it will run the lines
that follow and after that it will pick up the next sequence

        	#my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE
=>'Dna');#A BioPerl module was used here (Bio::Tools::SeqPattern in order to
give the program a better direction telling it what exactly the pattern is
about. If it's DNA, RNA or Protein. In this case it's DNA.

                my $id1 = $seq_obj->display_id();
#We use the $seq_obj->display_id() object here to be able to chop the fasta
header from each sequence and store it as the variable $id1

                     
				foreach ($seq_obj->seq =~ m/$pat/g){#for each sequence that contains the
pattern we are looking for, we start the count of the times the pattern
repeats itself
								++$count_of_pat;
							
							print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",#The Fasta Header,
the number of pattern repitions and the position where each repition was
found in each sequence is printed on the rough file
							$position + $-[0] + 1, "\n"; #This resets the position for the next
repetition
							$position = $position + length($seq_obj) - $patlen + 1;
							#print $-;
							#print "$count_of_pat\n";
							#print "$position\n";
							#print $seq_obj->seq, "\n";
							}#The positon is set to start from 1 rather than the default Perl
start position 0.
				
							
					}
					
					
        close MOTIFCOUNT;#With the file completelly scanned, the rough file
is closed

        open (SYM, "+< $rough") or die "The file doesn't exist";#The rough
file is open again and if it hasn't been created it prints out that it
doesn't exist

        open (TAB, ">> $final") or die "The gene list wasn't
transformed";#Another file is created and made writable, the final file.
This is done as can be seen in the following lines in order to substitute
any space by a tab and to print, as a header in the file, the motif we were
looking for.

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;#The regexp that substitutes each space
for a tab 
        		print TAB "$line";
        	}
        }
        close (SYM);#Closing both files the rough and the final
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;


Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
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From j.s.soares at gmail.com  Fri Oct 19 13:10:18 2007
From: j.s.soares at gmail.com (Djodja)
Date: Fri, 19 Oct 2007 06:10:18 -0700 (PDT)
Subject: [Bioperl-l]  Pattern recognition
Message-ID: <13293737.post@talk.nabble.com>


Hi all,

This is my first post. I am very puzzeled about a script that i wrote last
year, that was working fine, and all of sudden, with no change to the code
it just stopped doing what it was supposed to do. Basically I'm searching
for patterns on a whole genome database.

The pattern that I'm searching for at the moment is AACAAAG.

My script finds the pattern, no problem on regexps or anything. It also
searches the whole genome divided in fasta headers for each gene. The
problem is that I need to know the position of the pattern, relative to the
start of each gene. This is where the script goes weird. It doesn't reset
the counter to the start of each gene. It instead continues to count
patterns as if the genes aren't separated at all. Also I need the
information on how many repetitions of the pattern there are in each gene,
as above, it does not reset the counting of repetitions and instead gives me
the repitions in the whole genome.

here is the code:

#!/usr/lib/perl -w

use Bio::Perl;
use Bio::Seq ();
use Bio::SeqIO ();
use Bio::Tools::SeqPattern ();
use strict;
use warnings;




print 'Where is the file that you want to analise?';
chomp (my $Fasfile = <>) or die "No such file";
print "Where do you want to store the rough file?";
chomp (my $rough = <>);
print "Where do you want to store the final file?";
chomp (my $final = <>);

my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');

if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";


        while (my $seq_obj = $in->next_seq) {

                #my $id1 = $seq_obj->display_id();
				my $seq_length = length($seq_obj);
				#print "$seq_length\n";
				foreach ($seq_obj->seq =~ m/$pat/g){
								++$count_of_pat;
								
								my $id1 = $seq_obj->display_id();
								print $seq_obj->seq, "\n";							
								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
								$position + $-[0] + 1, "\n";
								$position = $position + length($seq_obj) - $patlen + 1;
								#print "$id1\n";
								#print "$count_of_pat\n";
								#print "$position\n";
								
								}
					
					#print "$seq_length\n";
					print $seq_obj->seq, "\n";
					}
					
					
        close MOTIFCOUNT;

        open (SYM, "+< $rough") or die "The file doesn't exist";

        open (TAB, ">> $final") or die "The gene list wasn't transformed";

	print TAB "Motif: $pat\n";
        while (my $line = <SYM>){

        	foreach ($line){
                	$line =~ s/\|/\t/g;
        		print TAB "$line";
        	}
        }
        close (SYM);
        close(TAB);

        print "The gene list was created and transformed successfully.\n\a"
}
exit;



Can anyone help me out? This is kind of in the way of my PhD progression.

All the best,

Djodja
-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From chemmeri at cgb.indiana.edu  Fri Oct 19 13:40:22 2007
From: chemmeri at cgb.indiana.edu (Chris Hemmerich)
Date: Fri, 19 Oct 2007 09:40:22 -0400 (EDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <13293737.post@talk.nabble.com>
References: <13293737.post@talk.nabble.com>
Message-ID: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>



Djoja,

Perhaps this is a problem with scope. Since you declare $position outside 
of

         while (my $seq_obj = $in->next_seq) {

it will not be reset for each sequence.  The line

 		$position = $position + length($seq_obj) - $patlen + 1;

will continue to increase $position for each sequence processed. From a 
quick look, I don't think you need $position at all in this script and can 
just print $-[0]+1.

Hope this helps,

  Chris


On Fri, 19 Oct 2007, Djodja wrote:

>
> Hi all,
>
> This is my first post. I am very puzzeled about a script that i wrote last
> year, that was working fine, and all of sudden, with no change to the code
> it just stopped doing what it was supposed to do. Basically I'm searching
> for patterns on a whole genome database.
>
> The pattern that I'm searching for at the moment is AACAAAG.
>
> My script finds the pattern, no problem on regexps or anything. It also
> searches the whole genome divided in fasta headers for each gene. The
> problem is that I need to know the position of the pattern, relative to the
> start of each gene. This is where the script goes weird. It doesn't reset
> the counter to the start of each gene. It instead continues to count
> patterns as if the genes aren't separated at all. Also I need the
> information on how many repetitions of the pattern there are in each gene,
> as above, it does not reset the counting of repetitions and instead gives me
> the repitions in the whole genome.
>
> here is the code:
>
> #!/usr/lib/perl -w
>
> use Bio::Perl;
> use Bio::Seq ();
> use Bio::SeqIO ();
> use Bio::Tools::SeqPattern ();
> use strict;
> use warnings;
>
>
>
>
> print 'Where is the file that you want to analise?';
> chomp (my $Fasfile = <>) or die "No such file";
> print "Where do you want to store the rough file?";
> chomp (my $rough = <>);
> print "Where do you want to store the final file?";
> chomp (my $final = <>);
>
> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>
> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>
>
>        while (my $seq_obj = $in->next_seq) {
>
>                #my $id1 = $seq_obj->display_id();
> 				my $seq_length = length($seq_obj);
> 				#print "$seq_length\n";
> 				foreach ($seq_obj->seq =~ m/$pat/g){
> 								++$count_of_pat;
>
> 								my $id1 = $seq_obj->display_id();
> 								print $seq_obj->seq, "\n";
> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
> 								$position + $-[0] + 1, "\n";
> 								$position = $position + length($seq_obj) - $patlen + 1;
> 								#print "$id1\n";
> 								#print "$count_of_pat\n";
> 								#print "$position\n";
>
> 								}
>
> 					#print "$seq_length\n";
> 					print $seq_obj->seq, "\n";
> 					}
>
>
>        close MOTIFCOUNT;
>
>        open (SYM, "+< $rough") or die "The file doesn't exist";
>
>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>
> 	print TAB "Motif: $pat\n";
>        while (my $line = <SYM>){
>
>        	foreach ($line){
>                	$line =~ s/\|/\t/g;
>        		print TAB "$line";
>        	}
>        }
>        close (SYM);
>        close(TAB);
>
>        print "The gene list was created and transformed successfully.\n\a"
> }
> exit;
>
>
>
> Can anyone help me out? This is kind of in the way of my PhD progression.
>
> All the best,
>
> Djodja
> -- 
> View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>


From smei_26 at yahoo.com  Fri Oct 19 17:51:48 2007
From: smei_26 at yahoo.com (Steven Mei)
Date: Fri, 19 Oct 2007 10:51:48 -0700 (PDT)
Subject: [Bioperl-l] Please help: GenBank ID map
Message-ID: <560962.35266.qm@web38802.mail.mud.yahoo.com>

Hi, 

I have list of GenBank ID inlcuding ids for EST, gemonics sequence and UniGene. I wish to map these ids to RefSeq Ids using BioPerl. Anyone know how to do this? Thanks

example of the GenBank Id list: 

NM_000137
BC004558
BF939919
AL031588
AI673812
NM_006024
AK024914
AK026008
NM_014823
AA523958
NM_001677
AW291083
AL049246
AF116615
AI672084


-- Mike

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 



From j.s.soares at gmail.com  Sat Oct 20 07:11:17 2007
From: j.s.soares at gmail.com (Djodja)
Date: Sat, 20 Oct 2007 00:11:17 -0700 (PDT)
Subject: [Bioperl-l] Pattern recognition
In-Reply-To: <Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
References: <13293737.post@talk.nabble.com>
	<Pine.LNX.4.64.0710190936300.4370@islay.cgb.indiana.edu>
Message-ID: <13307407.post@talk.nabble.com>


I will have to give you the credit here as well!

THank you so much Chris.

I have declared both $position and $count_of_pat inside the while loop.

Will rearrange the script and I'm going to make it a subroutine as I have
many other patterns to search for.

Thank you thank you thankyou.

Also, I am in England in Exeter. If you want I could look on ways to get you
here for a nice talk for you to expose your work.

Let me know.

Djodja

Chris Hemmerich wrote:
> 
> 
> 
> Djoja,
> 
> Perhaps this is a problem with scope. Since you declare $position outside 
> of
> 
>          while (my $seq_obj = $in->next_seq) {
> 
> it will not be reset for each sequence.  The line
> 
>  		$position = $position + length($seq_obj) - $patlen + 1;
> 
> will continue to increase $position for each sequence processed. From a 
> quick look, I don't think you need $position at all in this script and can 
> just print $-[0]+1.
> 
> Hope this helps,
> 
>   Chris
> 
> 
> On Fri, 19 Oct 2007, Djodja wrote:
> 
>>
>> Hi all,
>>
>> This is my first post. I am very puzzeled about a script that i wrote
>> last
>> year, that was working fine, and all of sudden, with no change to the
>> code
>> it just stopped doing what it was supposed to do. Basically I'm searching
>> for patterns on a whole genome database.
>>
>> The pattern that I'm searching for at the moment is AACAAAG.
>>
>> My script finds the pattern, no problem on regexps or anything. It also
>> searches the whole genome divided in fasta headers for each gene. The
>> problem is that I need to know the position of the pattern, relative to
>> the
>> start of each gene. This is where the script goes weird. It doesn't reset
>> the counter to the start of each gene. It instead continues to count
>> patterns as if the genes aren't separated at all. Also I need the
>> information on how many repetitions of the pattern there are in each
>> gene,
>> as above, it does not reset the counting of repetitions and instead gives
>> me
>> the repitions in the whole genome.
>>
>> here is the code:
>>
>> #!/usr/lib/perl -w
>>
>> use Bio::Perl;
>> use Bio::Seq ();
>> use Bio::SeqIO ();
>> use Bio::Tools::SeqPattern ();
>> use strict;
>> use warnings;
>>
>>
>>
>>
>> print 'Where is the file that you want to analise?';
>> chomp (my $Fasfile = <>) or die "No such file";
>> print "Where do you want to store the rough file?";
>> chomp (my $rough = <>);
>> print "Where do you want to store the final file?";
>> chomp (my $final = <>);
>>
>> my ($pat, $patlen, $count_of_pat, $position) = ("AACAAAG", 7, 0, 0);
>> my $pattern = new Bio::Tools::SeqPattern(-SEQ => $pat, -TYPE =>'Dna');
>>
>> if(my $in = Bio::SeqIO->new(-file => $Fasfile, -format => 'fasta' )) {
>>   	open (MOTIFCOUNT,">> $rough") or die "The gene list wasn't created";
>>
>>
>>        while (my $seq_obj = $in->next_seq) {
>>
>>                #my $id1 = $seq_obj->display_id();
>> 				my $seq_length = length($seq_obj);
>> 				#print "$seq_length\n";
>> 				foreach ($seq_obj->seq =~ m/$pat/g){
>> 								++$count_of_pat;
>>
>> 								my $id1 = $seq_obj->display_id();
>> 								print $seq_obj->seq, "\n";
>> 								print MOTIFCOUNT "$id1\t$count_of_pat\tposition ",
>> 								$position + $-[0] + 1, "\n";
>> 								$position = $position + length($seq_obj) - $patlen + 1;
>> 								#print "$id1\n";
>> 								#print "$count_of_pat\n";
>> 								#print "$position\n";
>>
>> 								}
>>
>> 					#print "$seq_length\n";
>> 					print $seq_obj->seq, "\n";
>> 					}
>>
>>
>>        close MOTIFCOUNT;
>>
>>        open (SYM, "+< $rough") or die "The file doesn't exist";
>>
>>        open (TAB, ">> $final") or die "The gene list wasn't transformed";
>>
>> 	print TAB "Motif: $pat\n";
>>        while (my $line = <SYM>){
>>
>>        	foreach ($line){
>>                	$line =~ s/\|/\t/g;
>>        		print TAB "$line";
>>        	}
>>        }
>>        close (SYM);
>>        close(TAB);
>>
>>        print "The gene list was created and transformed
>> successfully.\n\a"
>> }
>> exit;
>>
>>
>>
>> Can anyone help me out? This is kind of in the way of my PhD progression.
>>
>> All the best,
>>
>> Djodja
>> -- 
>> View this message in context:
>> http://www.nabble.com/Pattern-recognition-tf4652923.html#a13293737
>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 

-- 
View this message in context: http://www.nabble.com/Pattern-recognition-tf4652923.html#a13307407
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From avilella at gmail.com  Mon Oct 22 08:53:45 2007
From: avilella at gmail.com (Albert Vilella)
Date: Mon, 22 Oct 2007 09:53:45 +0100
Subject: [Bioperl-l] java runnables
Message-ID: <358f4d650710220153o4a941088qd5a109d546a1e140@mail.gmail.com>

Hi all,

A question related to java runnables in bioperl-run:

I would like to have a Pecan (http://www.bioperl.org/wiki/PECAN) runnable in
bioperl-run,
and there are a couple of java runnables already written, eponine and vista.

I was wondering if the current state of the java runnables satifies
everybody or if people
can think of a more clean or generic way of calling java from bioperl-run.

Comments?

Cheers,

    Albert.


From wgallin at ualberta.ca  Mon Oct 22 17:53:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 11:53:24 -0600
Subject: [Bioperl-l] Problem with EUtilities
Message-ID: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>

I've encountered a problem with retrieving a set of records using  
efetch.

Code snippet:

     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'efetch',
         -db      => 'protein',
         -rettype => 'genbank',
         -id      => \@ginumber_search
     );
     $file = 'temp_hold.gb';

     $gpeptfactory->get_Response( -file => $file );



If the array of gi numbers that I submit is large (482 elements does  
not give the problem but 1517 does) I am getting an error at the  
get_response step:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:144
-----------------------------------------------------------


Am I correct in thinking that the individual array elements are being  
submitted as part of the URI, and therefore a large array is  
exceeding the acceptable size limit for a URI?

If so, is there a workaround?  Breaking the large request into a set  
of smaller requests?
Or is there a way of submitting a file of gi numbers using  
EUtilities, rather than an array?

Warren Gallin


From cjfields at uiuc.edu  Mon Oct 22 18:16:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 13:16:19 -0500
Subject: [Bioperl-l] Problem with EUtilities
In-Reply-To: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
References: <ED0A57EF-D8A9-4641-8457-C411F6974F0B@ualberta.ca>
Message-ID: <DB401D8A-0DC9-46EB-89A9-58093B8FB171@uiuc.edu>


On Oct 22, 2007, at 12:53 PM, Warren Gallin wrote:

> I've encountered a problem with retrieving a set of records using
> efetch.
>
> Code snippet:
>
>      my $gpeptfactory = Bio::DB::EUtilities->new(
>          -eutil   => 'efetch',
>          -db      => 'protein',
>          -rettype => 'genbank',
>          -id      => \@ginumber_search
>      );
>      $file = 'temp_hold.gb';
>
>      $gpeptfactory->get_Response( -file => $file );
>
>
>
> If the array of gi numbers that I submit is large (482 elements does
> not give the problem but 1517 does) I am getting an error at the
> get_response step:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:144
> -----------------------------------------------------------
>
>
> Am I correct in thinking that the individual array elements are being
> submitted as part of the URI, and therefore a large array is
> exceeding the acceptable size limit for a URI?

Yes.

> If so, is there a workaround?  Breaking the large request into a set
> of smaller requests?
> Or is there a way of submitting a file of gi numbers using
> EUtilities, rather than an array?
>
> Warren Gallin

You can use epost and post your IDs first, then retrieve them.   
Alternatively, you can fetch them in small batches.  The following  
two code bits should help:

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_post_a_specific_list_of_UIDs_to_NCBI. 
27s_history_server.3F

http://www.bioperl.org/wiki/ 
HOWTO:EUtilities_Cookbook#How_do_I_retrieve_a_long_list_of_sequences_usi 
ng_a_query.3F

chris


From er at xs4all.nl  Mon Oct 22 16:05:29 2007
From: er at xs4all.nl (Erikjan)
Date: Mon, 22 Oct 2007 18:05:29 +0200 (CEST)
Subject: [Bioperl-l] postgres datatype: VARCHAR to TEXT - patch
Message-ID: <22811.156.83.0.216.1193069129.squirrel@webmail.xs4all.nl>

Hello,

Using load_seqdatabase.pl to load uniprot_sprot.dat into
postgres (8.2.5), biosql gave me:

ERROR:  value too long for type character varying(40)

(all fresh from cvs)

Changing 'VARCHAR(N)' to 'TEXT' fixed those errors.

Generally, VARCHAR[(N)], (=character varying) are probably
better replaced with 'TEXT' as VARCHAR(N) is implemented
as TEXT with a check on length.



Attached is a patch for the table definitions in
biosqldb-pg.sql; I haven't changed the other scripts, as I
don't know if you will agree with this improvement.

(The other table-creating scripts are probably also better
off with a change from VARCHAR (=character varying) to the
text datatype.)

(loading uniprot_sprot.dat took 20 hours to load, but now
without errors, so I won't complain :)


Thanks,

Erik



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From hangsyin at gmail.com  Mon Oct 22 22:30:10 2007
From: hangsyin at gmail.com (Hang)
Date: Mon, 22 Oct 2007 22:30:10 +0000 (UTC)
Subject: [Bioperl-l] Extract features from GFF
Message-ID: <loom.20071022T221835-291@post.gmane.org>

Hello,

I have a list of about 100,000 short genomic regions with paired start and end
coordinations on reference fly genome (R5.3). I also have GFF files from the
same genome release. I wonder how I can extract all overlapping features from
these regions.

For example:

region A is on chromosome 2L between 123,456 bp to 123,489 bp. What code should
I use to extract feature, like gene, CDS etc., that overlaps with this region?

Thank you in advance!

-- Hang



From wgallin at ualberta.ca  Tue Oct 23 00:28:55 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Mon, 22 Oct 2007 18:28:55 -0600
Subject: [Bioperl-l] More on EUtilities problem
Message-ID: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>

I seem to be missing something here.

I took the code from the HOWTO as a template and wrote the following  
code snippet (@gisearch_number is an array of gi numbers, prints out  
as expected and can be used to successfully download the relevant  
records using Batch Entrez):
______________________________________________________________

#Create new EUTILS  history object for submitting a large array of gi  
numbers
     my $gpeptfactory = Bio::DB::EUtilities->new(
         -eutil   => 'epost',
         -db      => 'protein',
         -id      => \@ginumber_search,
         -keep_histories => 1
     );

     my $count = @ginumber_search;


     my $history;
     if ($history = $gpeptfactory -> next_History){
    		print "Posted successfully\n";                            
#Prints as expected for successful history
     	print "WebEnv    : ", $history -> get_webenv,"\n";
     	print "Query_key : ",$history->get_query_key,"\n";
     }
     $file = 'temp_hold.gb';

     $gpeptfactory->set_parameters (-eutil => 'efetch',
     							   -rettype => 'genbank',
     							   -history => $history,
     							
	);
	my ($retmax, $retstart) = (300,0);
	my $retry = 0;
RETRIEVE_SEQS: while ($retstart < $count) {
	
     $gpeptfactory->set_parameters(
     						-retmax => $retmax,
                             -retstart => $retstart,
                             );
     eval{
         $gpeptfactory->get_Response(-file => $file);
         print "Output file is $file.\n";
     };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++ && goto RETRIEVE_SEQS;
     }
     else{
     	
     	my $retend = $retstart + $ retmax;
     	print "Loaded entries $retstart through $retend on retry # 
$retry.\n";

     	$retstart += $retmax;
     	$retry = 0;
     }
}

         $retr_seq = Bio::SeqIO->new(
             -file   => $file,
             -format => 'genbank'
         );

________________________________________________
At this point the program fails because there is no file written.

It appears that the get_Response method is not doing its thing.

Also, on each iteration of the loop enclosing the eval the first pass  
fails with the following error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Response Error
Request-URI Too Large
STACK: Error::throw
STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/ 
DB/GenericWebAgent.pm:184
STACK: Stable_gb_update.pl:177
-----------------------------------------------------------
  and then the second pass evaluates as correct - but the output file  
is never opened or written to.

I've tried to pass $file,  "$file" , ">>$file"  and a literal string  
of a file name, with and without the >>, but to no avail.

So I think that I must be missing something basic here, but I am  
unable to see what.

Any advice would be most welcome.

Warren Gallin




From cjfields at uiuc.edu  Tue Oct 23 00:43:31 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 19:43:31 -0500
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>


On Oct 22, 2007, at 5:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang

Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
depend on the GFF version of the data you have.

chris


From cjfields at uiuc.edu  Tue Oct 23 03:50:19 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 22 Oct 2007 22:50:19 -0500
Subject: [Bioperl-l] More on EUtilities problem
In-Reply-To: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
References: <345B6FBB-AA3F-45EC-BB62-FE4EA9525AED@ualberta.ca>
Message-ID: <52D724FE-A586-489A-81BE-F9AAA6963435@uiuc.edu>


On Oct 22, 2007, at 7:28 PM, Warren Gallin wrote:

> I seem to be missing something here.
>
> I took the code from the HOWTO as a template and wrote the following
> code snippet (@gisearch_number is an array of gi numbers, prints out
> as expected and can be used to successfully download the relevant
> records using Batch Entrez):
> ...

One problem (but not the main one):

>      $file = 'temp_hold.gb';

You don't indicate the file needs appending (such as when rewriting  
to the same file in the loop below); you should change it to:

$file = '>>temp_hold.gb';

The below section is the main issue:

>      $gpeptfactory->set_parameters (-eutil => 'efetch',
>      							   -rettype => 'genbank',
>      							   -history => $history,
>      							
> 	);

In general, unless you're absolutely sure you want to carry over  
parameters from the previous eutil search (such as when you are  
looping through and changing the retmax/retstart parameters below),  
use reset_parameters():

$gpeptfactory->reset_parameters(
        -eutil => 'efetch',
        -db  => 'protein',
        -rettype => 'genbank',
        -history => $history
);

What's I believe is happening is the id parameter setting from your  
first eutil search is carried over and is reposted in the URL (thus  
getting the error).  reset_parameters() resets all parameters to  
undef unless new parameter args are passed in, in which case those  
are set to the new values, so nothing carries over.

 From that point on everything works fine (though again you'll want  
to specify that you are appending to a file instead of overwriting it  
within the loop).

chris

> 	my ($retmax, $retstart) = (300,0);
> 	my $retry = 0;
> RETRIEVE_SEQS: while ($retstart < $count) {
> 	
>      $gpeptfactory->set_parameters(
>      						-retmax => $retmax,
>                              -retstart => $retstart,
>                              );
>      eval{
>          $gpeptfactory->get_Response(-file => $file);
>          print "Output file is $file.\n";
>      };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++ && goto RETRIEVE_SEQS;
>      }
>      else{
>      	
>      	my $retend = $retstart + $ retmax;
>      	print "Loaded entries $retstart through $retend on retry #
> $retry.\n";
>
>      	$retstart += $retmax;
>      	$retry = 0;
>      }
> }
>
>          $retr_seq = Bio::SeqIO->new(
>              -file   => $file,
>              -format => 'genbank'
>          );
>
> ________________________________________________
> At this point the program fails because there is no file written.
>
> It appears that the get_Response method is not doing its thing.
>
> Also, on each iteration of the loop enclosing the eval the first pass
> fails with the following error message:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Response Error
> Request-URI Too Large
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /Library/Perl/5.8.1/Bio/Root/Root.pm:357
> STACK: Bio::DB::GenericWebAgent::get_Response /Library/Perl/5.8.1/Bio/
> DB/GenericWebAgent.pm:184
> STACK: Stable_gb_update.pl:177
> -----------------------------------------------------------
>   and then the second pass evaluates as correct - but the output file
> is never opened or written to.
>
> I've tried to pass $file,  "$file" , ">>$file"  and a literal string
> of a file name, with and without the >>, but to no avail.
>
> So I think that I must be missing something basic here, but I am
> unable to see what.
>
> Any advice would be most welcome.
>
> Warren Gallin
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From barry.moore at genetics.utah.edu  Tue Oct 23 04:09:05 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:09:05 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <loom.20071022T221835-291@post.gmane.org>
References: <loom.20071022T221835-291@post.gmane.org>
Message-ID: <7691F0B8-9771-477F-A982-21360F769D4A@genetics.utah.edu>

Hang-

Something like this would work, although for simply querying the  
coordinates on GFF like that you could iterate over the file with  
your own while loop, split the columns and do the same thing with  
about as many lines.  You'll need to do each chromosome as a separate  
GFF file or add some code to the loop to check the chromosome  
($feature->seq_id I think).

     use Bio::Tools::GFF;

     my $coord_start = 12345;
     my $coord_end  = 67890;

     # specify input via -fh or -file
     my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version =>  
2);
     my $feature;
     # loop over the input stream
     while($feature = $gffio->next_feature()) {
	 if ($coord_start <= $feature->start && $coord_end >= $feature->end) {
	 	print $feature->gff_string;
	}
     }
     $gffio->close();

Barry

On Oct 22, 2007, at 4:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From barry.moore at genetics.utah.edu  Tue Oct 23 04:37:07 2007
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Mon, 22 Oct 2007 22:37:07 -0600
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <C837CA5E-4E55-4B23-8451-27E74426BB52@genetics.utah.edu>

Oh yeah, much better option if you've got a database running.  Look  
at the docs for the modules Chris suggested.  Something like:

my $db      = Bio::DB::SeqFeature::Store->new( -adaptor => 'DBI::mysql',
                                                  -dsn     =>  
'dbi:mysql:test',
                                                  -write   => 1 );
# load an entire GFF3 file, using the GFF3 loader...
my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    =>  
$db,
							   -verbose  => 1,
							   -fast     => 1);

$loader->load('./my_genome.gff3');

@features = $db->get_features_by_location(-seq_id=>'Chr1',- 
start=>4000,-end=>600000);

Barry

On Oct 22, 2007, at 6:43 PM, Chris Fields wrote:

>
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
>
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files
>> from the
>> same genome release. I wonder how I can extract all overlapping
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
>
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will
> depend on the GFF version of the data you have.
>
> chris
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



From sdavis2 at mail.nih.gov  Tue Oct 23 11:00:12 2007
From: sdavis2 at mail.nih.gov (Sean Davis)
Date: Tue, 23 Oct 2007 07:00:12 -0400
Subject: [Bioperl-l] Extract features from GFF
In-Reply-To: <CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
References: <loom.20071022T221835-291@post.gmane.org>
	<CD2B6D5F-230F-4C80-B358-FA3FE9E0EA09@uiuc.edu>
Message-ID: <471DD43C.8060203@mail.nih.gov>

Chris Fields wrote:
> On Oct 22, 2007, at 5:30 PM, Hang wrote:
> 
>> Hello,
>>
>> I have a list of about 100,000 short genomic regions with paired  
>> start and end
>> coordinations on reference fly genome (R5.3). I also have GFF files  
>> from the
>> same genome release. I wonder how I can extract all overlapping  
>> features from
>> these regions.
>>
>> For example:
>>
>> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
>> code should
>> I use to extract feature, like gene, CDS etc., that overlaps with  
>> this region?
>>
>> Thank you in advance!
>>
>> -- Hang
> 
> Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
> depend on the GFF version of the data you have.
> 
> chris

Not a bioperl solution, but still a very cool application, see:

http://main.g2.bx.psu.edu/

It is web-based and allows for set operations (intersection, union,
etc.) on genomic coordinates.  If you have two sets of regions of
interest, you can then ask (very quickly) for all regions that overlap,
contain, are distinct, etc.

Sean


From forrest_zhang at 163.com  Wed Oct 24 03:27:00 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Wed, 24 Oct 2007 11:27:00 +0800
Subject: [Bioperl-l]
	=?gb2312?B?tPC4tDogW0Jpb3BlcmwtbF0gbG9hZF9zZXFkYXRhYmFzZS5wbCBlcnJvcg==?=
In-Reply-To: <FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
Message-ID: <000101c815ed$bdafb2e0$390f18a0$@com>

Dear Chris:
	What's the result of test? In my computer, the test haven't been
passed.

Forrest Zhang

-----????-----
???: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
????: 2007?9?29? 6:03
???: Forrest Zhang
??: bioperl-l at bioperl.org BioPerl
??: Re: [Bioperl-l] load_seqdatabase.pl error

Okay, fixed the recursion (extra copy of a BasePersistentAdaptor  
module I was working which tripped it, so nothing in CVS).

Forrest, I get all tests passing.  I used a database without taxonomy  
loaded with bioperl-db and bioperl from cvs and it worked w/o  
problems.  I'll try working with your sequence when I have time this  
weekend.

chris

On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:

> I'm actually getting some odd recursion issues again; not sure what's
> causing it, but a reinstall of both bioperl and bioperl-db fixed it
> last time.  It may be related to the rollback, just not sure yet.
>
> I'll try tracking it down if it persists (bad pun).
>
> t/04swiss....ok 3/52
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> ---------------------------------------------------
> t/04swiss....ok
> All tests successful.
> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
> CPU)
>
> The specific error under verbose running is:
>
> --------------------- WARNING ---------------------
> MSG: recursion detected for Bio::Taxon object
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:680
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:691
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:677
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:658
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:629
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> BasePersistenceAdaptor.pm:586
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:252
> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
> PrimarySeqAdaptor.pm:229
> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/src/
> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:213
> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:244
> STACK toplevel t/04swiss.t:37
> ---------------------------------------------------
>
>
> chris
>
> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>
>> Chris let me know if you get stumped. I'm surprised that the special
>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>> assign ranks to them? I thought I filter them out. Needs to be looked
>> into too.), but at any rate I don't understand why they aren't being
>> accepted.
>>
>> Also, maybe we need a more verbose output here - Forrest, can you run
>> this with adding a --printerror argument. (I'm embarrassed to find
>> that this doesn't seem to be documented. Sigh.)
>>
>> 	-hilmar
>>
>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>
>>> If this is occurring using bioperl from CVS then I'll try taking a
>>> look at it.
>>>
>>> chris
>>>
>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>
>>>> Hilmar,
>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: The supplied lineage does not start near 'Phaseolus aureus' (I
>>>> was
>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>> | rosids
>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>> Euphyllophyta |
>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>> ---------------------------------------------------
>>>> Could not store Q40784:
>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>> by unique
>>>> key
>>>> STACK: Error::throw
>>>> STACK: Bio::Root::Root::throw
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:206
>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:244
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:169
>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:251
>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>> PersistentObject.pm:271
>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>> -----------------------------------------------------------
>>>> Sigh~~~~~~
>>>>
>>>> Forrest Zhang
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>> Lapp
>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>> To: Forrest
>>>> Cc: bioperl-l at bioperl.org
>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>
>>>> Forrest,
>>>>
>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>> the
>>>> code will try to use it to look up species and their lineage,  
>>>> rather
>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>> sequence record.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>
>>>>> Hi, all
>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>> swissport data.
>>>>> But the programe show some error as below:
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>> mysql
>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>> Could not store Q6DAH5:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>> subsp.
>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>> Pectobacterium |
>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>> Proteobacteria | Bacteria')
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>> STACK: Bio::Species::classification
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:552
>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:1305
>>>>> STACK:  
>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:973
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:852
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:182
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: load_seqdatabase.pl:620
>>>>> -----------------------------------------------------------
>>>>>
>>>>>  at load_seqdatabase.pl line 633
>>>>> ================================================================== 
>>>>> =
>>>>> =
>>>>> =
>>>>> =
>>>>> ======
>>>>> ===============================================
>>>>>
>>>>> How can I solve it, please help me, Thank you.
>>>>>
>>>>> Thanks
>>>>> Forrest zhang
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign



_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From cjfields at uiuc.edu  Wed Oct 24 04:21:00 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 23 Oct 2007 23:21:00 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000101c815ed$bdafb2e0$390f18a0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
Message-ID: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From martin.burkert at uni-bielefeld.de  Wed Oct 24 12:25:13 2007
From: martin.burkert at uni-bielefeld.de (Martin Burkert)
Date: Wed, 24 Oct 2007 14:25:13 +0200
Subject: [Bioperl-l] Problems parsing Glimmer output
Message-ID: <471F39A9.6050909@uni-bielefeld.de>

Hello,

i can't figure out why my Glimmer files can not be parsed from
Bio::Tools::Glimmer.

---- pbglimmer.pl ----
use strict;
use Bio::Tools::Glimmer;

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
my $predictionCount = 0;

while(my $gene = $parser->next_prediction()) {
	$predictionCount++;
	print $predictionCount.	':' .$gene->display_name().
				', '.$gene->start().
				', '.$gene->stop()."\n";
}
print "Total predictions: ".$predictionCount;

---- pb4.predict ----
>pb4
orf00001     1022     1138  +2     0.90
orf00002     1655     1131  -3     2.77
orf00003     1638     2390  +3     3.59
orf00004     3176     3472  +2     0.30
orf00006     4395     5561  +3     2.96
orf00008     5576     8719  +2     2.98
orf00012     8725    10152  +1     2.96
orf00013    10906    11019  +1     0.21
orf00014    12188    12292  +2     2.41
orf00017    12518    14077  +2     2.97
orf00019    15356    15246  -3     2.21
orf00020    17864    17748  -3     0.23
orf00021    18153    18037  -1     0.32
orf00023    19253    19462  +2     0.48
orf00025    21018    20902  -1     0.23
orf00027    21658    24708  +1     2.92
orf00030    26115    24898  -1     2.96
orf00031    26414    26112  -3     3.21
orf00032    28015    28473  +1     3.54
orf00033    28044    27223  -1     2.85
orf00037    30137    30033  -3     2.80
orf00041    30183    33152  +3     2.98
orf00045    34860    33637  -1     2.96
orf00047    35142    34909  -1     2.54
orf00050    36606    36737  +3     1.44
orf00052    37616    37789  +2     2.23
orf00054    37786    40344  +1     2.98
orf00056    40624    40505  -2     0.79
orf00057    42508    43890  +1     2.96
orf00059    44183    44680  +2     1.49
orf00060    44705    44908  +2     0.05
orf00063    44920    46632  +1     2.97
orf00068    47296    47865  +1     0.39
orf00071    47953    49134  +1     2.90
orf00072    49208    49318  +2     1.15
orf00074    51139    51270  +1     1.16
orf00083    58362    53767  -1     2.99
orf00088    60846    58783  -1     2.98
orf00090    63298    61394  -2     2.97
orf00093    65553    63295  -1     2.98
orf00095    65959    65588  -2     1.13
orf00096    66185    65964  -3     2.98
orf00098    66610    66933  +1     0.11
orf00099    67371    67658  +3     0.27
orf00102    71019    68134  -1     2.98
orf00103    71825    72628  +2     2.71
orf00105    75062    73740  -3     2.96
orf00106    75817    76221  +1     0.73
orf00109    78206    76734  -3     2.92
orf00113      198    79299  -3     4.22


The program always outputs "Total predictions: 0".

I also tried to force the parsing format to be just 'Glimmer'
(prokaryotic) and not 'GlimmerHmm'  with:

my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', -format =>
'Glimmer');

The pb4.predict was generated by glimmer3.02. I also tried to parse an
output from glimmer2.X, but without success.

Printing $parser with Data::Dumper outputs:

$VAR1 = bless( {
                 '_file' => 'pb4.predict',
                 '_preds_parsed' => 0,
                 '_analysis_date' => undef,
                 '_root_cleanup_methods' => [
                                              sub { "DUMMY" }
                                            ],
                 '_analysis_sbjct' => undef,
                 '_analysis_progVersion' => undef,
                 '_flush_on_write' => 1,
                 '_analysis_prog' => undef,
                 '_filehandle' => \*Symbol::GEN0,
                 '_analysis_query' => undef,
                 '_root_verbose' => 0,
                 '_preds' => []
               }, 'Bio::Tools::Glimmer' );

My installation:

Perl v5.8.8 built for MSWin32-x86-multi-thread
Bioperl 1.4

Thank you.

-- 
Viele Gr??e,

MARTIN BURKERT
mailto:martin.burkert at uni-bielefeld.de


From cjfields at uiuc.edu  Wed Oct 24 13:38:03 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 08:38:03 -0500
Subject: [Bioperl-l] Problems parsing Glimmer output
In-Reply-To: <471F39A9.6050909@uni-bielefeld.de>
References: <471F39A9.6050909@uni-bielefeld.de>
Message-ID: <37465B90-4A03-4A53-B4EF-BCC8296BAE2C@uiuc.edu>

Update to bioperl-live (from CVS).  The Glimmer parser was recently  
revised by Mark Johnson for Glimmer3 output.  I added a few fixes  
myself to correct start/end issues.

chris

On Oct 24, 2007, at 7:25 AM, Martin Burkert wrote:

> Hello,
>
> i can't figure out why my Glimmer files can not be parsed from
> Bio::Tools::Glimmer.
>
> ---- pbglimmer.pl ----
> use strict;
> use Bio::Tools::Glimmer;
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict');
> my $predictionCount = 0;
>
> while(my $gene = $parser->next_prediction()) {
> 	$predictionCount++;
> 	print $predictionCount.	':' .$gene->display_name().
> 				', '.$gene->start().
> 				', '.$gene->stop()."\n";
> }
> print "Total predictions: ".$predictionCount;
>
> ---- pb4.predict ----
>> pb4
> orf00001     1022     1138  +2     0.90
> orf00002     1655     1131  -3     2.77
> orf00003     1638     2390  +3     3.59
> orf00004     3176     3472  +2     0.30
> orf00006     4395     5561  +3     2.96
> orf00008     5576     8719  +2     2.98
> orf00012     8725    10152  +1     2.96
> orf00013    10906    11019  +1     0.21
> orf00014    12188    12292  +2     2.41
> orf00017    12518    14077  +2     2.97
> orf00019    15356    15246  -3     2.21
> orf00020    17864    17748  -3     0.23
> orf00021    18153    18037  -1     0.32
> orf00023    19253    19462  +2     0.48
> orf00025    21018    20902  -1     0.23
> orf00027    21658    24708  +1     2.92
> orf00030    26115    24898  -1     2.96
> orf00031    26414    26112  -3     3.21
> orf00032    28015    28473  +1     3.54
> orf00033    28044    27223  -1     2.85
> orf00037    30137    30033  -3     2.80
> orf00041    30183    33152  +3     2.98
> orf00045    34860    33637  -1     2.96
> orf00047    35142    34909  -1     2.54
> orf00050    36606    36737  +3     1.44
> orf00052    37616    37789  +2     2.23
> orf00054    37786    40344  +1     2.98
> orf00056    40624    40505  -2     0.79
> orf00057    42508    43890  +1     2.96
> orf00059    44183    44680  +2     1.49
> orf00060    44705    44908  +2     0.05
> orf00063    44920    46632  +1     2.97
> orf00068    47296    47865  +1     0.39
> orf00071    47953    49134  +1     2.90
> orf00072    49208    49318  +2     1.15
> orf00074    51139    51270  +1     1.16
> orf00083    58362    53767  -1     2.99
> orf00088    60846    58783  -1     2.98
> orf00090    63298    61394  -2     2.97
> orf00093    65553    63295  -1     2.98
> orf00095    65959    65588  -2     1.13
> orf00096    66185    65964  -3     2.98
> orf00098    66610    66933  +1     0.11
> orf00099    67371    67658  +3     0.27
> orf00102    71019    68134  -1     2.98
> orf00103    71825    72628  +2     2.71
> orf00105    75062    73740  -3     2.96
> orf00106    75817    76221  +1     0.73
> orf00109    78206    76734  -3     2.92
> orf00113      198    79299  -3     4.22
>
>
> The program always outputs "Total predictions: 0".
>
> I also tried to force the parsing format to be just 'Glimmer'
> (prokaryotic) and not 'GlimmerHmm'  with:
>
> my $parser = Bio::Tools::Glimmer->new(-file => 'pb4.predict', - 
> format =>
> 'Glimmer');
>
> The pb4.predict was generated by glimmer3.02. I also tried to parse an
> output from glimmer2.X, but without success.
>
> Printing $parser with Data::Dumper outputs:
>
> $VAR1 = bless( {
>                  '_file' => 'pb4.predict',
>                  '_preds_parsed' => 0,
>                  '_analysis_date' => undef,
>                  '_root_cleanup_methods' => [
>                                               sub { "DUMMY" }
>                                             ],
>                  '_analysis_sbjct' => undef,
>                  '_analysis_progVersion' => undef,
>                  '_flush_on_write' => 1,
>                  '_analysis_prog' => undef,
>                  '_filehandle' => \*Symbol::GEN0,
>                  '_analysis_query' => undef,
>                  '_root_verbose' => 0,
>                  '_preds' => []
>                }, 'Bio::Tools::Glimmer' );
>
> My installation:
>
> Perl v5.8.8 built for MSWin32-x86-multi-thread
> Bioperl 1.4
>
> Thank you.
>
> -- 
> Viele Gr??e,
>
> MARTIN BURKERT
> mailto:martin.burkert at uni-bielefeld.de
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From forrest_zhang at 163.com  Wed Oct 24 16:00:24 2007
From: forrest_zhang at 163.com (Forrest)
Date: Thu, 25 Oct 2007 00:00:24 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
Message-ID: <000001c81657$0067fd40$0137f7c0$@com>

Dear Chris,
	I was using different swissprot data all of the have some error about the taxon.
Maybe I should re-install bioperl and biosql. Could you give me the install protocol 
what you used.


Forrest Zhang

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu] 
Sent: Wednesday, October 24, 2007 12:21 PM
To: Forrest Zhang
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error

Forrest, it's working fine for me (no warnings):

cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe -- 
namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** -- 
format swiss Q40784.txt
Loading Q40784.txt ...
cjfields:~/tests/db_tests cjfields$

That was the sequence that failed (Q40784) and the format (swiss) you  
used, correct?

chris

On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:

> Dear Chris:
> 	What's the result of test? In my computer, the test haven't been
> passed.
>
> Forrest Zhang
>
> -----????-----
> ???: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
> ????: 2007?9?29? 6:03
> ???: Forrest Zhang
> ??: bioperl-l at bioperl.org BioPerl
> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>
> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
> module I was working which tripped it, so nothing in CVS).
>
> Forrest, I get all tests passing.  I used a database without taxonomy
> loaded with bioperl-db and bioperl from cvs and it worked w/o
> problems.  I'll try working with your sequence when I have time this
> weekend.
>
> chris
>
> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>
>> I'm actually getting some odd recursion issues again; not sure what's
>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>> last time.  It may be related to the rollback, just not sure yet.
>>
>> I'll try tracking it down if it persists (bad pun).
>>
>> t/04swiss....ok 3/52
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> ---------------------------------------------------
>> t/04swiss....ok
>> All tests successful.
>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =  1.51
>> CPU)
>>
>> The specific error under verbose running is:
>>
>> --------------------- WARNING ---------------------
>> MSG: recursion detected for Bio::Taxon object
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:680
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:691
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:677
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:658
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:629
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:586
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:252
>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> PrimarySeqAdaptor.pm:229
>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/ 
>> src/
>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/ 
>> cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>> BasePersistenceAdaptor.pm:213
>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm: 
>> 244
>> STACK toplevel t/04swiss.t:37
>> ---------------------------------------------------
>>
>>
>> chris
>>
>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>
>>> Chris let me know if you get stumped. I'm surprised that the special
>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI started to
>>> assign ranks to them? I thought I filter them out. Needs to be  
>>> looked
>>> into too.), but at any rate I don't understand why they aren't being
>>> accepted.
>>>
>>> Also, maybe we need a more verbose output here - Forrest, can you  
>>> run
>>> this with adding a --printerror argument. (I'm embarrassed to find
>>> that this doesn't seem to be documented. Sigh.)
>>>
>>> 	-hilmar
>>>
>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>
>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>> look at it.
>>>>
>>>> chris
>>>>
>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>
>>>>> Hilmar,
>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>
>>>>> --------------------- WARNING ---------------------
>>>>> MSG: The supplied lineage does not start near 'Phaseolus  
>>>>> aureus' (I
>>>>> was
>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales | eurosids I
>>>>> | rosids
>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>> Euphyllophyta |
>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>> ---------------------------------------------------
>>>>> Could not store Q40784:
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: create: object (Bio::Species) failed to insert or to be found
>>>>> by unique
>>>>> key
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:206
>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:244
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:169
>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>> BasePersistenceAdaptor.pm:251
>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>> PersistentObject.pm:271
>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>> -----------------------------------------------------------
>>>>> Sigh~~~~~~
>>>>>
>>>>> Forrest Zhang
>>>>>
>>>>>
>>>>> -----Original Message-----
>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>> Lapp
>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>> To: Forrest
>>>>> Cc: bioperl-l at bioperl.org
>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>
>>>>> Forrest,
>>>>>
>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>> the
>>>>> code will try to use it to look up species and their lineage,
>>>>> rather
>>>>> than inserting the lineage from whatever BioPerl parses out of the
>>>>> sequence record.
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>
>>>>>> Hi, all
>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>> swissport data.
>>>>>> But the programe show some error as below:
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>> mysql
>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>> Could not store Q6DAH5:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: The supplied lineage does not start near 'Erwinia carotovora
>>>>>> subsp.
>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>> Pectobacterium |
>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>> Proteobacteria | Bacteria')
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>> STACK: Bio::Species::classification
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:552
>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm: 
>>>>>> 281
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>> STACK:
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:973
>>>>>> STACK:  
>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:852
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:182
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: load_seqdatabase.pl:620
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>>  at load_seqdatabase.pl line 633
>>>>>> ================================================================= 
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> =
>>>>>> ======
>>>>>> ===============================================
>>>>>>
>>>>>> How can I solve it, please help me, Thank you.
>>>>>>
>>>>>> Thanks
>>>>>> Forrest zhang
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> -- 
>>> ===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign









From cjfields at uiuc.edu  Wed Oct 24 16:47:45 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Wed, 24 Oct 2007 11:47:45 -0500
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
 =?utf-8?q?rror?=
In-Reply-To: <000001c81657$0067fd40$0137f7c0$@com>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>
	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>
	<000101c815ed$bdafb2e0$390f18a0$@com>
	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>
	<000001c81657$0067fd40$0137f7c0$@com>
Message-ID: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Wed Oct 24 18:56:55 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 11:56:55 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
Message-ID: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>

Has anyone else encountered a problem parsing wu-blast output with
Bio::SearchIO ?

The ->next_hit method first returns the "unfiltered+1" sequence; that is,
the plus strand representation of the query sequence that is listed (before
the minus strand) before the summary of hits and e-values.

Then, the next time the next_hit method is called, it returns the second hit
on the list.

The only caveat to my "bug" report here is that I was searching a database
that included the query sequence, so the first hit was identical to the
query (and maybe somehow retained the "unfiltered+1" tag?) ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 19:39:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 12:39:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
Message-ID: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>

I'm relatively new to both objects and bioperl, and I'm having trouble
finding documentation on what values an attribute can have.  For example, in
Bio::Assembly::Contig the example script invokes the 'new' method with an
example filename and assigns the -format attribute (I think that's the
correct terminology) a value of 'phrap' ...

now, I'm wanting to process contig output from the cap3 program, so I'll try
assigning 'cap3' to the -format attribute (haven't tried yet so I don't know
if it will work), but where do I look for a complete list of what possible
values I can use?  I can't find it via either the Pdoc or CPAN documentation
links from the bioperl wiki pages.  Any help would be appreciated ...



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From David.Messina at sbc.su.se  Wed Oct 24 20:35:48 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:35:48 +0200
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
Message-ID: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>

Hi Joseph,

Could you post the blast report that's giving you trouble? And also could
you tell us what version of WU-BLAST you're running and what version of
BioPerl you're using?

I'd like to try and reproduce your problem.

Thanks,
Dave


From David.Messina at sbc.su.se  Wed Oct 24 20:59:12 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Wed, 24 Oct 2007 22:59:12 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
Message-ID: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>

I couldn't find the formats for Bio::Assembly::Contig in any of the
documentation either.

In situations like these, I poke around in the code for methods that deal
with whatever I'm looking for. In this case, I went to the pdoc for
Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
_guess_format method:

sub _guess_format {

   my $class = shift;
   my $arg   = shift;


return unless defined($arg);
   return 'ace'
 if ($arg =~ /\.ace\.\d+$/i);
   return 'phrap'
 if ($arg =~ /\.phrap\.out$/i);

}

So it looks like 'ace' and 'phrap' are the two assembly formats that are
supported.

The other place where the question of formats often comes up is with
sequence formats. Those are better documented, in the SeqIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats


Dave


From florent.angly at gmail.com  Wed Oct 24 21:25:25 2007
From: florent.angly at gmail.com (Florent Angly)
Date: Wed, 24 Oct 2007 14:25:25 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
Message-ID: <471FB845.2080201@gmail.com>

Dave,
Have a look in Bio::Assembly::Contig::IO, that's where all the supported 
assembly input/output formats are located. It's convenient to use the 
BioPerl Deobfuscator:
http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query 
<http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query>
'ace' and 'phrap' are the supported formats. The 'tigr' assembler format 
has been added in the CVS version recently too.
Florent


Dave Messina wrote:
> I couldn't find the formats for Bio::Assembly::Contig in any of the
> documentation either.
>
> In situations like these, I poke around in the code for methods that deal
> with whatever I'm looking for. In this case, I went to the pdoc for
> Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> _guess_format method:
>
> sub _guess_format {
>
>    my $class = shift;
>    my $arg   = shift;
>
>
> return unless defined($arg);
>    return 'ace'
>  if ($arg =~ /\.ace\.\d+$/i);
>    return 'phrap'
>  if ($arg =~ /\.phrap\.out$/i);
>
> }
>
> So it looks like 'ace' and 'phrap' are the two assembly formats that are
> supported.
>
> The other place where the question of formats often comes up is with
> sequence formats. Those are better documented, in the SeqIO HOWTO:
>
> http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
>
>
> Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>   



From joseph.fass at gmail.com  Wed Oct 24 21:43:08 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:43:08 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
Message-ID: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 21:45:29 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 14:45:29 -0700
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <471FB845.2080201@gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
Message-ID: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>

thanks, both of you!

On 10/24/07, Florent Angly <florent.angly at gmail.com> wrote:
>
> Dave,
> Have a look in Bio::Assembly::Contig::IO, that's where all the supported
> assembly input/output formats are located. It's convenient to use the
> BioPerl Deobfuscator:
>
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> <
> http://bioperl.org/cgi-bin/deob_interface.cgi?Search=&module=&sort_order=by+method&search_string=bio%3A%3Aassembly%3A%3Aio&Filter=Submit+Query
> >
> 'ace' and 'phrap' are the supported formats. The 'tigr' assembler format
> has been added in the CVS version recently too.
> Florent
>
>
> Dave Messina wrote:
> > I couldn't find the formats for Bio::Assembly::Contig in any of the
> > documentation either.
> >
> > In situations like these, I poke around in the code for methods that
> deal
> > with whatever I'm looking for. In this case, I went to the pdoc for
> > Bio::Assembly::Contig. In the synopsis, the assembly is loaded with
> > Bio::Assembly::IO->new, and in Bio::Assembly::IO's Pdoc I found the
> > _guess_format method:
> >
> > sub _guess_format {
> >
> >    my $class = shift;
> >    my $arg   = shift;
> >
> >
> > return unless defined($arg);
> >    return 'ace'
> >  if ($arg =~ /\.ace\.\d+$/i);
> >    return 'phrap'
> >  if ($arg =~ /\.phrap\.out$/i);
> >
> > }
> >
> > So it looks like 'ace' and 'phrap' are the two assembly formats that are
> > supported.
> >
> > The other place where the question of formats often comes up is with
> > sequence formats. Those are better documented, in the SeqIO HOWTO:
> >
> > http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats
> >
> >
> > Dave
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From jason at bioperl.org  Wed Oct 24 22:18:09 2007
From: jason at bioperl.org (Jason Stajich)
Date: Wed, 24 Oct 2007 18:18:09 -0400
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
Message-ID: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>

I'm pretty sure we fixed this problem after 1.4 so current "unstable"  
code a try first and let us know nif that solves the problem.

also - copy+paste of BLAST files on mailing list doesn't work so well  
so either a link to  URL or posting the file in a bugzilla bug  
(bugzilla.open-bio.org) make it easier for someone to try this at home.

-jason
On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:

> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what  
> you find.
>
> Joe
>
[SNIP]
--
Jason Stajich
jason at bioperl.org



From joseph.fass at gmail.com  Wed Oct 24 22:53:41 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 15:53:41 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
Message-ID: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>

I just updated to 1.5.2 via CPAN, and verified that that worked, and re-ran
my code ... same problem: it's still picking up "unfiltered+1" as the first
->next_hit result from wu-blast output.  This is a different issue than the
fixed bug (ID: 1649) I just found on bugzilla; that bug concerned the hit
sequences.  I'll post a report on bugzilla along with some files to try it
with (please let me know if what I upload there is incomplete).

Thanks for the quick attention, all!

~joe




On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> I'm pretty sure we fixed this problem after 1.4 so current "unstable" code
> a try first and let us know nif that solves the problem.
>
> also - copy+paste of BLAST files on mailing list doesn't work so well so
> either a link to  URL or posting the file in a bugzilla bug (
> bugzilla.open-bio.org) make it easier for someone to try this at home.
>
> -jason
> On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
>
> Hi Dave,
>
> here's my code, followed by a sample wu-blast report (below).
> I'm using bioperl version 1.4
> Thanks for looking into it, and I'd be very curious to know what you find.
>
> Joe
>
> [SNIP]
> --
> Jason Stajich
> jason at bioperl.org
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From joseph.fass at gmail.com  Wed Oct 24 23:25:50 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Wed, 24 Oct 2007 16:25:50 -0700
Subject: [Bioperl-l] problem parsing WU-blast output
In-Reply-To: <195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
References: <195e25cb0710241156n51ec42basf93a24c531f73c16@mail.gmail.com>
	<628aabb70710241335g14b4eed9r5c1c0dc6abeabd74@mail.gmail.com>
	<195e25cb0710241443l7e996cbds92a68f145937aad8@mail.gmail.com>
	<6A3F5B20-BCA6-4D74-BBBE-E764C3EA77C8@bioperl.org>
	<195e25cb0710241553pf0b6c0ega0bd8887b88dfde2@mail.gmail.com>
Message-ID: <195e25cb0710241625o8b92fe0y65925025fc9144c0@mail.gmail.com>

There's a script and sample input file to demonstrate this in Bugzilla, bug#
2388 <http://bugzilla.open-bio.org/show_bug.cgi?id=2388>

~joe



On 10/24/07, Joseph Fass <joseph.fass at gmail.com> wrote:
>
> I just updated to 1.5.2 via CPAN, and verified that that worked, and
> re-ran my code ... same problem: it's still picking up "unfiltered+1" as the
> first ->next_hit result from wu-blast output.  This is a different issue
> than the fixed bug (ID: 1649) I just found on bugzilla; that bug concerned
> the hit sequences.  I'll post a report on bugzilla along with some files to
> try it with (please let me know if what I upload there is incomplete).
>
> Thanks for the quick attention, all!
>
> ~joe
>
>
>
>
> On 10/24/07, Jason Stajich <jason at bioperl.org > wrote:
> >
> >  I'm pretty sure we fixed this problem after 1.4 so current "unstable"
> > code a try first and let us know nif that solves the problem.
> >
> > also - copy+paste of BLAST files on mailing list doesn't work so well so
> > either a link to  URL or posting the file in a bugzilla bug (
> > bugzilla.open-bio.org) make it easier for someone to try this at home.
> >
> > -jason
> > On Oct 24, 2007, at 5:43 PM, Joseph Fass wrote:
> >
> > Hi Dave,
> >
> > here's my code, followed by a sample wu-blast report (below).
> > I'm using bioperl version 1.4
> > Thanks for looking into it, and I'd be very curious to know what you
> > find.
> >
> > Joe
> >
> > [SNIP]
> > --
> > Jason Stajich
> > jason at bioperl.org
> >
> >
>
>
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
>



-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From simona_bazzocchi at yahoo.it  Thu Oct 25 03:46:53 2007
From: simona_bazzocchi at yahoo.it (simona bazzocchi)
Date: Thu, 25 Oct 2007 05:46:53 +0200 (CEST)
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
Message-ID: <594278.55585.qm@web27710.mail.ukl.yahoo.com>

Hi all, 
I'd like to parse my blast file to outuput in a html file filtering on percent identity, (75% identical or better). So I've just copied and pasted to create my perl file.
I launched this command:
perl searchIO.pl blast_file.txt
But it returned this error: "t
Bareword found where operator expected at searchIO.pl line 26, near "->length E"
        (Missing operator before E?)
syntax error at searchIO.pl line 26, near "->length E"
syntax error at searchIO.pl line 30, near "<gt"
Execution of searchIO.pl aborted due to compilation errors."
Here below you can find searchIO.pl
thanks



#!/usr/bin/perl
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;

my $in = new Bio::SearchIO(-format => 'blast',
                             -file   => shift @ARGV);

my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);


# to filter your output
my $MinLength = 100; # need a variable with scope outside the method
sub hsp_filter { 
      my $hsp = shift;
      return 1 if $hsp->length('total') > $MinLength;
  }
sub result_filter { 
      my $result = shift;
      return $hsp->num_hits > 0;
  }

  sub hit_filter { 
      my $hit = shift;
      return $hit->length E<gt> 100; # test if length of the hit sequence
                                     # long enough    
  }
  my $writer = new Bio::SearchIO::Writer::TextResultWriter(
       -filters => { 'HIT' =E<gt> \&hit_filter }  
      );


my $out = new Bio::SearchIO(-writer => $writer);
$out->write_result($in->next_result);

# can also set the filter via the writer object
$writer->filter('RESULT', \&result_filter);


 		
---------------------------------
Yahoo! Mail: gratis 1GB per i messaggi, antispam, antivirus, POP3


From torsten.seemann at infotech.monash.edu.au  Thu Oct 25 04:20:13 2007
From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann)
Date: Thu, 25 Oct 2007 14:20:13 +1000
Subject: [Bioperl-l] Bio::SearchIO::Writer::HTMLResultWriter problem
In-Reply-To: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
References: <594278.55585.qm@web27710.mail.ukl.yahoo.com>
Message-ID: <a79f6a4b0710242120g13e9a55dq710d004745b7e68b@mail.gmail.com>

Simona

> So I've just copied and pasted to create my perl file.
> syntax error at searchIO.pl line 26, near "->length E"
> syntax error at searchIO.pl line 30, near "<gt"
>   sub hit_filter {
>       my $hit = shift;
>       return $hit->length E<gt> 100; # test if length of the hit sequence

You have a Perl syntax error due to cutting and pasting from code in
PerlDoc format. It should read:

  return $hit->length > 100;  # not "E<gt>

-- 
--Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University
--Tel +61 3 9905 9010


From forrest_zhang at 163.com  Thu Oct 25 06:35:19 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 14:35:19 +0800
Subject: [Bioperl-l] =?utf-8?b?562U5aSNOiAgbG9hZF9zZXFkYXRhYmFzZS5wbCBl?=
	=?utf-8?q?rror?=
In-Reply-To: <D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
References: <000501c800d9$dc9c8e90$95d5abb0$@com>	<2461576A-1A15-45E2-A14F-AEED6ACD6007@gmx.net>	<000101c8017d$c4643360$4d2c9a20$@com>	<8C9CDFBD-200C-4CD6-8295-7833D2CD3758@uiuc.edu>	<9917490A-B7AF-4AE6-9C78-AD516700155B@gmx.net>	<EECC931E-C7B5-485E-B059-4A7A9A7C092E@uiuc.edu>	<FD7C7306-92E1-49D9-93E4-EDFBF09E1A1A@uiuc.edu>	<000101c815ed$bdafb2e0$390f18a0$@com>	<4B5DC028-D0DD-4708-A884-9400AD3DD4BB@uiuc.edu>	<000001c81657$0067fd40$0137f7c0$@com>
	<D0A6A96C-34E9-4147-B0ED-32C74EDD361B@uiuc.edu>
Message-ID: <000001c816d1$38d70250$aa8506f0$@com>

Dear Chris,
	I try you protocol, but the taxonomy problem is still existent. And the new problem about " The table 'comment' is full" is coming.
The error example like below:
	
Could not store Q6DA52: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The supplied lineage does not start near 'Erwinia carotovora subsp. atroseptica' (I was supplied 'Erwinia carotovora subsp. | Pectobacterium | Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria | Proteobacteria | Bacteria')
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::Species::classification /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:552
STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:281
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1305
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:973
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:852
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:182
STACK: Bio::DB::Persistent::PersistentObject::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:244
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:169
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed, values were ("-!- CATALYTIC ACTIVITY: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
-!- PATHWAY: Metabolic intermediate biosynthesis; chorismate
    biosynthesis; chorismate from D-erythrose 4-phosphate and PEP:
    step 3/7.
-!- PATHWAY: Context: Aromatic amino acids biosynthesis.
-!- SUBUNIT: Homodimer (By similarity).
-!- SIMILARITY: Belongs to the type-I 3-dehydroquinase family.
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
","1") FKs (12352)
The table 'comment' is full
---------------------------------------------------
Could not store Q723F8: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Comment) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: load_seqdatabase.pl:630
-----------------------------------------------------------

 at load_seqdatabase.pl line 643
	

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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Bioperl-l at lists.open-bio.org
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From forrest_zhang at 163.com  Thu Oct 25 08:16:34 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:34 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000101c816df$600c5c40$202514c0$@com>



-----Original Message-----
From: Forrest Zhang [mailto:forrest_zhang at 163.com] 
Sent: Thursday, October 25, 2007 4:16 PM
To: 'Chris Fields'
Subject: RE: [Bioperl-l] ??: load_seqdatabase.pl error

Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 08:16:58 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:16:58 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
	=?utf-8?q?=2Epl_error?=
Message-ID: <000201c816df$6c956fb0$45c04f10$@com>


Chris,
	Faint, the other kind error about "The table 'reference' is full" when I was loading uniprot_sprot_human data.
	Maybe the biosqldb-mysql.sql of my downloaded have some bugs. Where can I download the appropriate version? 


Loading uniprot_sprot_human.dat ...

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich P.C., Hermanns H.M.",""Characterization of the signaling capacities of the novel gp130-like cytokine receptor."","J. Biol. Chem. 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
The table 'reference' is full
---------------------------------------------------
Could not store Q8NI17: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:217
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
STACK: /usr/bin/bp_load_seqdatabase.pl:623
-----------------------------------------------------------

 at /usr/bin/bp_load_seqdatabase.pl line 636



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 12:48 AM
To: Forrest
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error

I use the exact procedure on the web site using Build.PL, just using  
bioperl-live and bioperl-db:

http://www.bioperl.org/wiki/ 
Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_. 
27Build.PL.27

You may have some tests fail, but >98% should pass (if not all of  
them).  Install anyway.

Prior to the bioperl-db tests I loaded a database with the BioSQL  
schema, then just ran:

perl Build.PL
./Build
./Build test
./Build install

with the proper configuration; everything passes, with one warning  
for Unigene I think (which is normal).  I install taxonomy afterwards.

One thing to note: make sure you do not have multiple bioperl  
versions installed (either db or live).  Note where the above distros  
install and then check which version is being used by using:

perldoc -l 'Bio::Root::Root'

If it isn't pointing at the same install directory then perl is using  
another BioPerl installation elsewhere in @INC, which needs to be  
removed.

chris

On Oct 24, 2007, at 11:00 AM, Forrest wrote:

> Dear Chris,
> 	I was using different swissprot data all of the have some error  
> about the taxon.
> Maybe I should re-install bioperl and biosql. Could you give me the  
> install protocol
> what you used.
>
>
> Forrest Zhang
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Wednesday, October 24, 2007 12:21 PM
> To: Forrest Zhang
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl error
>
> Forrest, it's working fine for me (no warnings):
>
> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl --safe --
> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
> format swiss Q40784.txt
> Loading Q40784.txt ...
> cjfields:~/tests/db_tests cjfields$
>
> That was the sequence that failed (Q40784) and the format (swiss) you
> used, correct?
>
> chris
>
> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>
>> Dear Chris:
>> 	What's the result of test? In my computer, the test haven't been
>> passed.
>>
>> Forrest Zhang
>>
>> -----????-----
>> ???: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>> ????: 2007?9?29? 6:03
>> ???: Forrest Zhang
>> ??: bioperl-l at bioperl.org BioPerl
>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>
>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>> module I was working which tripped it, so nothing in CVS).
>>
>> Forrest, I get all tests passing.  I used a database without taxonomy
>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>> problems.  I'll try working with your sequence when I have time this
>> weekend.
>>
>> chris
>>
>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>
>>> I'm actually getting some odd recursion issues again; not sure  
>>> what's
>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>> last time.  It may be related to the rollback, just not sure yet.
>>>
>>> I'll try tracking it down if it persists (bad pun).
>>>
>>> t/04swiss....ok 3/52
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> ---------------------------------------------------
>>> t/04swiss....ok
>>> All tests successful.
>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =   
>>> 1.51
>>> CPU)
>>>
>>> The specific error under verbose running is:
>>>
>>> --------------------- WARNING ---------------------
>>> MSG: recursion detected for Bio::Taxon object
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:680
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:691
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:677
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child / 
>>> Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:658
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:629
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:586
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/ 
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:252
>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> PrimarySeqAdaptor.pm:229
>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>> src/
>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>> cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>> BasePersistenceAdaptor.pm:213
>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/cjfields/
>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>> 244
>>> STACK toplevel t/04swiss.t:37
>>> ---------------------------------------------------
>>>
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>
>>>> Chris let me know if you get stumped. I'm surprised that the  
>>>> special
>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI  
>>>> started to
>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>> looked
>>>> into too.), but at any rate I don't understand why they aren't  
>>>> being
>>>> accepted.
>>>>
>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>> run
>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>> that this doesn't seem to be documented. Sigh.)
>>>>
>>>> 	-hilmar
>>>>
>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>
>>>>> If this is occurring using bioperl from CVS then I'll try taking a
>>>>> look at it.
>>>>>
>>>>> chris
>>>>>
>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>
>>>>>> Hilmar,
>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>
>>>>>> --------------------- WARNING ---------------------
>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>> aureus' (I
>>>>>> was
>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |  
>>>>>> eurosids I
>>>>>> | rosids
>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>> Euphyllophyta |
>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>> ---------------------------------------------------
>>>>>> Could not store Q40784:
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: create: object (Bio::Species) failed to insert or to be  
>>>>>> found
>>>>>> by unique
>>>>>> key
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:206
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:244
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:169
>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>> BasePersistenceAdaptor.pm:251
>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>> PersistentObject.pm:271
>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>> -----------------------------------------------------------
>>>>>> Sigh~~~~~~
>>>>>>
>>>>>> Forrest Zhang
>>>>>>
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Hilmar
>>>>>> Lapp
>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>> To: Forrest
>>>>>> Cc: bioperl-l at bioperl.org
>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>
>>>>>> Forrest,
>>>>>>
>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs, and
>>>>>> the
>>>>>> code will try to use it to look up species and their lineage,
>>>>>> rather
>>>>>> than inserting the lineage from whatever BioPerl parses out of  
>>>>>> the
>>>>>> sequence record.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>
>>>>>>> Hi, all
>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>> swissport data.
>>>>>>> But the programe show some error as below:
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>> mysql
>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>> Could not store Q6DAH5:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: The supplied lineage does not start near 'Erwinia  
>>>>>>> carotovora
>>>>>>> subsp.
>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>> Pectobacterium |
>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>> Proteobacteria | Bacteria')
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>> STACK: Bio::Species::classification
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:552
>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>> 281
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>> STACK:
>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>> ================================================================ 
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> =
>>>>>>> ======
>>>>>>> ===============================================
>>>>>>>
>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>
>>>>>>> Thanks
>>>>>>> Forrest zhang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> -- 
>>>>>> ===========================================================
>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>> ===========================================================
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> Christopher Fields
>>>>> Postdoctoral Researcher
>>>>> Lab of Dr. Robert Switzer
>>>>> Dept of Biochemistry
>>>>> University of Illinois Urbana-Champaign
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> -- 
>>>> ===========================================================
>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>> ===========================================================
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




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From forrest_zhang at 163.com  Thu Oct 25 08:06:27 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Thu, 25 Oct 2007 16:06:27 +0800
Subject: [Bioperl-l] FW:  problem parsing WU-blast output
Message-ID: <000201c816dd$f5c5e5f0$e151b1d0$@com>

Hi, Joe
	My this script(wublast.pl) maybe is useful for you. You can get the
subsequence by using query range and hit range.
	The script is below, and the file name is wublast.pl.

use strict;
use Bio::SearchIO;

die "Usage:perl wublast <File>\n"
      unless @ARGV==1;
my $inputfile = $ARGV[0];
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => $inputfile);
print "query","\t","hit","\t","total_length","\t",
      "query_lenth","\t","hit_length","\t",
      "percent_identity","\t","score","\t","evalue","\t","rank",
      "\t","query range","\t","hit range","\n";

while( my $result = $in->next_result ) {
    my $image=$result->query_name;

    while( my $hit = $result->next_hit ) {
	while( my $hsp = $hit->next_hsp ) {

	print $image,"\t",$hit->name,"\t",$hsp->length('total'),"\t",
	      $hsp->length('query'),"\t",$hsp->length('hit'),"\t",
	    $hsp->percent_identity,"\t",$hsp->score,"\t",$hsp->evalue,"\t",
 
$hsp->rank,"\t",$hsp->start('query'),",",$hsp->end('query'),"\t",
            $hsp->start('hit'),",",$hsp->end('hit'),"\n";

	}  
    }
}


Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
Sent: Thursday, October 25, 2007 5:43 AM
To: Dave Messina
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] problem parsing WU-blast output

Hi Dave,

here's my code, followed by a sample wu-blast report (below).
I'm using bioperl version 1.4
Thanks for looking into it, and I'd be very curious to know what you find.

Joe



***************code***************
#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::SeqIO;

# note: processes only the first result (first query sequence) of the blast
report!

my $usage = "usage: collect_hits.pl <blast report> <sequence database
(fasta)> <output_file>\n";
my $reportfile = shift || die $usage;
# open Blast report for reading in hit IDs
my $in  = Bio::SearchIO->new(-file => $reportfile,
                             -format => 'blast');

# open database (fasta format) for searching for hit IDs
my $databasefile = shift || die $usage;

# open output file (fasta format) for writing out IDs and sequences of Blast
hits
my $hitsfile = shift || die $usage;
my $out = Bio::SeqIO->new(-file => ">$hitsfile",
                          -format => 'fasta');

# get result from Blast report (only one!)
my $result = $in->next_result(); print "query: " .
$result->query_name()."\n";
#my $dummy = $result->next_hit; print "1st hit: " . $dummy->name() . "\n"; #
for debugging
#$dummy = $result->next_hit; print "2nd hit: " . $dummy->name() . "\n"; #
debugging
# then loop through hits, finding matching IDs in database and writing out
full fasta-format sequences
while (my $hit = $result->next_hit) {
  # find hit ID in database file to fill in sequence and write corresponding
sequence to output file
  my $seq = Bio::Seq->new( -id => $hit->name() ); # create Seq object with
hit name
  print "seq_id: " . $seq->id."\n";
  # open database file
  my $db = Bio::SeqIO->new(-file => $databasefile,
               -format => 'fasta');
  # now look through database sequences to pull out correct sequence for ID
from Blast hit
  my $still_looking = 1;
  do {
    my $db_seq = $db->next_seq();
    #print $seq->id() . " ... " . $db_seq->id() . "\n";
    if ($seq->id() eq $db_seq->id()) {
      $seq->seq($db_seq->seq);
      $still_looking = 0;
    } # if
  } while ($still_looking);
  # then write sequence (in fasta format) to output_file
  $out->write_seq($seq);
  print "found a sequence\n";
} # while







********************blast report*************************

BLASTN 2.0MP-WashU [04-May-2006] [linux26-x64-I32LPF64 2006-05-10T17:22:28]

Copyright (C) 1996-2006 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2006) http://blast.wustl.edu

Notice:  this program and its default parameter settings are optimized to
find
nearly identical sequences rapidly.  To identify weak protein similarities
encoded in nucleic acid, use BLASTX, TBLASTN or TBLASTX.

Query=  962_177_14574088_5489_46110_045.ab1
        (676 letters)
>Unfiltered+1
TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC
AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
CCCAACAATCCTACTT
>Unfiltered-1
AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
TCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAGCATGG
CCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGGCTTTC
CCTGTAATTAACAAATTGATTACCATTAGGAGAAGCAAGTGTGATGATGTCGAGTGAGAG
TAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAAATCGGCATCAGCATGT
TTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAACACGGTAGTTTTCAAGA
TTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCATATTTG
TTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAGAAGGGGTTGTTTTGTGTTCTT
GAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAAAGGAGACA
GAAAGTGATGCCAGGA

Database:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
           260,642 sequences; 158,813,828 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done


Smallest
                                                                       Sum
                                                              High
Expectation
Sequences producing High-scoring Segment Pairs:              Score
E(N)      N

962_177_14574088_5489_46110_045.ab1                           3380  2.0e-147
1
962_191_14579666_5489_46288_070.ab1                           2705  6.4e-117
1
962_307_14625348_5489_47135_029.ab1                           2314  2.8e-99
1
962_370_14650238_5489_47797_032.ab1                           2054  1.8e-87
1
962_400_14670294_5489_48184_096.ab1                           2040  7.2e-87
1
962_79_14536329_16654_45346_033.ab1                           1928  7.8e-82
1
962_187_14578095_5489_46263_022.ab1                           1764  2.3e-74
1
962_309_14626130_16654_47155_078.ab1                          1263  1.1e-51
1
962_45_14523164_5489_45006_087.ab1                            1160  3.7e-47
1
962_394_14659720_16654_47971_045.ab1                          1146  1.6e-46
1
962_61_14529390_16654_45210_020.ab1                           1077  2.1e-43
1
962_177_14574088_16654_46114_045.ab1                           955  7.5e-38
1
962_282_14615493_16654_46934_055.ab1                           891  1.3e-34
1
962_248_14601477_16654_46676_055.ab1                           687  1.0e-25
1
962_196_14581545_16654_48111_005.ab1                           633  3.0e-23
1


>962_177_14574088_5489_46110_045.ab1
        Length = 676

  Plus Strand HSPs:

 Score = 3380 (513.2 bits), Expect = 2.0e-147, P = 2.0e-147
 Identities = 676/676 (100%), Positives = 676/676 (100%), Strand = Plus /
Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGTTCC
120

Query:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 ACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCT
180

Query:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 CCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACA
240

Query:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 CCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGT
300

Query:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 AATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCA
360

Query:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 ATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCT
420

Query:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 TCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTA
480

Query:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTC
540

Query:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   541 ACAGATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTT
600

Query:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   601 GCAATTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAG
660

Query:   661 CCCAACAATCCTACTT 676
             ||||||||||||||||
Sbjct:   661 CCCAACAATCCTACTT 676


>962_191_14579666_5489_46288_070.ab1
        Length = 664

  Plus Strand HSPs:

 Score = 2705 (411.9 bits), Expect = 6.4e-117, P = 6.4e-117
 Identities = 541/541 (100%), Positives = 541/541 (100%), Strand = Plus /
Plus

Query:   136 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA
195
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:     1 ACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTCAGA 60

Query:   196 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
255
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 ATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTCCTA
120

Query:   256 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
315
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   121 AACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATCACT
180

Query:   316 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
375
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   181 ACTCTCACTCGACATCATCACACTTGCTTCTCCTAATGGTAATCAATTTGTTAATTACAG
240

Query:   376 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
435
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 GGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAG
300

Query:   436 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
495
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   301 GCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACG
360

Query:   496 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
555
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   361 AGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAG
420

Query:   556 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
615
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   421 CGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAA
480

Query:   616 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
675
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   481 ATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACT
540

Query:   676 T 676
             |
Sbjct:   541 T 541


>962_307_14625348_5489_47135_029.ab1
        Length = 687

  Minus Strand HSPs:

 Score = 2314 (353.2 bits), Expect = 2.8e-99, P = 2.8e-99
 Identities = 558/629 (88%), Positives = 558/629 (88%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:    72 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
131

Query:   617 -ATTT-A-GAGA-GAAA---TTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGA
565
              || | | | || ||||   || ||||||||||||||||||  | |||||| |     ||
Sbjct:   132 CATCTCATGTGAAGAAAAATTTACAAGTTAGAATAAAAAAAAAT-TAGTTC-G-----GA
184

Query:   564 AAAAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTC
505
             ||  ||    |||||||||||||||||| |||||||| |||| ||||||||||| |||||
Sbjct:   185 AAGCAG----TACTTGAAATCTGTGAGGATTGTTAACGGGTACGGCGAGTTTGACTATTC
240

Query:   504 TGAGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
445
             ||||||||||||| || | |||||||||||||||||||||||||||||||||||||||||
Sbjct:   241 TGAGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCT
300

Query:   444 GAGCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
385
             ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Sbjct:   301 GAGCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTA
360

Query:   384 TGGCTTTCCCTGTAATTAACAAATTGATTAC---CA-T--T--AGGAGAAGCAAGTGTGA
333
             ||||| |||||||||||||||||||||||||   || |  |  |||||||||||||||||
Sbjct:   361 TGGCTCTCCCTGTAATTAACAAATTGATTACAATCAATGGTGCAGGAGAAGCAAGTGTGA
420

Query:   332 TGATGTCGAGTGAGAGTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGGAA
273
             |||| | |||||||  ||| ||||||||||||||||||||||||||||||| ||||||||
Sbjct:   421 TGATTTTGAGTGAG--TAGCGATTAGTTGATTACTTACCATTAAGGACAACTAGGAGGAA
478

Query:   272 ATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
213
             ||||||||||||||| | ||||||||||||||||||||||||||||||||||||||||||
Sbjct:   479 ATCGGCATCAGCATGGTGAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACAAC
538

Query:   212 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCG
153
             |||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||
Sbjct:   539 ACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTCTGGAGGACACG
598

Query:   152 AAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAA 96
             |||||||||||||| ||| |||||||||||||||||||   |||| |||  |||||||||
Sbjct:   599 AAGGTGACCATATTGGTTTCTGAATAGAGTGTGGAACCACCTGTCAGAGTCGAAGTAGAA
658

Query:    95 GGGGTTGTTTTGTGTTCTTGAATCAGACT 67
             |||||| ||||||  |||||| ||  |||
Sbjct:   659 GGGGTTATTTTGTCCTCTTGATTCCAACT 687


>962_370_14650238_5489_47797_032.ab1
        Length = 581

  Plus Strand HSPs:

 Score = 2054 (314.2 bits), Expect = 1.8e-87, P = 1.8e-87
 Identities = 468/514 (91%), Positives = 468/514 (91%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             |||| |||||||||||||||||||| ||||||||||||||| |  | ||||| |||||||
Sbjct:    74 TCCTTGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGGGA--A-CACCAAGAGAGCC
130

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| || ||||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   131 AAGAAGAGTCGGAATCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
190

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   191 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
250

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   251 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
310

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   311 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
370

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACATCATCACACTTGCTTCTCCT--A--AT-
352
             ||||||||||||||| ||||||  |||| | |||||||||||||||||||||  |  ||
Sbjct:   371 AGTAATCAACTAATCGCTACTC--ACTCAAAATCATCACACTTGCTTCTCCTGCACCATT
428

Query:   353 G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGG
409
             |   ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Sbjct:   429 GATTGTAATCAATTTGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGG
488

Query:   410 CAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
469
             ||||||||||| |||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   489 CAGAGACTCCTACATTCTTGAGCAGGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTT
548

Query:   470 CTTTTTGGTTAACCCTAATGAAAACGAGAATCTC 503
             ||||||||| |||||| | || ||||||||||||
Sbjct:   549 CTTTTTGGT-AACCCTGACGACAACGAGAATCTC 581


>962_400_14670294_5489_48184_096.ab1
        Length = 641

  Plus Strand HSPs:

 Score = 2040 (312.1 bits), Expect = 7.2e-87, P = 7.2e-87
 Identities = 488/564 (86%), Positives = 488/564 (86%), Strand = Plus / Plus

Query:   123 ACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCC
182
             ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||||||||||
Sbjct:     1 ACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAACGCTCC 60

Query:   183 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
242
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:    61 AAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACC
120

Query:   243 CTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAA
302
             |||||||||||| | ||||||||||||||||||||||| |||||||||||||||||||||
Sbjct:   121 CTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTAAGTAA
180

Query:   303 TCAACTAATCACTACTCTCACTCGA-CATCATCACA--CTTGCTTCT-C-CTAATG---G
354
             |||||||||| |||||| | | | | ||||| |||   ||| || || | | | ||   |
Sbjct:   181 TCAACTAATCGCTACTCACTCACAATCATCA-CACTTTCTTTCTCCTGCACCATTGATTG
239

Query:   355 TAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
414
             ||||||||| |||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct:   240 TAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAG
299

Query:   415 ACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
474
             |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   300 ACTCCTACATTCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTT
359

Query:   475 TGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACA
534
             ||||||||||| | || |||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   360 TGGTTAACCCTGACGACAACGAGAATCTCAGAATAGTCAAACTCGCCATACCCGTTAACA
419

Query:   535 ACCCTCACAGATTTCAAGTAGCGCCTTTTTT-CTGATCCTGAACTATAACTTTTTTTATT
593
             | ||||||||||||||||||  |||||     || ||  |    | |  ||| |   ||
Sbjct:   420 ATCCTCACAGATTTCAAGTACTGCCTTCCGAACTAATTTTTT--T-TCCCTTCTAACATG
476

Query:   594 CTAACTTGCAATTTCTCTCTAAAT-TAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAG
652
             | |  || |     || | | |   ||||||||||  ||| ||||||||||||| |||||
Sbjct:   477 CGATTTTTCTCCA-CT-TGTGATGATAAATGCTTGGCCTGTAGGACTTTTTCCTATCTAG
534

Query:   653 CACAGAAGCCCAACAATCCTACTT 676
             ||||||||||||||||||||||||
Sbjct:   535 CACAGAAGCCCAACAATCCTACTT 558


>962_79_14536329_16654_45346_033.ab1
        Length = 675

  Plus Strand HSPs:

 Score = 1928 (295.3 bits), Expect = 7.8e-82, P = 7.8e-82
 Identities = 472/553 (85%), Positives = 472/553 (85%), Strand = Plus / Plus

Query:    77 AAGAA-CACAAAACAACCCCTTCTACTTCAGCTCCGACA-G-G-TTCCACACTCTATTCA
132
             ||||  || || |||||||||||||||||| |||||||| | | ||||||||||||| ||
Sbjct:     6 AAGAGTCAGAAGACAACCCCTTCTACTTCAACTCCGACAAGTGGTTCCACACTCTATACA 65

Query:   133 GCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAACGCTCCAAACAAATTC
192
             | ||| |||||||||||||||| || ||||| |||||||||||||||||| |||||||||
Sbjct:    66 GAAACCAATATGGTCACCTTCGTGTGCTCCAGAGGTTCGACCAACGCTCCGAACAAATTC
125

Query:   193 AGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
252
             |||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct:   126 AGAATCTTGAAAACTACCGTCTTGTAGAGTTCAAGTCCAAACCCAACACCCTCCTTCTTC
185

Query:   253 CTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTAAGTAATCAACTAATC
312
             || | || |||||||||||||| |||||  |||||||||| |||||||||| |||||||
Sbjct:   186 CTCACCACGCTGATGCCGATTTGCTCCTATTTGTCCTTAACGGTAAGTAATAAACTAATA
245

Query:   313 ACTACTC-TCACTCGACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTT
364
             |   ||  | ||  || | | ||| | ||||||||||  ||   || ||   ||||| ||
Sbjct:   246 ATCGCTAGTAACA-GA-A-CTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTT
302

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             ||||||||||||   | || || |||| |||||||||||||| |||||||| |||| |||
Sbjct:   303 GTTAATTACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACAT
362

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||| |||| ||||| |||||||||||||||| |||||||||| |||||||
Sbjct:   363 TCTTGAGCAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCC
422

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             | | || |||||| |||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   423 TGACGACAACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAT
482

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  |||||||  ||||| |  ||||| | |||||||| || |||||||||
Sbjct:   483 ATTTCAAGTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCAT
539

Query:   605 TTTCTCTCTAAAT 617
             |||||||||||||
Sbjct:   540 TTTCTCTCTAAAT 552

 Score = 1188 (184.3 bits), Expect = 2.1e-48, P = 2.1e-48
 Identities = 358/471 (76%), Positives = 358/471 (76%), Strand = Plus / Plus

Query:   220 AGTTCAAGTCCAAACCCAACACCCTCCTTCTTC-CTAAACATGCTGATGCCGATTTCCTC
278
             ||| |||  ||||  ||  | || || ||| || | |  | || ||  |      ||||
Sbjct:   159 AGTCCAAACCCAACACC--CTCCTTC-TTCCTCACCACGC-TGATGCCGATTTGCTCCTA
214

Query:   279 CTTGTTGTCCTTAATG-GTAAGTAATCAACTAATCACTACTCTCACTCGACATCATCACA
337
              ||||  |      |  |||| ||| | | ||||| ||| |  ||    || ||||
Sbjct:   215 TTTGTCCTTAACGGTAAGTAA-TAAACTAATAATCGCTAGTAACAGA--ACTTCATATTT
271

Query:   338 -CTTGCTTCTCCTAA-TGGTA---ATCAATTTGTTAATTACAGGGAAAGCCATACTCACC
392
              ||| || | |  || || ||   ||||| ||||||||||||||   | || || ||||
Sbjct:   272 GCTT-CTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGGACCCGTAATCACA
330

Query:   393 TTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCATGCTCAGAAGATC
452
             |||||||||||||| |||||||| |||| |||||||||||||||| |||| ||||| |||
Sbjct:   331 TTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGATGCCCAGAAAATC
390

Query:   453 CCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAATCTCAGAATAATC
512
             ||||||||||||| |||||||||| |||||||| | || |||||| ||||||||||||||
Sbjct:   391 CCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGATCTCAGAATAATC
450

Query:   513 AAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCCTTTTTTCTGATCC
572
             |||||||||||||| |||||||||||||||| ||||||||||  |||||||  ||||| |
Sbjct:   451 AAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCCTTTT--CTGATTC
508

Query:   573 TGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T----A-AA-TGCT
625
               ||||| | |||||||| || ||||||||| ||||||||||||| |    | || || |
Sbjct:   509 CCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGTGACGATAAATGTT
567

Query:   626 TGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCTACTT 676
             ||  ||| ||||||||||| | |||||||||||||||||||| ||||||||
Sbjct:   568 TGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCTACTT 618


>962_187_14578095_5489_46263_022.ab1
        Length = 590

  Plus Strand HSPs:

 Score = 1764 (270.7 bits), Expect = 2.3e-74, P = 2.3e-74
 Identities = 410/453 (90%), Positives = 410/453 (90%), Strand = Plus / Plus

Query:     1 TCCTGGCATCACTTTCTGTCTCCTTTGGCATTGTACACCGGCAGCAGCACCATGAGAGCC 60
             ||||||||||||||||||||||||| |||||||||||||||  | ||||||| |||||||
Sbjct:   144 TCCTGGCATCACTTTCTGTCTCCTTCGGCATTGTACACCGG--G-AGCACCAAGAGAGCC
200

Query:    61 AGGAAGAGTCTGATTCAAGAACACAAAACAACCCCTTCTACTTCAGCTCCGACAGGT--T
118
             | |||||||| ||  |||||  |||||| |||||||||||||||  ||| |||||||  |
Sbjct:   201 AAGAAGAGTCGGAACCAAGAGGACAAAATAACCCCTTCTACTTCGACTCTGACAGGTGGT
260

Query:   119 -CCACACTCTATTCAGCAACAAATATGGTCACCTTCGGGTCCTCCACAGGTTCGACCAAC
177
              ||||||||||||||| ||| |||||||||||||||| |||||||| |||||||||||||
Sbjct:   261 TCCACACTCTATTCAGAAACCAATATGGTCACCTTCGTGTCCTCCAGAGGTTCGACCAAC
320

Query:   178 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
237
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   321 GCTCCAAACAAATTCAGAATCTTGAAAACTACCGTGTTGTAGAGTTCAAGTCCAAACCCA
380

Query:   238 ACACCCTCCTTCTTCCTAAACATGCTGATGCCGATTTCCTCCTTGTTGTCCTTAATGGTA
297
             ||||||||||||||||| | ||||||||||||||||||||||| ||||||||||||||||
Sbjct:   381 ACACCCTCCTTCTTCCTCACCATGCTGATGCCGATTTCCTCCTAGTTGTCCTTAATGGTA
440

Query:   298 AGTAATCAACTAATCACTACTCTCACTCGACA-TCATCACACTTGCTT-CTCCT--A--A
351
             ||||||||||||||| ||||||  |||| ||| ||||||||||| ||| |||||  |  |
Sbjct:   441 AGTAATCAACTAATCGCTACTC--ACTC-ACAATCATCACACTTTCTTTCTCCTGCACCA
497

Query:   352 T-G---GTAATCAATTTGTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGAC
407
             | |   |||||||||| |||||||||||||| ||||||||||||||||||||||||||||
Sbjct:   498 TTGATTGTAATCAATTCGTTAATTACAGGGAGAGCCATACTCACCTTGGTGAACCCTGAC
557

Query:   408 GGCAGAGACTCCTTCATTCTTGAGCAAGGCCAT 440
             ||||||||||||| |||||||||||||||||||
Sbjct:   558 GGCAGAGACTCCTACATTCTTGAGCAAGGCCAT 590


>962_309_14626130_16654_47155_078.ab1
        Length = 531

  Plus Strand HSPs:

 Score = 1263 (195.6 bits), Expect = 1.1e-51, P = 1.1e-51
 Identities = 281/312 (90%), Positives = 281/312 (90%), Strand = Plus / Plus

Query:   365 GTTAATTACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCAT
424
             |||||||||||| | ||||||||||||||||||||||||||||||||||||||| |||||
Sbjct:     1 GTTAATTACAGGAAGAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCATTCAT 60

Query:   425 TCTTGAGCAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
484
             ||||||||||||||||| ||| | ||||||||||||||||||||||||||||||||||||
Sbjct:    61 TCTTGAGCAAGGCCATGTTCAAAGGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCC
120

Query:   485 TAATGAAAACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAG
544
             ||| || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Sbjct:   121 TAACGACAACGACAATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACAA
180

Query:   545 ATTTCAAGTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAA
604
             ||||||||||  ||||| | |  ||| |   ||||||||| ||||||||||||||| |||
Sbjct:   181 ATTTCAAGTACTGCCTTCTGT--GATTCCATACTATAACTGTTTTTATTCTAACTTTCAA
238

Query:   605 TTTCTCTCTAAATTAAATGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             ||||||||||||| ||||| || | ||| ||||||||||||| |||||||||||||| ||
Sbjct:   239 TTTCTCTCTAAAT-AAATGTTTCTCCTGTAGGACTTTTTCCTATCTAGCACAGAAGCTCA
297

Query:   665 ACAATCCTACTT 676
              |||||||||||
Sbjct:   298 GCAATCCTACTT 309


>962_45_14523164_5489_45006_087.ab1
        Length = 697

  Plus Strand HSPs:

 Score = 1160 (180.1 bits), Expect = 3.7e-47, P = 3.7e-47
 Identities = 302/364 (82%), Positives = 302/364 (82%), Strand = Plus / Plus

Query:   327 ACATCATCACACTTGCTTCTCCT-AA---TGGTA---ATCAATTTGTTAATTACAGGGAA
379
             | | | ||| | ||||||||||  ||   || ||   ||||| ||||||||||||||
Sbjct:    13 AGAACTTCATATTTGCTTCTCCGCAAAAATGATAGTGATCAAGTTGTTAATTACAGGTGG 72

Query:   380 AGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAGCAAGGCCA
439
             | || || |||| |||||||||||||| |||||||| |||| |||||||||||||||| |
Sbjct:    73 ACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAGCAAGGCGA
132

Query:   440 TGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAAAACGAGAA
499
             ||| ||||| |||||||||||||||| |||||||||| |||||||| | || |||||| |
Sbjct:   133 TGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGACAACGAGGA
192

Query:   500 TCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAAGTAGCGCC
559
             ||||||||||||||||||||||||||| |||||||||||||||| ||||||||||  |||
Sbjct:   193 TCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAAGTACTGCC
252

Query:   560 TTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCTCTAAAT-T
618
             ||||  ||||| |  ||||| | |||||||| || ||||||||| ||||||||||||| |
Sbjct:   253 TTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCTCTAAATGT
309

Query:   619 -A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCAACAATCCT
672
              |  |  | || |||  ||| ||||||||||| | |||||||||||||||||||| ||||
Sbjct:   310 GACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCAACAGTCCT
369

Query:   673 ACTT 676
             ||||
Sbjct:   370 ACTT 373


>962_394_14659720_16654_47971_045.ab1
        Length = 708

  Minus Strand HSPs:

 Score = 1146 (178.0 bits), Expect = 1.6e-46, P = 1.6e-46
 Identities = 284/333 (85%), Positives = 284/333 (85%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTA-
618
             ||||||||||||||||||||||||||||| ||||||||||||| |||  ||||||||||
Sbjct:   374 AAGTAGGATTGTTGGGCTTCTGTGCTAGATAGGAAAAAGTCCTACAGGCCAAGCATTTAT
433

Query:   617 -ATTTAGAGAGAAATTGCAAGTTAGAA-T-A-AA-AAAAGTTATAGTTCAGGATCAGAAA
563
              || |   | |||     || ||| || | | || ||||   | |  | ||  || ||||
Sbjct:   434 CATCTCATGTGAAGAAA-AATTTACAAGTTAGAATAAAAAAAAAAAAT-AGT-TCGGAAA
490

Query:   562 AAAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTG
503
               ||    ||||||||||||||||||||||||||| |||| ||||||||||| |||||||
Sbjct:   491 GCAG----TACTTGAAATCTGTGAGGGTTGTTAACGGGTACGGCGAGTTTGACTATTCTG
546

Query:   502 AGATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
443
             ||||||||||| || | |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   547 AGATTCTCGTTGTCGTCAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGA
606

Query:   442 GCATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
383
             ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct:   607 GCATGGCCTTGCTCAAGAATGTAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATG
666

Query:   382 GCTTTCCCTGTAATTAACAAATTGATTACCATT 350
             ||| |||||||||||||| |||||||||| | |
Sbjct:   667 GCTCTCCCTGTAATTAACGAATTGATTACAAAT 699


>962_61_14529390_16654_45210_020.ab1
        Length = 696

  Plus Strand HSPs:

 Score = 1077 (167.6 bits), Expect = 2.1e-43, P = 2.1e-43
 Identities = 265/312 (84%), Positives = 265/312 (84%), Strand = Plus / Plus

Query:   372 ACAGGGAAAGCCATACTCACCTTGGTGAACCCTGACGGCAGAGACTCCTTCATTCTTGAG
431
             |||||   | || || |||| |||||||||||||| |||||||| |||| ||||||||||
Sbjct:     1 ACAGGTGGACCCGTAATCACATTGGTGAACCCTGATGGCAGAGAATCCTACATTCTTGAG 60

Query:   432 CAAGGCCATGCTCAGAAGATCCCTGCAGGAACCACTTTCTTTTTGGTTAACCCTAATGAA
491
             |||||| |||| ||||| |||||||||||||||| |||||||||| |||||||| | ||
Sbjct:    61 CAAGGCGATGCCCAGAAAATCCCTGCAGGAACCATTTTCTTTTTGATTAACCCTGACGAC
120

Query:   492 AACGAGAATCTCAGAATAATCAAACTCGCCATACCTGTTAACAACCCTCACAGATTTCAA
551
             |||||| |||||||||||||||||||||||||||| |||||||||||||||| |||||||
Sbjct:   121 AACGAGGATCTCAGAATAATCAAACTCGCCATACCCGTTAACAACCCTCACATATTTCAA
180

Query:   552 GTAGCGCCTTTTTTCTGATCCTGAACTATAACTTTTTTTATTCTAACTTGCAATTTCTCT
611
             |||  |||||||  ||||| |  ||||| | |||||||| || ||||||||| |||||||
Sbjct:   181 GTACTGCCTTTT--CTGATTCCCAACTA-ACCTTTTTTTCTTTTAACTTGCATTTTCTCT
237

Query:   612 CTAAAT-T-A--A--A-TGCTTGTTCTGCAGGACTTTTTCCTTTCTAGCACAGAAGCCCA
664
             |||||| | |  |  | || |||  ||| ||||||||||| | |||||||||||||||||
Sbjct:   238 CTAAATGTGACGATAAATGTTTGCCCTGTAGGACTTTTTCTTATCTAGCACAGAAGCCCA
297

Query:   665 ACAATCCTACTT 676
             ||| ||||||||
Sbjct:   298 ACAGTCCTACTT 309


>962_177_14574088_16654_46114_045.ab1
        Length = 625

  Minus Strand HSPs:

 Score = 955 (149.3 bits), Expect = 7.5e-38, P = 7.5e-38
 Identities = 191/191 (100%), Positives = 191/191 (100%), Strand = Minus /
Plus

Query:   676 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
617
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   435 AAGTAGGATTGTTGGGCTTCTGTGCTAGAAAGGAAAAAGTCCTGCAGAACAAGCATTTAA
494

Query:   616 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
557
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   495 TTTAGAGAGAAATTGCAAGTTAGAATAAAAAAAGTTATAGTTCAGGATCAGAAAAAAGGC
554

Query:   556 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
497
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct:   555 GCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGAGATTC
614

Query:   496 TCGTTTTCATT 486
             |||||||||||
Sbjct:   615 TCGTTTTCATT 625


>962_282_14615493_16654_46934_055.ab1
        Length = 274

  Minus Strand HSPs:

 Score = 891 (139.7 bits), Expect = 1.3e-34, P = 1.3e-34
 Identities = 191/207 (92%), Positives = 191/207 (92%), Strand = Minus /
Plus

Query:   561 AAGGCGCTACTTGAAATCTGTGAGGGTTGTTAACAGGTATGGCGAGTTTGATTATTCTGA
502
             |||||  |||||||||||||||||| |||||||| |||||||||||||||| ||||||||
Sbjct:    68 AAGGCAGTACTTGAAATCTGTGAGGATTGTTAACGGGTATGGCGAGTTTGACTATTCTGA
127

Query:   501 GATTCTCGTTTTCATTAGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
442
             |||||||||| || |  |||||||||||||||||||||||||||||||||||||||||||
Sbjct:   128 GATTCTCGTTGTCGTCTGGGTTAACCAAAAAGAAAGTGGTTCCTGCAGGGATCTTCTGAG
187

Query:   441 CATGGCCTTGCTCAAGAATGAAGGAGTCTCTGCCGTCAGGGTTCACCAAGGTGAGTATGG
382
             ||||||||||||||| |||| ||||||||||||||||||||||| |||||||||||||||
Sbjct:   188 CATGGCCTTGCTCAATAATGTAGGAGTCTCTGCCGTCAGGGTTCCCCAAGGTGAGTATGG
247

Query:   381 CTTTCCCTGTAATTAACAAATTGATTA 355
             || |||||| ||||||| | |||||||
Sbjct:   248 CTCTCCCTGCAATTAACGATTTGATTA 274


>962_248_14601477_16654_46676_055.ab1
        Length = 566

  Minus Strand HSPs:

 Score = 687 (109.1 bits), Expect = 1.0e-25, P = 1.0e-25
 Identities = 203/273 (74%), Positives = 203/273 (74%), Strand = Minus /
Plus

Query:   333 ATGATGTCGAGTGAGA-GTAGTGATTAGTTGATTACTTACCATTAAGGACAACAAGGAGG
275
             ||||  |  | | ||| ||||| |  |||  |||||| |||  ||||||| |  ||||||
Sbjct:     1 ATGAAATTTAATCAGAAGTAGT-A--AGTA-ATTACTGACCGCTAAGGACGAGGAGGAGG 56

Query:   274 AAATCGGCATCAGCATGTTTAGGAAGAAGGAGGGTGTTGGGTTTGGACTTGAACTCTACA
215
             ||||| || || ||||| | ||| ||||| ||||||| |||| |||||| |||||| |||
Sbjct:    57 AAATCAGCGTCTGCATGGTGAGGGAGAAGAAGGGTGTGGGGTCTGGACTCGAACTCCACA
116

Query:   214 ACACGGTAGTTTTCAAGATTCTGAATTTGTTTGGAGC---GTTGGTCGAACCTGTGGAGG
158
             |||||||||| |  ||| |||||||  ||| ||||||   ||||||| || || || |||
Sbjct:   117 ACACGGTAGTCTCGAAGGTTCTGAAGCTGTGTGGAGCTTCGTTGGTCAAAGCTCTGAAGG
176

Query:   157 ACCCGAAGGTGACCATATTTGTTGCTGAATAGAGTGTGGAACCTGTCGGAGCTGAAGTAG 98
             |  || | |||||| | || |||  |||| |||||| |||| || |  ||  ||||||
Sbjct:   177 ATACGGATGTGACCGTGTTGGTTCTTGAAAAGAGTGCGGAATCTATTCGACATGAAGTGA
236

Query:    97 AAGGGGTTGTTTTGTGTTCTTGAATCAGACTCT 65
             || |||||| | ||||||  ||| || || |||
Sbjct:   237 AAAGGGTTGGTCTGTGTTTGTGAGTCTGAGTCT 269


>962_196_14581545_16654_48111_005.ab1
        Length = 538

  Minus Strand HSPs:

 Score = 633 (101.0 bits), Expect = 3.0e-23, P = 3.0e-23
 Identities = 169/204 (82%), Positives = 169/204 (82%), Strand = Minus /
Plus

Query:   201 CAAGATTCTGAATTTGTTTGGAGCGTTGGTCGAACCTGTGGAGGACCCGAAGGTGACCAT
142
             ||||||||||||||||||| |  |||||||||||||| ||||||||||| || |||||||
Sbjct:     2 CAAGATTCTGAATTTGTTTCGTACGTTGGTCGAACCTCTGGAGGACCCGGAGATGACCAT 61

Query:   141 ATTTGTTGCTGAATAGAGTGTGGAACC---TGTCGGAGCTGAAGTAGAAGGGGTTGTTTT 85
             ||| |||  ||||||||||||||||||   | ||||||||||||| ||| ||||| ||||
Sbjct:    62 ATTGGTTTTTGAATAGAGTGTGGAACCACCTATCGGAGCTGAAGTGGAAAGGGTTATTTT
121

Query:    84 GTGTTCTTGAATCAGACTCTTCCTGGCTCTCATGGTGCTGCTGCCGGTGTACAATGCCAA 25
             ||  ||| |  |  |||||||  ||||| || ||||||| | |  | ||||||||||| |
Sbjct:   122 GT--TCTCG--T--GACTCTTGTTGGCTTTCTTGGTGCT-C-GT-GATGTACAATGCCTA
172

Query:    24 AGGAGACAGAAAGTGATGCCAGGA 1
             |||| ||||||| |||||||||||
Sbjct:   173 AGGAAACAGAAACTGATGCCAGGA 196


Parameters:
  E=1e-20
  evalues
  echofilter
  -o Cowpea962_177_14574088_5489_46110_045.ab1.wu.n

  ctxfactor=2.00

  Query                        -----  As Used  -----    -----  Computed
----
  Strand MatID Matrix name     Lambda    K       H      Lambda    K       H
   +1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a
   -1      0   +5,-4           0.192   0.182   0.357    same    same    same
               Q=10,R=10       0.104   0.0151  0.0600    n/a     n/a     n/a

  Query
  Strand MatID  Length  Eff.Length     E     S  W   T   X   E2      S2
   +1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119
   -1      0      676       676   9.9e-21  611 11 n/a  73  0.049    80
                                                      134  0.048   119


Statistics:

  Database:  ../../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Title:  ../Cowpea1X/Cowpea_all_GSS_clean.fasta
   Posted:  2:44:50 PM PDT Oct 19, 2007
   Created:  2:44:50 PM PDT Oct 19, 2007
   Format:  XDF-1
   # of letters in database:  158,813,828
   # of sequences in database:  260,642
   # of database sequences satisfying E:  15
  No. of states in DFA:  245 (490 KB)
  Total size of DFA:  548 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  2
  Search cpu time:  1.19u 0.04s 1.23t   Elapsed:  00:00:00
  Total cpu time:  1.20u 0.04s 1.24t   Elapsed:  00:00:00
  Start:  Fri Oct 19 14:51:16 2007   End:  Fri Oct 19 14:51:16 2007













On 10/24/07, Dave Messina <David.Messina at sbc.su.se> wrote:
>
> Hi Joseph,
>
> Could you post the blast report that's giving you trouble? And also could
> you tell us what version of WU-BLAST you're running and what version of
> BioPerl you're using?
>
> I'd like to try and reproduce your problem.
>
> Thanks,
> Dave
>
>


-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)
_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
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From David.Messina at sbc.su.se  Thu Oct 25 08:52:14 2007
From: David.Messina at sbc.su.se (Dave Messina)
Date: Thu, 25 Oct 2007 10:52:14 +0200
Subject: [Bioperl-l] general question about possible attribute values
In-Reply-To: <195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
References: <195e25cb0710241239tb83aafapd96c6c109eb95467@mail.gmail.com>
	<628aabb70710241359y24e25208p351545bec44e48b2@mail.gmail.com>
	<471FB845.2080201@gmail.com>
	<195e25cb0710241445ha86414h2df5e2cf9f9ca4eb@mail.gmail.com>
Message-ID: <628aabb70710250152l6218fa1as78b9ab23731f1530@mail.gmail.com>

Ah, wonderful -- thanks Florent! Man, that Deobfuscator sure is useful. :)

Dave


From cjfields at uiuc.edu  Thu Oct 25 13:07:23 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Thu, 25 Oct 2007 08:07:23 -0500
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICDnrZTlpI06ICBsb2FkX3NlcWRhdGFiYXNl?=
 =?utf-8?q?=2Epl_error?=
In-Reply-To: <000201c816df$6c956fb0$45c04f10$@com>
References: <000201c816df$6c956fb0$45c04f10$@com>
Message-ID: <F7F03A54-34F1-45A8-8141-7E785F0FB555@uiuc.edu>

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign






From joseph.fass at gmail.com  Thu Oct 25 21:50:02 2007
From: joseph.fass at gmail.com (Joseph Fass)
Date: Thu, 25 Oct 2007 14:50:02 -0700
Subject: [Bioperl-l] what's the optimal way to search a fasta file for
	matching ID's?
Message-ID: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>

I would appreciate any advice, big or small, on this ...

I've got a decent-sized database ... 90,000 sequences or so in a single
fasta-format file.  Then, I've got sequence ID's from that database that
show up in blast reports.  I want to collect those ID's and their sequences
(for the purposes of exploring possible contigs).  Since the blast report
only includes sub-sequences (from alignments) of my sequences, I want to
parse the report, then match each hit ID against an ID in the database, so I
can pull out its full sequence.  Is there a faster way to do this than
opening the database file each time I have a new hit ID, so I can search it
from beginning to end?  If I push each sequence onto a list or hash, it's
liable to chew up a lot of RAM, I'm guessing.  Any suggestions?

Thanks in advance,
~joe

-- 
Joseph Fass
joseph.fass at gmail.com  ||  joefass at hotmail.com
970.227.5928 (c)  ||  530.754.7978 (w)


From MEC at stowers-institute.org  Thu Oct 25 22:17:04 2007
From: MEC at stowers-institute.org (Cook, Malcolm)
Date: Thu, 25 Oct 2007 17:17:04 -0500
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
Message-ID: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>

If you have the fasta database already indexed for blast searching, then
you should use fastacmd, which comes with the blast package, for
extracting (sub)sequences based on ID (and indices).

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph Fass
> Sent: Thursday, October 25, 2007 4:50 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] what's the optimal way to search a fasta 
> file formatching ID's?
> 
> I would appreciate any advice, big or small, on this ...
> 
> I've got a decent-sized database ... 90,000 sequences or so 
> in a single fasta-format file.  Then, I've got sequence ID's 
> from that database that show up in blast reports.  I want to 
> collect those ID's and their sequences (for the purposes of 
> exploring possible contigs).  Since the blast report only 
> includes sub-sequences (from alignments) of my sequences, I 
> want to parse the report, then match each hit ID against an 
> ID in the database, so I can pull out its full sequence.  Is 
> there a faster way to do this than opening the database file 
> each time I have a new hit ID, so I can search it from 
> beginning to end?  If I push each sequence onto a list or 
> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any 
> suggestions?
> 
> Thanks in advance,
> ~joe
> 
> --
> Joseph Fass
> joseph.fass at gmail.com  ||  joefass at hotmail.com
> 970.227.5928 (c)  ||  530.754.7978 (w)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



From jason at bioperl.org  Fri Oct 26 04:57:52 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 00:57:52 -0400
Subject: [Bioperl-l] what's the optimal way to search a fasta file
	formatching ID's?
In-Reply-To: <CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
References: <195e25cb0710251450o6de39784s546131f86c12deb8@mail.gmail.com>
	<CED81D34E37D5043A1211565277A51E50A2ED2DC@exchkc02.stowers-institute.org>
Message-ID: <8F627E8A-EE44-4953-9A90-F82BC69C15D9@bioperl.org>

or see Bio::DB::Fasta if you want a bioperl soln.

On Oct 25, 2007, at 6:17 PM, Cook, Malcolm wrote:

> If you have the fasta database already indexed for blast searching,  
> then
> you should use fastacmd, which comes with the blast package, for
> extracting (sub)sequences based on ID (and indices).
>
> Malcolm Cook
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, Missouri
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Joseph  
>> Fass
>> Sent: Thursday, October 25, 2007 4:50 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] what's the optimal way to search a fasta
>> file formatching ID's?
>>
>> I would appreciate any advice, big or small, on this ...
>>
>> I've got a decent-sized database ... 90,000 sequences or so
>> in a single fasta-format file.  Then, I've got sequence ID's
>> from that database that show up in blast reports.  I want to
>> collect those ID's and their sequences (for the purposes of
>> exploring possible contigs).  Since the blast report only
>> includes sub-sequences (from alignments) of my sequences, I
>> want to parse the report, then match each hit ID against an
>> ID in the database, so I can pull out its full sequence.  Is
>> there a faster way to do this than opening the database file
>> each time I have a new hit ID, so I can search it from
>> beginning to end?  If I push each sequence onto a list or
>> hash, it's liable to chew up a lot of RAM, I'm guessing.  Any
>> suggestions?
>>
>> Thanks in advance,
>> ~joe
>>
>> --
>> Joseph Fass
>> joseph.fass at gmail.com  ||  joefass at hotmail.com
>> 970.227.5928 (c)  ||  530.754.7978 (w)
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org



From forrest_zhang at 163.com  Fri Oct 26 08:21:56 2007
From: forrest_zhang at 163.com (Forrest Zhang)
Date: Fri, 26 Oct 2007 16:21:56 +0800
Subject: [Bioperl-l] =?utf-8?b?Rlc6ICBGVzogIOetlOWkjTogIGxvYWRfc2VxZGF0?=
	=?utf-8?q?abase=2Epl_error?=
Message-ID: <000701c817a9$4733fb40$d59bf1c0$@com>

Chris,
	I am using --safe to loading sequence. Maybe I would load species data one by one.
It seem be OK now.

	Thanks for your help so much Chris.

Forrest Zhang


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
Sent: Thursday, October 25, 2007 9:07 PM
To: Forrest Zhang; BioSQL
Cc: bioperl-l at bioperl.org BioPerl
Subject: Re: [Bioperl-l] FW: ??: load_seqdatabase.pl error

Forrest,

I'm cross-posting this to BioSQL.  Maybe you can get more response  
there (I'm not the best person to ask about bioperl-db).

BioSQL can be found here:

http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/

The 'table x is full' probably has to do with the second (more  
critical) error, that being the sequence may already appears in the  
database ('failed to insert or be found by unique key').  Are you  
loading sequences  using --safe mode?

chris

On Oct 25, 2007, at 3:16 AM, Forrest Zhang wrote:

> Chris,
> 	Faint, the other kind error about "The table 'reference' is full"  
> when I was loading uniprot_sprot_human data.
> 	Maybe the biosqldb-mysql.sql of my downloaded have some bugs.  
> Where can I download the appropriate version?
>
>
> Loading uniprot_sprot_human.dat ...
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed,  
> values were ("Dreuw A., Radtke S., Pflanz S., Lippok B.E., Heinrich  
> P.C., Hermanns H.M.",""Characterization of the signaling capacities  
> of the novel gp130-like cytokine receptor."","J. Biol. Chem.  
> 279:36112-36120(2004).","CRC-12B29F06AAD1641A","","","") FKs (157046)
> The table 'reference' is full
> ---------------------------------------------------
> Could not store Q8NI17:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: create: object (Bio::Annotation::Reference) failed to insert  
> or to be found by unique key
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ 
> Root/Root.pm:359
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:206
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK:  
> Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/ 
> lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/ 
> AnnotationCollectionAdaptor.pm:217
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/BioSQL/SeqAdaptor.pm:224
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/ 
> perl5/site_perl/5.8.8/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
> STACK: Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/ 
> site_perl/5.8.8/Bio/DB/Persistent/PersistentObject.pm:271
> STACK: /usr/bin/bp_load_seqdatabase.pl:623
> -----------------------------------------------------------
>
>  at /usr/bin/bp_load_seqdatabase.pl line 636
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> bounces at lists.open-bio.org] On Behalf Of Chris Fields
> Sent: Thursday, October 25, 2007 12:48 AM
> To: Forrest
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] ??: load_seqdatabase.pl error
>
> I use the exact procedure on the web site using Build.PL, just using
> bioperl-live and bioperl-db:
>
> http://www.bioperl.org/wiki/
> Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_.
> 27Build.PL.27
>
> You may have some tests fail, but >98% should pass (if not all of
> them).  Install anyway.
>
> Prior to the bioperl-db tests I loaded a database with the BioSQL
> schema, then just ran:
>
> perl Build.PL
> ./Build
> ./Build test
> ./Build install
>
> with the proper configuration; everything passes, with one warning
> for Unigene I think (which is normal).  I install taxonomy afterwards.
>
> One thing to note: make sure you do not have multiple bioperl
> versions installed (either db or live).  Note where the above distros
> install and then check which version is being used by using:
>
> perldoc -l 'Bio::Root::Root'
>
> If it isn't pointing at the same install directory then perl is using
> another BioPerl installation elsewhere in @INC, which needs to be
> removed.
>
> chris
>
> On Oct 24, 2007, at 11:00 AM, Forrest wrote:
>
>> Dear Chris,
>> 	I was using different swissprot data all of the have some error
>> about the taxon.
>> Maybe I should re-install bioperl and biosql. Could you give me the
>> install protocol
>> what you used.
>>
>>
>> Forrest Zhang
>>
>> -----Original Message-----
>> From: Chris Fields [mailto:cjfields at uiuc.edu]
>> Sent: Wednesday, October 24, 2007 12:21 PM
>> To: Forrest Zhang
>> Cc: bioperl-l at bioperl.org
>> Subject: Re: [Bioperl-l] ??: [Bioperl-l] load_seqdatabase.pl  
>> error
>>
>> Forrest, it's working fine for me (no warnings):
>>
>> cjfields:~/tests/db_tests cjfields$ perl load_seqdatabase.pl -- 
>> safe --
>> namespace swissprot --dbname bioseqdb --dbuser **** --dbpass **** --
>> format swiss Q40784.txt
>> Loading Q40784.txt ...
>> cjfields:~/tests/db_tests cjfields$
>>
>> That was the sequence that failed (Q40784) and the format (swiss) you
>> used, correct?
>>
>> chris
>>
>> On Oct 23, 2007, at 10:27 PM, Forrest Zhang wrote:
>>
>>> Dear Chris:
>>> 	What's the result of test? In my computer, the test haven't been
>>> passed.
>>>
>>> Forrest Zhang
>>>
>>> -----????-----
>>> ???: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] ?? Chris Fields
>>> ????: 2007?9?29? 6:03
>>> ???: Forrest Zhang
>>> ??: bioperl-l at bioperl.org BioPerl
>>> ??: Re: [Bioperl-l] load_seqdatabase.pl error
>>>
>>> Okay, fixed the recursion (extra copy of a BasePersistentAdaptor
>>> module I was working which tripped it, so nothing in CVS).
>>>
>>> Forrest, I get all tests passing.  I used a database without  
>>> taxonomy
>>> loaded with bioperl-db and bioperl from cvs and it worked w/o
>>> problems.  I'll try working with your sequence when I have time this
>>> weekend.
>>>
>>> chris
>>>
>>> On Sep 28, 2007, at 11:10 AM, Chris Fields wrote:
>>>
>>>> I'm actually getting some odd recursion issues again; not sure
>>>> what's
>>>> causing it, but a reinstall of both bioperl and bioperl-db fixed it
>>>> last time.  It may be related to the rollback, just not sure yet.
>>>>
>>>> I'll try tracking it down if it persists (bad pun).
>>>>
>>>> t/04swiss....ok 3/52
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> ---------------------------------------------------
>>>> t/04swiss....ok
>>>> All tests successful.
>>>> Files=1, Tests=52,  2 wallclock secs ( 1.33 cusr +  0.18 csys =
>>>> 1.51
>>>> CPU)
>>>>
>>>> The specific error under verbose running is:
>>>>
>>>> --------------------- WARNING ---------------------
>>>> MSG: recursion detected for Bio::Taxon object
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:680
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:691
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:677
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_process_child /
>>>> Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:658
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:629
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create_persistent /
>>>> Users/cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:586
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:252
>>>> STACK Bio::DB::BioSQL::PrimarySeqAdaptor::store_children /Users/
>>>> cjfields/src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> PrimarySeqAdaptor.pm:229
>>>> STACK Bio::DB::BioSQL::SeqAdaptor::store_children /Users/cjfields/
>>>> src/
>>>> core/bioperl-db/blib/lib/Bio/DB/BioSQL/SeqAdaptor.pm:217
>>>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /Users/
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/BioSQL/
>>>> BasePersistenceAdaptor.pm:213
>>>> STACK Bio::DB::Persistent::PersistentObject::create /Users/ 
>>>> cjfields/
>>>> src/core/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm:
>>>> 244
>>>> STACK toplevel t/04swiss.t:37
>>>> ---------------------------------------------------
>>>>
>>>>
>>>> chris
>>>>
>>>> On Sep 28, 2007, at 10:53 AM, Hilmar Lapp wrote:
>>>>
>>>>> Chris let me know if you get stumped. I'm surprised that the
>>>>> special
>>>>> ranks ('eurosids I' etc) show up in the lineage (has NCBI
>>>>> started to
>>>>> assign ranks to them? I thought I filter them out. Needs to be
>>>>> looked
>>>>> into too.), but at any rate I don't understand why they aren't
>>>>> being
>>>>> accepted.
>>>>>
>>>>> Also, maybe we need a more verbose output here - Forrest, can you
>>>>> run
>>>>> this with adding a --printerror argument. (I'm embarrassed to find
>>>>> that this doesn't seem to be documented. Sigh.)
>>>>>
>>>>> 	-hilmar
>>>>>
>>>>> On Sep 28, 2007, at 1:00 AM, Chris Fields wrote:
>>>>>
>>>>>> If this is occurring using bioperl from CVS then I'll try  
>>>>>> taking a
>>>>>> look at it.
>>>>>>
>>>>>> chris
>>>>>>
>>>>>> On Sep 27, 2007, at 10:15 PM, Forrest Zhang wrote:
>>>>>>
>>>>>>> Hilmar,
>>>>>>> 	I have already pre-loaded the NCBI taxonomy using
>>>>>>> load_ncbi_taxonomy.pl yet. The error message show:
>>>>>>>
>>>>>>> --------------------- WARNING ---------------------
>>>>>>> MSG: The supplied lineage does not start near 'Phaseolus
>>>>>>> aureus' (I
>>>>>>> was
>>>>>>> supplied 'Vigna | Papilionoideae | Fabaceae | Fabales |
>>>>>>> eurosids I
>>>>>>> | rosids
>>>>>>> | core eudicotyledons | eudicotyledons | Magnoliophyta |
>>>>>>> Euphyllophyta |
>>>>>>> Embryophyta | Streptophytina | Viridiplantae | Eukaryota')
>>>>>>> ---------------------------------------------------
>>>>>>> Could not store Q40784:
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: create: object (Bio::Species) failed to insert or to be
>>>>>>> found
>>>>>>> by unique
>>>>>>> key
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:357
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:206
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:244
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>> PersistentObject.pm:271
>>>>>>> STACK: /usr/bin/bp_load_seqdatabase.pl:633
>>>>>>> -----------------------------------------------------------
>>>>>>> Sigh~~~~~~
>>>>>>>
>>>>>>> Forrest Zhang
>>>>>>>
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of  
>>>>>>> Hilmar
>>>>>>> Lapp
>>>>>>> Sent: Friday, September 28, 2007 6:17 AM
>>>>>>> To: Forrest
>>>>>>> Cc: bioperl-l at bioperl.org
>>>>>>> Subject: Re: [Bioperl-l] load_seqdatabase.pl error
>>>>>>>
>>>>>>> Forrest,
>>>>>>>
>>>>>>> have you preloaded the NCBI taxonomy as suggested in the BioSQL
>>>>>>> installation guidelines? SwissProt format has NCBI taxon IDs,  
>>>>>>> and
>>>>>>> the
>>>>>>> code will try to use it to look up species and their lineage,
>>>>>>> rather
>>>>>>> than inserting the lineage from whatever BioPerl parses out of
>>>>>>> the
>>>>>>> sequence record.
>>>>>>>
>>>>>>> 	-hilmar
>>>>>>>
>>>>>>> On Sep 27, 2007, at 3:41 AM, Forrest wrote:
>>>>>>>
>>>>>>>> Hi, all
>>>>>>>>     I install the biosql, and bioperl-db. I want to import
>>>>>>>> swissport data.
>>>>>>>> But the programe show some error as below:
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>> perl load_seqdatabase.pl -dbuser root -dbname bioseqdb -driver
>>>>>>>>> mysql
>>>>>>>> -namespace swissprot -format swiss ~/uniprot/uniprot_sprot.dat
>>>>>>>> Loading /home/forrest/uniprot/uniprot_sprot.dat ...
>>>>>>>> Could not store Q6DAH5:
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: The supplied lineage does not start near 'Erwinia
>>>>>>>> carotovora
>>>>>>>> subsp.
>>>>>>>> atroseptica' (I was supplied 'Erwinia carotovora subsp. |
>>>>>>>> Pectobacterium |
>>>>>>>> Enterobacteriaceae | Enterobacteriales | Gammaproteobacteria |
>>>>>>>> Proteobacteria | Bacteria')
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359
>>>>>>>> STACK: Bio::Species::classification
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm:174
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::AUTOLOAD
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:552
>>>>>>>> STACK: Bio::DB::BioSQL::SpeciesAdaptor::populate_from_row
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/SpeciesAdaptor.pm:
>>>>>>>> 281
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::_build_object
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:1305
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:973
>>>>>>>> STACK:
>>>>>>>> Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:852
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:182
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:244
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:169
>>>>>>>> STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/BioSQL/
>>>>>>>> BasePersistenceAdaptor.pm:251
>>>>>>>> STACK: Bio::DB::Persistent::PersistentObject::store
>>>>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Persistent/
>>>>>>>> PersistentObject.pm:271
>>>>>>>> STACK: load_seqdatabase.pl:620
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>>  at load_seqdatabase.pl line 633
>>>>>>>> =============================================================== 
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> =
>>>>>>>> ======
>>>>>>>> ===============================================
>>>>>>>>
>>>>>>>> How can I solve it, please help me, Thank you.
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>> Forrest zhang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioperl-l mailing list
>>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>> -- 
>>>>>>> ===========================================================
>>>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>>>> ===========================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>> Christopher Fields
>>>>>> Postdoctoral Researcher
>>>>>> Lab of Dr. Robert Switzer
>>>>>> Dept of Biochemistry
>>>>>> University of Illinois Urbana-Champaign
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>> -- 
>>>>> ===========================================================
>>>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>>>> ===========================================================
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Robert Switzer
>>> Dept of Biochemistry
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign




_______________________________________________
Bioperl-l mailing list
Bioperl-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/bioperl-l






From avilella at gmail.com  Fri Oct 26 09:33:09 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 10:33:09 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
Message-ID: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>

Hi all,

I was looking at the Gumby runnable, which is pretty cool. But I got an
error
when running the tests (see below). Can other people reproduce this?

It seems to me that the runnable is expecting a tree object, not the
filename for a tree...

avilella at magneto:~/bioperl/vanilla/bioperl-run$ perl t/Gumby.t
1..124
ok 1 - use Bio::Tools::Run::Phylo::Gumby;
ok 2 - use Bio::AlignIO;
ok 3 - use Bio::TreeIO;
ok 4 - use Bio::DB::Taxonomy;
ok 5 - use Bio::Tools::GFF;
ok 6 - Found input alignment file
ok 7 - Found input tree file
ok 8 - Found input gff file
ok 9 - The object isa Bio::Tools::Run::Phylo::Gumby
ok 10 - has a created method not in args
ok 11 - quiet was set
ok 12 - program_dir returned correct default
ok 13 - Correct exe default name
Can't call method "value" without a package or object reference at
/home/avilella/bioperl/vanilla/bioperl-live/Bio/Tools/Phylo/Gumby.pm line
136, <GEN2> line 6.
# Looks like you planned 124 tests but only ran 13.
# Looks like your test died just after 13.


From bix at sendu.me.uk  Fri Oct 26 10:10:41 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 11:10:41 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <4721BD21.9060805@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got
> an error when running the tests (see below). Can other people
> reproduce this?
> 
> It seems to me that the runnable is expecting a tree object, not the 
> filename for a tree...

No, most likely this is another thing broken by the SeqFeature changes.
I'm going to go ahead and try out some of my proposals in the
'Bio::SeqFeature::Annotated API change' thread.


From Rohit.Ghai at mikrobio.med.uni-giessen.de  Fri Oct 26 11:30:43 2007
From: Rohit.Ghai at mikrobio.med.uni-giessen.de (Rohit Ghai)
Date: Fri, 26 Oct 2007 13:30:43 +0200
Subject: [Bioperl-l] cannot run emboss from bioperl on windows
Message-ID: <4721CFE3.4060805@mikrobio.med.uni-giessen.de>

Dear all,

I have emboss installed on a windows machine. (Embosswin). I can run
this from the dos command line and the path is present. However, when I 
try to call
an emboss application from bioperl I get a "Application not found error"


   my $f = Bio::Factory::EMBOSS->new();
   # get an EMBOSS application  object from the factory
   my $fuzznuc = $f->program('fuzznuc');
     $fuzznuc->run(
                   { -sequence  => $infile,
                         -pattern   => $motif,
                        -outfile   => $outfile                       
               });
  gives the following error

-------------------- WARNING ---------------------
MSG: Application [fuzznuc] is not available!
---------------------------------------------------
Can't call method "run" on an undefined value at searchPatterns.pl line 
102.

Can somebody help me fix this ?

best regards
Rohit

-- 

Dr. Rohit Ghai
Institute of Medical Microbiology
Faculty of Medicine
Justus-Liebig University
Frankfurter Strasse 107
35392 - Giessen
GERMANY

Tel  :	0049 (0)641-9946413
Fax  :	0049 (0)641-9946409
Email:  Rohit.Ghai at mikrobio.med.uni-giessen.de



From cjfields at uiuc.edu  Fri Oct 26 12:51:26 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 07:51:26 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <4721BD21.9060805@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<4721BD21.9060805@sendu.me.uk>
Message-ID: <D2A5B64D-9534-4421-A6B5-6EA607F3D649@uiuc.edu>


On Oct 26, 2007, at 5:10 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I got
>> an error when running the tests (see below). Can other people
>> reproduce this?
>>
>> It seems to me that the runnable is expecting a tree object, not the
>> filename for a tree...
>
> No, most likely this is another thing broken by the SeqFeature  
> changes.
> I'm going to go ahead and try out some of my proposals in the
> 'Bio::SeqFeature::Annotated API change' thread.

I was able to repeat it on my end.  If you have a fix for it  
involving B::SF::A then definitely go ahead.

chris


From bix at sendu.me.uk  Fri Oct 26 14:48:27 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 15:48:27 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
Message-ID: <4721FE3B.2080507@sendu.me.uk>

Hilmar Lapp wrote:
> 
> On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:
> 
>> seq_id()
>>   Usage   : $obj->seq_id($newval)
>>   Function: holds a string corresponding to the unique
>>             seq_id of the sequence underlying the feature
>>             (e.g. database accession or primary key).
>>   Returns : a Bio::Annotation::SimpleValue object representing the
>>             seq_id.
> 
> type() and source() should be ontology-typed in a TypedSeqFeatureI (and 
> therefore be instances of Bio::Annotation::OntologyTerm, not 
> Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't 
> understand what the benefit of typing seq_id() any stronger than a 
> string would be.

Would there be any problem with having source() return a string, but 
still allow access to the OntologyTerm object via 
get_Annotations('source')? (Ditto with type?)

I think that's the way I'm going to go for now.


From bix at sendu.me.uk  Fri Oct 26 16:52:59 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:52:59 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
 problem with Genewise.t
In-Reply-To: <470DFD98.4030603@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
Message-ID: <47221B6B.5000604@sendu.me.uk>

Sendu Bala wrote:
> Following Chris's changes to SF::Annotated et al., lots of existing user 
> code breaks. Also, at least some Bioperl code breaks, notably 
> Bio::DB::SeqFeature::Store, which in mysql mode calls 
> _get_location_and_bin() which calls $feature->seq_id which ends up 
> storing something like 'Bio::Annotation::SimpleValue=HASH(0x1f435d0)' in 
> the database, instead of an actual sequence id (which completely breaks 
> searching by seq_id).
> 
> I propose its API be changed to be more consistent with 
> Bio::SeqFeatureI, eg. instead of:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : a Bio::Annotation::SimpleValue object representing the
>             seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> we have:
> 
> seq_id()
>   Usage   : $obj->seq_id($newval)
>   Function: holds a string corresponding to the unique
>             seq_id of the sequence underlying the feature
>             (e.g. database accession or primary key).
>   Returns : string representing the seq_id.
>   Args    : on set, some string or a Bio::Annotation::SimpleValue object.
> 
> This would apply to seq_id(), name(), type(), source(), phase() and 
> frame(). Internally the implementation could store the string value in a 
> SimpleValue object.

I've now done this except for type() and source(), since these aren't in 
Generic. Instead we have source_tag() and primary_tag() accepting and 
returning strings.

source() and type() return objects as before, but now only accept 
objects when setting for consistency.


One test that pops up with an error is t/Genewise.t
I don't understand what's causing the problem. Can anyone help?


From bix at sendu.me.uk  Fri Oct 26 16:53:43 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Fri, 26 Oct 2007 17:53:43 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
Message-ID: <47221B97.10209@sendu.me.uk>

Albert Vilella wrote:
> Hi all,
> 
> I was looking at the Gumby runnable, which is pretty cool. But I got an
> error

This should now be fixed (update live and run). If you run into any 
other problems please let me know.


From cjfields at uiuc.edu  Fri Oct 26 17:48:55 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 12:48:55 -0500
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <47221B97.10209@sendu.me.uk>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
Message-ID: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>


On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:

> Albert Vilella wrote:
>> Hi all,
>>
>> I was looking at the Gumby runnable, which is pretty cool. But I  
>> got an
>> error
>
> This should now be fixed (update live and run). If you run into any
> other problems please let me know.

Works now!

chris


From jason at bioperl.org  Fri Oct 26 18:22:42 2007
From: jason at bioperl.org (Jason Stajich)
Date: Fri, 26 Oct 2007 14:22:42 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change,
	problem with Genewise.t
In-Reply-To: <47221B6B.5000604@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk> <47221B6B.5000604@sendu.me.uk>
Message-ID: <053BEEDD-9C6A-4FE8-BCFD-6FD9C70537DB@bioperl.org>

fixed

> One test that pops up with an error is t/Genewise.t
> I don't understand what's causing the problem. Can anyone help?

--
Jason Stajich
jason at bioperl.org



From avilella at gmail.com  Fri Oct 26 18:29:37 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:29:37 +0100
Subject: [Bioperl-l] bioperl-run gumby tests fail for me
In-Reply-To: <34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
References: <358f4d650710260233y5ef6a075n982d4bd2c34198e5@mail.gmail.com>
	<47221B97.10209@sendu.me.uk>
	<34D5F1F2-D3A0-4D0E-A919-C8C9D1CBD96A@uiuc.edu>
Message-ID: <358f4d650710261129v13758f55g2dbc6d788f0e7618@mail.gmail.com>

for me too, thanks Sendu :)

On 10/26/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
> On Oct 26, 2007, at 11:53 AM, Sendu Bala wrote:
>
> > Albert Vilella wrote:
> >> Hi all,
> >>
> >> I was looking at the Gumby runnable, which is pretty cool. But I
> >> got an
> >> error
> >
> > This should now be fixed (update live and run). If you run into any
> > other problems please let me know.
>
> Works now!
>
> chris
>


From avilella at gmail.com  Fri Oct 26 18:45:29 2007
From: avilella at gmail.com (Albert Vilella)
Date: Fri, 26 Oct 2007 19:45:29 +0100
Subject: [Bioperl-l] problems to use parsing of rst in
	Bio::Tools::Run::Phylo::PAML::Codeml
In-Reply-To: <41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
References: <471CD625.7090605@rennes.inra.fr>
	<41D0D5A5-5A8D-4FA0-BBDB-D702D09B2805@bioperl.org>
Message-ID: <358f4d650710261145k3e174c5aj94cd69b9ef9a356f@mail.gmail.com>

Hi Claude,

Did you submit the bug in bugzilla?

Or if you want, can you attach me a tar.gz with your script and input file
so I can have a look at this?

Cheers,

    Albert.

On 10/24/07, Jason Stajich <jason at bioperl.org> wrote:
>
> Claude - Will try and take a look when I have time, but pretty overwhelmed
> with other things for the time being - best bet is to also submit this as a
> bug to bugzilla.open-bio.org
>
> -jason
> On Oct 22, 2007, at 12:56 PM, Claude Rispe wrote:
>
> Dear Dr Stajich
> We have difficulty using this bioperl module to run Paml, when we try to
> parse the reconstruction of ancestral sites (rst). I send a workable extract
> of our program,  and two example fasta files (alignments). The program
> seems to work fine (at least for running codeml) and generates a correct rst
> file (by visual inspection) but we have two problems when we try to parse
> the results.
>
> 1/ we have 36 taxa and 11 internal nodes (see attached .nwk file).
> However, when we use the functions of "get_rst_persite", they do not work
> for node 36 (the last terminal node) and for node 47 (the last internal
> node): they return errors. However, inspecting visually the rst file, there
> are no problemes with these sequences.
>
> 2/ if alignments contain gaps (as eg. the file b1630.fas-GBL), the
> get_rst_persite returns wrong values.It seems the references are not
> correct (gaps being ignored ?) and so we obtain codons which are different
> from those actually expected for most sequences!
>
> May be you will have a bit of time to have a glance at our code and
> example files. We might have not written the code correctly (I am not an
> expert at this task). Thanks a lot in advance for any advice or feedback,
> Claude Rispe
> #!usr/bin/perl -w
>
> use Bio::SeqIO;
> use Bio::AlignIO;
> use Bio::Tools::Phylo::PAML;
> use Bio::Tools::Run::Phylo::PAML::Codeml;
> use Bio::TreeIO;
> use Bio::Tree::TreeI;
>
> use strict;
>
>
> my $treeio=Bio::TreeIO->new(-file =>"entero_topo.nwk", -format=>"newick");
> my $tree=$treeio->next_tree();
>
>
>    # runs PAML and gets encestral sequences (for internal nodes)
> ------------------------------------------------------------
>       my $in=Bio::AlignIO->new(-file => "b3298.fas-GBL",-format  =>
> 'fasta');
>       while ( my $aln=$in->next_aln() ) {
>          my $kaks_factory=new Bio::Tools::Run::Phylo::PAML::Codeml (
> -tree=> $tree, -save_tempfiles=> 'TRUE', -dir=>'/tmp', -params=>
> {'runmode'=>0,'seqtype'=>1,'model'=>0,'RateAncestor'=>1} );
>          $kaks_factory->alignment($aln);
>          my($rc,$parser)= $kaks_factory->run();
>  my $result=$parser->next_result;
>
>
>          # parsing of ancestral states and of mutations along branches
> ------------------------------------------------------------
>  my @trees = $result->get_rst_trees;
>  my $persite = $result->get_rst_persite;
>  my $nbsites=scalar(@$persite)-1;
>  print "$nbsites\n";
>     for my $t ( @trees ) {
>                for my $node ( $t->get_nodes ) {
>                    next unless $node->ancestor; # skip root node
>    printf "node:%s     ancestor: %s  node is leaf?
> %s\n",$node->id,$node->ancestor->id,$node->is_Leaf;
>    if ($node->id=~/^(\d*)/) {
>        for( my $i=1;$i<=$nbsites;$i++) {
>          print " $i ",$persite->[$i]->[$1]->{'codon'}, '
> ',$persite->[$i]->[$1]->{'aa'}," ";
>          unless ($node->is_Leaf) {print "
> ",$persite->[$i]->[$1]->{'prob'}," ";}
>
>
>        }
>    }
>            print "\n";
>                }
>
>
>            }
>
>
>
>
>       }
>
> Eco3
>
> GTCGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Erwca
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCGTTAACG
> TCAATTTTCG GTATCGGTAA AACTCGGTCG CAGGCTATTT GTGCTGCAAC GGAGATTGCC
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG ATAAGCTGCG TGACGAAGTT
> GCCAAGTTTG TTGTAGAAGG TGATCTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTT
> ATGGACCTTG GTACTTATCG TGGTTTGCGT CATCGTCGTG GTCTGCCGGT TCGCGGTCAG
> CGTACCAAGA CTAACGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Shig1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGTCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep3
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Klebs
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCACAAAC ATACCGTTAT CGCTTTAACC
> GCTATTTTCG GTATCGGCAA AACCCGTTCT AAAGCCATCT GCGCTGAAAC GGGCATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATTG ATATTCTGCG TGAAGCAGTA
> GGTAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GTTGCTACCG TGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yent
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCGTTAACT
> GCGATCTACG GCATCGGTAA GACCCGTTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yep5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Yeps1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Eco10
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Yep6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ATACCGTTAT CGCTTTAACT
> GCGATCTTCG GCATCGGCAA AACTCGCTCA CAGGCTATCT GTGTTGCTGC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATCG AGAAGCTGCG TGACGAAGTT
> GCCAAGTACG TTGTAGAAGG TGATCTGCGT CGTGAGGTGA CCCTGAGCAT CAAGCGTCTG
> ATGGACCTTG GGACTTATCG TGGTTTGCGT CATCGTCGTG GTCTACCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCGATCAA GAAA
>
> Styphim
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Enterob
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAAAAAC ATGCTGTGAT CGCATTAACT
> TCGATCTATG GCGTCGGCAA GACCCGTTCC AAAGCCATTT TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAGTTA GCATGAGCAT CAAGCGCCTT
> ATGGACCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGCCAG
> CGCACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sty1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGTGCA AACCGATCAA GAAA
>
> Eco5
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco4
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco7
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco6
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Serrp
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTAAT CGCCTTAACG
> TCGATCTTCG GAATCGGTAA AACCCGCTCA CAGTCTATCT GTGCGTCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAAATTG AACAGCTGCG TGAAGCAGTC
> GCCAAATTCA CTGTAGAAGG TGATTTGCGT CGTGAAGTTA CCCTGAGCAT CAAGCGTCTG
> ATGGATCTTG GTACTTACCG TGGTTTGCGT CATCGTCGTG GTCTGCCAGT TCGCGGTCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCGCGTA AACCAATCAA GAAA
>
> Sodalis
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAAC ATACCGTTAT TGCCCTAACG
> TCAATCTACG GTATCGGCAA AACCCGCTCG CAGCACATCT GCGCGGCTAC GGGTATTGCT
> GAACATGTTA AGATCAGTGA GCTGTCTGAA GAGCAGATTG ACACGCTGCG TGAAGCAGTT
> ACCAAGTTTG TTGTCGAAGG CGATCTGCGC CGTGAAGTCA CCCTGAGTAT CAAGCGTCTG
> ATGGACCTTG GTACCTATCG TGGTTTGCGT CATCGTCGTG GTCTTCCGGT TCGCGGTCAG
> CGTACCAAGA CCAATGCCCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent2
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Sent1
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAAC ACGCCGTGAT CGCGTTAACT
> TCGATCTACG GTGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAAATGTTA AGATCAGTGA GCTGTCTGAA GAACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGCCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCTCG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Pholu
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCAGAAGC ATACCGTGAT CGCTTTAACA
> TCGATCTACG GAATTGGCAA AACTCGCTCC CAAGCCATTT GTGCTGCGGC GGGTATTGCT
> GAGCATGTTA AGATCAGCGA GCTGTCTGAA GAGCAAATTG ATAAGCTGCG TGACGAAGTT
> GCCAAATACG TTGTAGAAGG CGATTTGCGT CGTGAAGTAA CCCTGAGCAT CAAACGTCTG
> ATGGATCTTG GTACTTATCG TGGTTTACGT CACCGTCGTG GTCTACCTGT TCGCGGCCAG
> CGTACTAAGA CCAACGCACG TACCCGTAAG GGTCCACGTA AGCCGATCAA GAAA
>
> Eco9
>
> GTGGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco8
>
> GTAGCCCGTA TAGCAGGCAT TAACATTCCT GATCATAAGC ATGCCGTAAT CGCATTAACT
> TCGATTTATG GCGTCGGCAA GACCCGTTCT AAAGCCATCC TGGCTGCAGC GGGTATCGCT
> GAAGATGTTA AGATCAGTGA GCTGTCTGAA GGACAAATCG ACACGCTGCG TGACGAAGTT
> GCCAAATTTG TCGTTGAAGG TGATCTGCGC CGTGAAATCA GCATGAGCAT CAAGCGCCTG
> ATGGATCTTG GTTGCTATCG CGGTTTGCGT CATCGTCGTG GTCTCCCGGT TCGCGGTCAG
> CGTACCAAGA CCAACGCACG TACCCGTAAG GGTCCGCGCA AACCGATCAA GAAA
>
> Eco3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTAT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TTCTGGCCGA AGCTCTCGTC
> CTCAAACTAC GCAAGCAGTC GGTAGCTGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGT
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGT TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TGTGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTGGCGGG CTTATTAGTC TGGATGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTTG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig6
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig4
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig5
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGCGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTAGCGCCAT GGTGGATGGT CGTACTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAATA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTCAAAACCT CTGTCCGCGC AGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGTGGC GTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACTATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCAGTT ACTGCTTCTA CGACCAATCG TGGTCGGCTG
> ATGTTCGGCG CGCTGGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig2
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGCT GATATGAACA CACTACACTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Erwca
>
> ATGGCTTTTA TTGCGAGTTC ACCGTTCACA CATAACCAGC AGCGCACGCA GCGCATCATG
> CTGTGGGTTA TTCTGGCCTG CCTGCCGGGC ATGTTGGCGC AGGTCTATTT CTTTGGCTAC
> GGCAACCTGA TTCAGGTCGG GCTGGCGTCT GCCACCGCAC TCATTGCGGA AGGCGTGACG
> CTGTCACTGA GGAAATTTGC GGTTCGTACC ACCCTGGCTG ATAATTCCGC GTTACTGACC
> GCCGTGCTGC TCGGAATCAG TCTACCGCCA TTAGCGCCCT GGTGGATGGT GGTCATGGCA
> ACCGTCTTCG CTATCATTAT CGCTAAACAG CTGTATGGCG GATTAGGGCA AAATCCCTTT
> AACCCCGCGA TGATTGGTTA TGTGGTGTTG CTGATCTCTT TCCCTGTCCA GATGACGAGC
> TGGCTGCCAC CCGAGCCGCT GCAAACCATC TCGCTTAGTT TCCATGACTC GCTAGTCATC
> ATTTTTACCG GACACACGCC TGACGGGCAT ACCATGCAGC AGCTGATGCA CAATGTTGAT
> GGCGTGAGTC AGGCCACCCC GCTGGATACG TTTAAAACCA GCTTACGTTC CGGCCAAACG
> CCACAGAACA TCCTGCAACA GCCGATGTTT GCACAATCAC TGTCTGGTAT TGGCTGGCAG
> TGGGTTAATA TCGGTTTTCT CATCGGCGGG CTGTTCTTGC TGATGCGCGG CACGATTCGC
> TGGCATATTC CAGTCAGTTT CCTGCTGTCG CTGATGTTCT GCGCCCTGCT AAGCTGGATC
> ATCGCGCCGG ATAAATTTGC CCAACCGATG TTACATCTGT TGTCCGGTGC GACCATGCTC
> GGCGCATTTT TCATCGCCAC AGATCCCGTT ACAGCATCAA CCACGAACCG GGGCCGTCTG
> ATTTTCGGTG CGTTGATTGG GTTACTGGTG TGGCTGATTC GCACCTATGG CGGCTACCCA
> GACGGCGTTG CCTTTGCCGT TCTACTGGCG AACATCACCG TCCCGCTGAT CGACTATTAC
> ACCAAGCCAC GTGCTTACGG CCACCATCGC
>
> Shig3
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCATCG GTTAGTACTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAGCAGTC GGTAGCCGCA ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTGTATGGCG GTCTGGGGCA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCCTGGTT TTATCGACGC CATACAGGTT
> ATTTTCAGCG GGCATACCGC CAGTGGTGGT GATATGAACA CACTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC CTGTGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGTGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Shig1
>
> ATGGTATTCA TAGCTAGCTC CCCTTATACC CATAACCAGC GCCAGACATC GCGCATTATG
> CTGTTGGTGT TGCTCGCAGC CGTGCCAGGA ATCGCAGCGC AACTGTGGTT TTTTGGTTGG
> GGTACTCTCG TTCAGATCCT GTTGGCGTCG GTCAGTGCTC TGTTAGCCGA AGCTCTCGTA
> CTCAAACTAC GCAAACAGTC GGTAGCCGCC ACGTTGAAAG ATAACTCAGC ATTGCTGACA
> GGCTTATTGC TGGCGGTAAG TATTCCCCCC CTCGCGCCAT GGTGGATGGT CGTGCTGGGT
> ACGGTGTTTG CGGTGATCAT CGCTAAACAG TTATATGGCG GTCTGGGACA AAACCCGTTT
> AATCCGGCAA TGATTGGTTA TGTGGTCTTA CTGATCTCCT TCCCGGTGCA GATGACCAGC
> TGGTTACCGC CACATGAAAT TGCGGTCAAC ATCCTTGGTT TTATCGACGC CATCCAGGTT
> ATTTTCAGCG GTCATACCGC CAGTGGTGGT GATATGAACA CGCTACGCTT AGGTATTGAT
> GGCATTAGTC AGGCGACACC GCTGGATACA TTTAAAACCT CTGTCCGTGC CGGTCATTCG
> GTTGAACAGA TTATGCAATA TCCGATCTAC AGCGGTATTC TGGCGGGCGC TGGTTGGCAA
> TGGGTAAATC TCGCCTGGCT GGCTGGCGGC GTATGGTTGC TATGGCAGAA AGCGATTCGC
> TGGCATATTC CCCTCAGCTT CTTAGTAACG CTGGCGTTAT GCGCAACGTT GGGCTGGTTG
> TTCTCACCAG AAACACTGGC AGCACCGCAA ATTCATCTGC TGTCTGGAGC GACCATGCTC
> GGCGCATTCT TTATTTTGAC TGACCCGGTT ACCGCTTCTA CGACCAATCG TGGTCGTCTT
> ATTTTCGGCG CGCTTGCGGG CTTATTAGTC TGGTTGATCC GCAGTTTCGG CGGCTATCCT
> GACGGCGTGG CTTTTGCCGT CCTGCTGGCG AACATCACGG TTCCTCTGAT CGATTACTAC
> ACGCGTCCGC GCGTCTACGG CCATCGCAAA
>
> Yep2
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep3
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Klebs
>
> ATGGTTTTCA TCGCAAGCTC CCCCTATACC CATAACCAGC GGCAGACCTC GCGTATTATG
> CTGCTGGTGC TGCTCGCCGC TGTGCCTGGC ATTGTGGTCC AGACCTGGTT TTTCGGCTGG
> GGCACCGTAC TGCAGATTGT CCTCGCCGCC CTGACGGCCT GGGCGACCGA AGCCGCTATT
> CTCAAACTGC GTAAACAGCC TGTTGCTGCC ACGCTGAAAG ATAATTCCGC CCTGCTCACC
> GGCCTGCTGC TGGCGGTGAG TATTCCGCCA CTGGCCCCGT GGTGGATGGT GGTGCTCGGC
> ACTGCCTTTG CCGTAGTCAT TGCCAAGCAG TTGTACGGAG GCCTGGGCCA TAACCCCTTC
> AACCCGGCAA TGATCGGCTA TGTCGTGCTG CTGATTTCGT TCCCGGTGCA GATGACCTCC
> TGGCTGCCTT CCTATGAGAT AGCCGCCCAT ATCCCGGCAT TCAGCGACGC GCTGCAGATG
> ATCTTCACCG GTCATACCGC CGCCGGAGGC GACATGGCCA GTCTGCGGCT GGGTATCGAC
> GGCGTCAGCC AGGCCACCCC GCTGGATACC TTTAAAACCT CCCTGCATGC CGGACATAGC
> GTTCAGCAGG TGCTGCAATT GCCGGTCTAC GGCGGCGTGC TGGCAGGTCT GGGCTGGCAG
> TGGGTGAATA TCGCCTGGCT GGCAGGCGGC CTTTTCCTGC TGTGGCAGAA GGCGATCCGC
> TGGCATATCC CGGTCAGCTT CCTTGTTAGC CTCGGCCTGT GCGCCACCCT CGGCTGGATT
> TTTTCGCCGC AGAGCCTGGC CTCACCGCAG ATGCATTTGC TCTCCGGGGC GACCATGCTT
> GGCGCCTTCT TTATCCTGAC CGATCCGGTG ACGGCCTCAA CAACCAACCG CGGCCGTCTG
> ATCTTTGGCG CCCTCGCTGG CCTGCTGGTC TGGCTCATCC GCAGCTTCGG TGGTTATCCG
> GACGGCGTGG CGTTTGCCGT TCTGCTGGCG AATATTACCG TGCCGCTGAT CGATTACTAC
> ACGCGCCCGC GCGTATATGG CCACCGT---
>
> Yep1
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yent
>
> ---------A TAGCCAGTTC CCCTTTTACG CATAATCAAC GTAGCACCCG CAGTATTATG
> CTGCTGGTTA TTTTAGCCTG CATTCCGGGG ATTATCGCCC AGACTTACTT CTTTGGTTAT
> GGCAGCCTAA TCCAAGTTGC ACTGGCTATA ATGACCGCCG TGCTGGCCGA AGGCGCTGTC
> TTGCATTTAC GTAAACAGCC GGTACTGACA CGATTACAGG ATAACTCTGC CCTGCTCACT
> GGCTTATTGT TAGGTATCAG TCTGCCGCCA CTTGCCCCTT GGTGGATGAT TGTTCTGGGT
> ACGGCATTTG CCATTATTAT TGCCAAACAA CTTTACGGCG GTTTAGGTCA GAATCCGTTT
> AATCCTGCCA TGGTCGGCTA TGTTGTACTA CTGATTTCAT TCCCAGTACA AATGACCAGT
> TGGCTTCCTC CTCTGCCATT ACAGGGAACG CCGGTTGGAT TCTATGACAG CTTATTAACT
> ATTTTCACCG GATTCACCCA AAATGGTGCC GATATTCACC AACTGCAGAT TGGCTATGAT
> GGGATAAGTC AGGCCACGCC TCTCGATAAC TTTAAAACCT CACTGCGCTC C---CAACCC
> GTGGAACAGA TTCTGCAACA ACCGATTTTT ACCGCGGGGC TGGCGGGTAT TGGTTGGCAA
> TGGATTAACC TCGGTTTTCT GGCGGGCGGT CTGTTGCTGC TATGGCGTAA AGCCATCCAC
> TGGCATATTC CGGTGAGTTT CCTATTGGCT TTGGCAGGTT GTGCTGCTAT CAGTTGGATG
> ATTGCGCCAC ACAGCTTCGC CCCCCCTATG TTGCATCTGT TTTCCGGTGC CACCATGTTG
> GGTGCTTTCT TTATTGCCAC CGATCCGGTC AGCGCCTCGA CAACACCTCG TGGTCGGCTG
> ATTTTCGGCG CATTGATTGG TATTTTGGTG TGGCTGATTC GCGTTTACGG CGGTTATCCC
> GATGGGGTAG CATTTGCGGT GCTGCTGGCC AACATCTGTG TTCCACTGAT TGATCACTAC
> ACTCAACCAC GCGTTTATGG TCATCAGCGC
>
> Yep4
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yep5
>
> ATGAAATTCA TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTACTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATA CCGGCTTTCT GGTTGGCGGC TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
> GGTGCATTTT TCATTGCTAC CGATCCTGTC AGTGCCTCTA CAACACCCCG TGGCCGCCTG
> ATATTTGGTG CCCTCATTGG TATTCTGGTG TGGCTAATCC GGGTATATGG CGGCTATCCG
> GATAGTGTTG CTTTTGCCGT GTTGCTCGCC AATATTACAG TTCCGTTGAT TGACCACTAT
> ACCCAACCTC GGGTCTATGG CCATAAAAGC
>
> Yeps2
>
> ---------A TTGCCAGTTC CCCTTTTACC CACAATCAAC GCAGTACCCG TCGTATTATG
> CTGCTGGTTA TTCTGGCCTG TATTCCGGGG ATTATCGCCC AGACTTACTT CTTCGGTTAT
> GGCAGCCTGA TTCAAGTCAT GCTGGCTATG ATCACTGCAC TGTTGGCCGA AGGTGCCGTA
> TTGCAGTTAC GTAAACAACC CGTCATGGCG CGGTTACAAG ATAACTCAGC CCTGCTGACT
> GCCTTATTGT TGGGGATAAG CCTCCCCCCA TTGGCCCCCT GGTGGATGAT CGTGCTGGGC
> ACGCTATTTG CTATTGTCAT TGCCAAACAA CTCTATGGTG GCCTAGGGCA GAACCCGTTT
> AACCCGGCAA TGGTCGGTTA TGTTGTGCTC CTTATTTCAT TTCCGGTACA AATGACCAGT
> TGGCTGCCAC CGCTACCGTT GCAAGGAACG TCGGTGGGAT TCTATGACAG TCTCTTAACC
> ATTTTCACCG GTTATACCCA CAGTGGTGAG AATATTCATC AGCTCCAAGT TGGCTATGAC
> GGCATCAGCC AAGCGACGCC ACTGGATACG TTTAAGACCT CGCTACGTTC A---CAGCCA
> GCAGATCAAA TTCTGCAACA GCCCATATTT GGCGGTGTGC TGGCGGGTTT AGGCTGGCAA
> TGGGTTAATC TCGGCTTTCT GGTTGGCGGT TTATTGCTAC TGTGGCGTAA AGCTATTCAC
> TGGCATATTC CCGTGAGCTT CCTGCTCGCC TTAGGAGGTT GTGCCGCAGT GAGCTGGATG
> ATTGCTCCAC AAAGCTTTGC CTCACCAATG CTACATTTGT TCTCCGGTGC CACCATGTTA
>
> ...
>
> [Message clipped]


From hlapp at gmx.net  Fri Oct 26 23:32:00 2007
From: hlapp at gmx.net (Hilmar Lapp)
Date: Fri, 26 Oct 2007 19:32:00 -0400
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4721FE3B.2080507@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
Message-ID: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>


On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:

> Would there be any problem with having source() return a string,  
> but still allow access to the OntologyTerm object via  
> get_Annotations('source')? (Ditto with type?)

Do I interpret your second email that you abandoned this plan? I.e.,  
source() and type() return objects? I think that's the right way.  
(Otherwise source() is redundant with source_tag().)

	-hilmar
-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







From bix at sendu.me.uk  Fri Oct 26 23:47:11 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 00:47:11 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
Message-ID: <47227C7F.9010709@sendu.me.uk>

Hilmar Lapp wrote:
> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
> 
>> Would there be any problem with having source() return a string,  
>> but still allow access to the OntologyTerm object via  
>> get_Annotations('source')? (Ditto with type?)
> 
> Do I interpret your second email that you abandoned this plan? I.e.,  
> source() and type() return objects? I think that's the right way.  
> (Otherwise source() is redundant with source_tag().)

Yes, I abandoned the above plan. I've left source() as a SimpleValue, at 
least until issues with DB::Store are resolved wrt ontologies (it stores 
the entire ontology for each feature in the database, increasing storage 
requirments > 800x).


From cjfields at uiuc.edu  Sat Oct 27 03:39:09 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Fri, 26 Oct 2007 22:39:09 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <47227C7F.9010709@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
Message-ID: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>


On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> On Oct 26, 2007, at 10:48 AM, Sendu Bala wrote:
>>
>>> Would there be any problem with having source() return a string,
>>> but still allow access to the OntologyTerm object via
>>> get_Annotations('source')? (Ditto with type?)
>>
>> Do I interpret your second email that you abandoned this plan? I.e.,
>> source() and type() return objects? I think that's the right way.
>> (Otherwise source() is redundant with source_tag().)
>
> Yes, I abandoned the above plan. I've left source() as a  
> SimpleValue, at
> least until issues with DB::Store are resolved wrt ontologies (it  
> stores
> the entire ontology for each feature in the database, increasing  
> storage
> requirments > 800x).

Do you mean SeqFeature::Store or OntologyStore (I'm guessing the  
latter)?

chris


From bix at sendu.me.uk  Sat Oct 27 07:03:12 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Sat, 27 Oct 2007 08:03:12 +0100
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
Message-ID: <4722E2B0.3050503@sendu.me.uk>

Chris Fields wrote:
> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>> I've left source() as a SimpleValue, at least until issues with
>> DB::Store are resolved wrt ontologies (it stores the entire
>> ontology for each feature in the database, increasing storage 
>> requirments > 800x).
> 
> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the 
> latter)?

Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you 
set the type() as well of course; the only reason I don't suffer from 
that is that I deliberately avoid setting the type on my features.


From cjfields at uiuc.edu  Sat Oct 27 14:53:59 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Sat, 27 Oct 2007 09:53:59 -0500
Subject: [Bioperl-l] Bio::SeqFeature::Annotated API change
In-Reply-To: <4722E2B0.3050503@sendu.me.uk>
References: <470DFD98.4030603@sendu.me.uk>
	<FD63B6C4-4ED3-4B39-BF0C-B1B78342C196@gmx.net>
	<4721FE3B.2080507@sendu.me.uk>
	<B5DE8388-44C1-416B-A450-5D6270BFB0E9@gmx.net>
	<47227C7F.9010709@sendu.me.uk>
	<68E7E40E-8569-4BE9-AB76-92266E081CC9@uiuc.edu>
	<4722E2B0.3050503@sendu.me.uk>
Message-ID: <C69BF9A1-1B61-4CE6-80F2-0941D6DB31AB@uiuc.edu>


On Oct 27, 2007, at 2:03 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>>> I've left source() as a SimpleValue, at least until issues with
>>> DB::Store are resolved wrt ontologies (it stores the entire
>>> ontology for each feature in the database, increasing storage
>>> requirments > 800x).
>>
>> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the
>> latter)?
>
> Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you
> set the type() as well of course; the only reason I don't suffer from
> that is that I deliberately avoid setting the type on my features.

Makes sense if you're using $store->add_SeqFeatures (it stores a  
serializized SF along with the data via Storable, so the  
OntologyStore probably goes along for the ride).  If we make type  
checking optional and lazily create the OntologyStore singleton it  
would probably reduce the space, as you wouldn't create it unless  
needed.  Or you could map it over to a DB::SeqFeature after  
validating the type.

Just noticed something: DB::SeqFeature uses type() and source() as  
synonyms of primary_tag() and source_tag(); both use strings instead  
of SimpleValues.

chris


From snaphit at planet.nl  Thu Oct 25 08:07:00 2007
From: snaphit at planet.nl (Jelle86)
Date: Thu, 25 Oct 2007 01:07:00 -0700 (PDT)
Subject: [Bioperl-l]  get_Stream_by_gi: Memory going up every call.
Message-ID: <13401838.post@talk.nabble.com>


Hi, 
I have a problem when using Bio::DB::GenBank->get_Stream_by_gi . My usage
memory for the perl script keeps going up each time a piece of the list is
downloaded. 
I have a gilist, that consist of about 1300 gi's, and i split it in pieces
of 100gi's since get_stream_by_gi doesn't work on more than 300 or so (don't
know why..). 
But either way, using this constructing makes the script take more and more
memory each time 100entries are downloaded. For 1300 gi's not a problem, but
i'm planning on doing it for at least 200.000 gi's.
How can i solve it. At the end of the end of the loops and end of the usage
of the package genbankQuery I empty all the used objects with undef. 
Below are some snippets of my code. Is there a way to find out what actually
causes the problem and more how to solve it?


I use:
perl 5.8.8.822
bioper1.5.2
winxp
behind a proxy


=========
ESTdownload;
makeChunks(){
  while (@small_list = splice(@{$gilist_ref->{gilist}}, 0, 100)) {
        $self->callStream(\@small_list);
 }
}
callStream(){
  $smallref=shift;#contains @small_list ref.
  my $query = genbankQuery->new(ids=>$smallref);
  my $part_result = $query->streamQuery();
}
=========
genbankQuery;
new{
  
  my $self = {
			ids => '',			
			@_,					
		    };
  $self->{gb}=Bio::DB::GenBank->new();
}
streamQuery(){
  my $stream_obj = $self->{gb}->get_Stream_by_gi(\@ids);
  my $seq_obj;       
  #Step through the results 
  while ($seq_obj = $stream_obj->next_seq) {
    #make lines from features and return them in an array ref
  }
}
_____________
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13401838
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From snaphit at planet.nl  Fri Oct 26 12:42:13 2007
From: snaphit at planet.nl (Jelle86)
Date: Fri, 26 Oct 2007 05:42:13 -0700 (PDT)
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13401838.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com>
Message-ID: <13426480.post@talk.nabble.com>


Ok I stripped a lot. And this is causing the problem:

use Bio::DB::Genbank;
sub new(){
  my $invocant = shift;
  my $class = ref($invocant) || $invocant;
  my $self = {@_};
  $self->{gb} = Bio::DB::GenBank->new();
  bless $self, $class;
  return $self;
}

sub streamQuery(){
	my $self = shift;        
	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
        while (my $seq_obj = $stream_obj->next_seq) {
                
        }
}

Both subs (new and streamQuery) are called several times with a new
accessionlist. 
Removing the while loop, will use a bit less memory. But the memory usage is
still going up.
-- 
View this message in context: http://www.nabble.com/get_Stream_by_gi%3A-Memory-going-up-every-call.-tf4689188.html#a13426480
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.



From wgallin at ualberta.ca  Mon Oct 29 04:03:24 2007
From: wgallin at ualberta.ca (Warren Gallin)
Date: Sun, 28 Oct 2007 22:03:24 -0600
Subject: [Bioperl-l] Not catching an error in EUtilities
Message-ID: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>

I've been having an intermittent problem, when the NCBI service that  
is accessed by EUtilities (in particular efetch) is not available.

I have the calls enclosed in eval statements, but an exception is not  
thrown.  Instead I find that the  file that should contain the  
results of the efetch only has the following text:

Error: The resource is temporarily unavailable

So it appears that this is not generating an exception (maybe that is  
not desireable in general, but it would be useful in my case).

The result is that my script tries to access the file using  
Bio::Seq::IO, and the expected text is not there.

The relevant snippet of code and the output are copied below.

The only way that I can think of to catch this outcome is to open the  
file and check the firt three lines for this text, and then go back  
and redo the efetch if this particular text is found.

Is this behaviour considered a bug, or just an outcome that needs to  
be checked for when code is written using efetch?

If so, is there a standard way of checking for this?

Thanks,

Warren Gallin

[Code that successfully executes an epost and retrieves the history]

   RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
         -eutil   => 'efetch',
         -rettype => 'genbank',
         -db      => 'protein',
         -history => $history
     );};
     if ($@){
     	print "efetch error trapped\n$@\n";
     	goto RETRIEVE_LIST;

     }

     $file1 = ">" . $file1;
     $retry = 0;
     eval { $prot_eutil->get_Response( -file => $file1 ); };
     if ($@) {
         die "Server error: $@.  Try again later" if $retry == 5;
         print STDERR "$@\n";
         print STDERR "Server error, redo #$retry\n";
         $retry++;
         sleep(5);
         goto RETRIEVE_LIST;
     }
     else {
         print "efetch ran on $loop_bottom through $loop_top.\n";
     }

The output to the terminal from this part of the code is:

efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 15:42:43 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 10:42:43 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <5AEAE8C4-2E18-4BBE-A470-8CB398949BEA@uiuc.edu>


On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
>
> Error: The resource is temporarily unavailable
>
> So it appears that this is not generating an exception (maybe that is
> not desireable in general, but it would be useful in my case).
>
> The result is that my script tries to access the file using
> Bio::Seq::IO, and the expected text is not there.
>
> The relevant snippet of code and the output are copied below.
>
> The only way that I can think of to catch this outcome is to open the
> file and check the firt three lines for this text, and then go back
> and redo the efetch if this particular text is found.
>
> Is this behaviour considered a bug, or just an outcome that needs to
> be checked for when code is written using efetch?
...
> If so, is there a standard way of checking for this?

I may have already mentioned this (it is mentioned in the POD), but  
it's worth repeating: if you running a script to post more than 100  
requests you should be running it btwn 9pm and 5am ET per NCBI's rules:

http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

I have built in a way to pass in an LWP::UserAgent-related callback  
to get_Response() using the -cb parameter, primarily to allow piping  
data to a child process for instance.  This could also be used for  
checking the initial data retrieved and throwing if an error is  
returned.  I haven't extensively tested this yet; I can try running a  
stress test to see if I can trigger an efetch error and catch it in  
the callback.  If I can get something working I'll post it later  
today and may incorporate it into EUtilities in CVS.

A bit of background: efetch is the only eutil that doesn't have a  
specific parser (Bio::Tools::EUtilities) attached to it, primarily b/ 
c the data retrieved is very diverse (seq/pubmed/snp/etc data in XML,  
asn.1, text, HTML).  All other eutils besides efetch generate error  
codes via the HTTP::Response header (the norm) or in the XML  
returned; both of the previous types are errors that EUtilities  
catches and throws, so an eval{} works.  efetch errors seen to be  
atypical and may be related to the server load or specific database  
availability.

chris

> Thanks,
>
> Warren Gallin
>
> [Code that successfully executes an epost and retrieves the history]
>
>    RETRIEVE_LIST: eval {$prot_eutil->reset_parameters(
>          -eutil   => 'efetch',
>          -rettype => 'genbank',
>          -db      => 'protein',
>          -history => $history
>      );};
>      if ($@){
>      	print "efetch error trapped\n$@\n";
>      	goto RETRIEVE_LIST;
>
>      }
>
>      $file1 = ">" . $file1;
>      $retry = 0;
>      eval { $prot_eutil->get_Response( -file => $file1 ); };
>      if ($@) {
>          die "Server error: $@.  Try again later" if $retry == 5;
>          print STDERR "$@\n";
>          print STDERR "Server error, redo #$retry\n";
>          $retry++;
>          sleep(5);
>          goto RETRIEVE_LIST;
>      }
>      else {
>          print "efetch ran on $loop_bottom through $loop_top.\n";
>      }
>
> The output to the terminal from this part of the code is:
>
> efetch ran on 0 through 300.



From cjfields at uiuc.edu  Mon Oct 29 16:06:24 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 11:06:24 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <13426480.post@talk.nabble.com>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
Message-ID: <8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>

It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From cjfields at uiuc.edu  Mon Oct 29 20:45:53 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Mon, 29 Oct 2007 15:45:53 -0500
Subject: [Bioperl-l] Not catching an error in EUtilities
In-Reply-To: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
References: <D1174CA3-BAF0-44DB-AEF8-95CAD5802740@ualberta.ca>
Message-ID: <A5708C31-CA39-43D8-ADE2-E1791D3332C7@uiuc.edu>

Warren,

For efetch the following works for me; it include a simple callback  
to check the initial data chunk (note the die in the callback and the  
extra call to check the header) and prints to the file if no error is  
detected, otherwise it retries.  I'll see if there is an easy way to  
integrate this into EUtilities.


# after eutil calls

open (my $SEQFILE, '>', $file) || die "Can't write to file:$!";
my $expected;
my $bytes = 0;

RETRIEVE_SEQS:
while ($retstart < $count) {
      $gpeptfactory->set_parameters(
		-retmax => $retmax,
                 -retstart => $retstart,
                              );
      my $response;
      eval{
         $response= $gpeptfactory->get_Response(-cb => sub {
            my ($chunk, $res) = @_;
             if ($bytes == 0 && $chunk =~ m{^Error:(.*)}i) {
                 die "$1\n";
             }
             $bytes += length($chunk);
             print $SEQFILE $chunk;
         });
      };
      if ($@ || $response->header('x-died')) {
          my $error = $@ || $response->header('x-died');
          die "Server error: $error.  Try again later" if $retry == 5;
          print STDERR "$error\n";
          print STDERR "Server error, redo #$retry\n";
          $retry++ && redo RETRIEVE_SEQS;
      } else  {
      	my $retend = $retstart + $retmax;
      	print "Loaded entries ",$retstart+1," through $retend on retry  
# $retry.\n";
      	$retstart += $retmax;
      	$retry = 0;
         $bytes = 0; # important!
         undef $expected ;
      }
}

close $SEQFILE;

chris

On Oct 28, 2007, at 11:03 PM, Warren Gallin wrote:

> I've been having an intermittent problem, when the NCBI service that
> is accessed by EUtilities (in particular efetch) is not available.
>
> I have the calls enclosed in eval statements, but an exception is not
> thrown.  Instead I find that the  file that should contain the
> results of the efetch only has the following text:
> ...
> If so, is there a standard way of checking for this?
>
> Thanks,
>
> Warren Gallin
...


From wenbinye at gmail.com  Tue Oct 30 11:46:55 2007
From: wenbinye at gmail.com (Ye Wenbin)
Date: Tue, 30 Oct 2007 19:46:55 +0800
Subject: [Bioperl-l] console version of Deobfuscator
Message-ID: <op.t00dohrc52p72k@tsinghua-64dc66>

Hi, all.
I wrote a console version of Deobfuscator. I think it is easy to
use and more efficient to query and search.
Hope it is helpful!
You can download it from:
http://search.cpan.org/CPAN/authors/id/Y/YE/YEWENBIN/deob-0.02.tar.gz

-- 
Best regards.
Ye Wenbin


From cjfields at uiuc.edu  Tue Oct 30 12:10:41 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 07:10:41 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
Message-ID: <2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>

What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From snaphit at planet.nl  Tue Oct 30 08:51:40 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 09:51:40 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>

This doesn't seem to work. It still keeps using more memory. I already tried it once and didn't seem to make a difference. But gave it another try. But as I said, it doesn't solve the problem.


-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Mon 10/29/2007 5:06 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It may be based on the mode (set by -retrievaltype) in which the  
sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI  
module has the documentation for this parameter.  If you are making  
tons of calls to get_Seq*/get_Stream* methods it may lead to  
substantial increases in memory until the child processes finish up  
parsing each data stream.

You can possibly add in a wait() in between sequence retrieval calls,  
or try setting the Bio::DB::GenBank instance to 'tempfile' or  
'io_string' (the former always worked faster for me):

$self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');

chris

On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:

> Ok I stripped a lot. And this is causing the problem:
>
> use Bio::DB::Genbank;
> sub new(){
>   my $invocant = shift;
>   my $class = ref($invocant) || $invocant;
>   my $self = {@_};
>   $self->{gb} = Bio::DB::GenBank->new();
>   bless $self, $class;
>   return $self;
> }
>
> sub streamQuery(){
> 	my $self = shift;
> 	my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
>         while (my $seq_obj = $stream_obj->next_seq) {
>
>         }
> }
>
> Both subs (new and streamQuery) are called several times with a new
> accessionlist.
> Removing the while loop, will use a bit less memory. But the memory  
> usage is
> still going up.
> -- 
> View this message in context: http://www.nabble.com/get_Stream_by_gi 
> %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From jason at bioperl.org  Tue Oct 30 15:16:59 2007
From: jason at bioperl.org (Jason Stajich)
Date: Tue, 30 Oct 2007 11:16:59 -0400
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>

Denis -
Not sure - the list members will know more.

-jason
Begin forwarded message:

> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
> Date: October 30, 2007 7:41:29 AM EDT
> To: <jason at bioperl.org>
> Subject: Pairwaise_kaks.pl
>
> Good morning,
>
> I'm attempting to set up the pairwise_kaks script here.
>
> I have successfully used an older version in a previous position so  
> I am
> somewhat familiar with it.
>
> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
> And have bioperl             in /usr/local/bioperl-1.5.2_100
>
>
> When I try to run the script I get the following
>
> Can't locate object method "_set_from_args" via package
> "Bio::Tools::Run::Alignment::Clustalw" at
> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>
> I'm not sure how to resolve this so I refer to a higher authority
>
> Merci
>
> Dennis Prickett
>
> Institute for Animal Health
> Compton nr Newbury
> Berkshire
> RG20 7NN
>
> Switchboard: +44  (0)1635 578411
> Central Fax: +44  (0)1635 57723
>

--
Jason Stajich
jason at bioperl.org



From cjfields at uiuc.edu  Tue Oct 30 15:33:34 2007
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue, 30 Oct 2007 10:33:34 -0500
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
In-Reply-To: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
Message-ID: <2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>

It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





From bix at sendu.me.uk  Tue Oct 30 16:10:42 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Tue, 30 Oct 2007 16:10:42 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
Message-ID: <47275782.2010200@sendu.me.uk>

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package
>> "Bio::Tools::Run::Alignment::Clustalw" at
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably 
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the 
same place. Ie. 1.5.2 release packages or CVS, not both.


From bix at sendu.me.uk  Wed Oct 31 11:36:09 2007
From: bix at sendu.me.uk (Sendu Bala)
Date: Wed, 31 Oct 2007 11:36:09 +0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
	<8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>
Message-ID: <472868A9.2090706@sendu.me.uk>

dennis prickett (IAH-C) wrote:
> Sendu
> 
> Thanks for the quick response.  
> 
> Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
> the bioperl core package.
> 
> But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

No, that's still 1.5.2 with minor installation-related patches ( 
http://www.bioperl.org/wiki/Release_1.5.2#Updates ). You'll need to 
install bioperl-live from CVS, or bioperl-run-1.5.2_100.


From dennis.prickett at bbsrc.ac.uk  Wed Oct 31 11:32:35 2007
From: dennis.prickett at bbsrc.ac.uk (dennis prickett (IAH-C))
Date: Wed, 31 Oct 2007 11:32:35 -0000
Subject: [Bioperl-l] Fwd: Pairwaise_kaks.pl
In-Reply-To: <47275782.2010200@sendu.me.uk>
References: <8975119BCD0AC5419D61A9CF1A923E9504751E7D@iahce2ksrv1.iah.bbsrc.ac.uk>
	<6C8860B8-6CE7-4F31-A77B-0D5D983A68E3@bioperl.org>
	<47275782.2010200@sendu.me.uk>
Message-ID: <8975119BCD0AC5419D61A9CF1A923E9504751E7F@iahce2ksrv1.iah.bbsrc.ac.uk>

Sendu

Thanks for the quick response.  

Yes I do have the mixed setup as you describe-  bioperl-run from CVS and
the bioperl core package.

But.. to resolve the issue - would installing bioperl 1.5.2_102 work? 

Thanks 

Dennis Prickett

-----Original Message-----
From: Sendu Bala [mailto:bix at sendu.me.uk] 
Sent: 30 October 2007 16:11
To: Jason Stajich
Cc: bioperl-l list; dennis prickett (IAH-C)
Subject: Re: [Bioperl-l] Fwd: Pairwaise_kaks.pl

Jason Stajich wrote:
> Denis -
> Not sure - the list members will know more.
>
>> From: "dennis prickett \(IAH-C\)" <dennis.prickett at bbsrc.ac.uk>
>
>> I have installed bioperl-run in /usr/local/bioperl_run-1.5.2
>> And have bioperl             in /usr/local/bioperl-1.5.2_100
>>
>>
>> When I try to run the script I get the following
>>
>> Can't locate object method "_set_from_args" via package 
>> "Bio::Tools::Run::Alignment::Clustalw" at 
>> Bio/Tools/Run/Alignment/Clustalw.pm line 409.
>>
>> I'm not sure how to resolve this so I refer to a higher authority

_set_from_args() first arrived in Jan 2007, after 1.5.2 was released. 
This means you actually have some kind of mixed setup where you probably
have bioperl-run from CVS and bioperl-core 1.5.2.

The solution is to make sure you have core and run packages from the
same place. Ie. 1.5.2 release packages or CVS, not both.



From snaphit at planet.nl  Tue Oct 30 14:56:10 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Tue, 30 Oct 2007 15:56:10 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>

I just made a test script which shows the problem.
The second while loop will cause the program to use more and more memory without releasing it.

I will post the bug later today.

Jelle

code:
use Bio::DB::GenBank;
use strict;
use warnings;
my @arraylist = (157043286,157043285,157043189); #use couple of hundreds gi's to see the issue
while (my @small_list = splice(@arraylist, 0, 100)) {
        my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
        my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);        
        while (my $seq_obj = $stream_obj->next_seq) {
            #this is what causes the problem...
        }        
}

-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 1:10 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
What happens if you create a new Bio::DB::GenBank instance each time  
within streamQuery() instead of using a cached instance?  Does the  
memory issue go away?

I'll try to look into it when I can; if you could file a bug on this  
it would help track it:

http://www.bioperl.org/wiki/Bugs

chris

On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:

> This doesn't seem to work. It still keeps using more memory. I  
> already tried it once and didn't seem to make a difference. But  
> gave it another try. But as I said, it doesn't solve the problem.
>
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Mon 10/29/2007 5:06 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> It may be based on the mode (set by -retrievaltype) in which the
> sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> module has the documentation for this parameter.  If you are making
> tons of calls to get_Seq*/get_Stream* methods it may lead to
> substantial increases in memory until the child processes finish up
> parsing each data stream.
>
> You can possibly add in a wait() in between sequence retrieval calls,
> or try setting the Bio::DB::GenBank instance to 'tempfile' or
> 'io_string' (the former always worked faster for me):
>
> $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>
> chris
>
> On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
>
> > Ok I stripped a lot. And this is causing the problem:
> >
> > use Bio::DB::Genbank;
> > sub new(){
> >   my $invocant = shift;
> >   my $class = ref($invocant) || $invocant;
> >   my $self = {@_};
> >   $self->{gb} = Bio::DB::GenBank->new();
> >   bless $self, $class;
> >   return $self;
> > }
> >
> > sub streamQuery(){
> >       my $self = shift;
> >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self->{ids});
> >         while (my $seq_obj = $stream_obj->next_seq) {
> >
> >         }
> > }
> >
> > Both subs (new and streamQuery) are called several times with a new
> > accessionlist.
> > Removing the while loop, will use a bit less memory. But the memory
> > usage is
> > still going up.
> > --
> > View this message in context: http://www.nabble.com/get_Stream_by_gi
> > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From snaphit at planet.nl  Wed Oct 31 10:07:38 2007
From: snaphit at planet.nl (snaphit at planet.nl)
Date: Wed, 31 Oct 2007 11:07:38 +0100
Subject: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
References: <13401838.post@talk.nabble.com> <13426480.post@talk.nabble.com>
	<8F6EB080-1F27-4B48-824C-8E58F9672A49@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F16@CPEXBE-EML18.kpnsp.local>
	<2A6A5C06-FFD7-4EC7-89BA-CA0DD565CEBD@uiuc.edu>
	<FC9EDB791DBD6444B2843787456FDCB0F98F17@CPEXBE-EML18.kpnsp.local>
	<2EE8B8E1-8E9A-4B1C-83B8-BE983EFDE657@uiuc.edu>
Message-ID: <FC9EDB791DBD6444B2843787456FDCB0F98F1A@CPEXBE-EML18.kpnsp.local>

I installed S/SE/SENDU/bioperl-1.5.2_102.tar.gz using cpan -force -notest.
And now running the script doesn't use that much memory. Although it keeps going up, but just a little bit every call. For 14000 +/-20mb (starts at 16mb).

Before I used this bioperl version (only one I was able to install using PPM):
Bioinformatics Toolkit 1.5.2 RC2
Version:	1.5.1.9992
Released:	2006-10-02

I first replaced the modules you mentioned, but it didn't help. So I thought before I report the bug, I will try to install the package with cpan. It gave some errors at first, so I used force and notest. And now it seems to work. I get the output I expect and a lot less memory usage. 

So if you don't see anything on your windows machine, I won't report the bug.

Thanks,
Jelle



-----Original Message-----
From: Chris Fields [mailto:cjfields at uiuc.edu]
Sent: Tue 10/30/2007 4:33 PM
To: snaphit at planet.nl
Cc: Bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
 
It appears to be Win32-specific; I retrieved ~1000 ESTs from Solanum  
lycopersicum and retrieved them in this loop w/o appreciable memory  
loss on my MacBook; I'll try WinXP later today.  If you can, also try  
downloading the Bio::DB::GenBank/NCBIHelper/WebDBSeqI modules from  
CVS and replacing your local copies with those to see if the problem  
still persists.

chris

On Oct 30, 2007, at 9:56 AM, <snaphit at planet.nl> wrote:
> I just made a test script which shows the problem.
> The second while loop will cause the program to use more and more  
> memory without releasing it.
>
> I will post the bug later today.
>
> Jelle
>
> code:
> use Bio::DB::GenBank;
> use strict;
> use warnings;
> my @arraylist = (157043286,157043285,157043189); #use couple of  
> hundreds gi's to see the issue
> while (my @small_list = splice(@arraylist, 0, 100)) {
>         my $gb = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
>         my $stream_obj =  $gb->get_Stream_by_gi(\@small_list);
>         while (my $seq_obj = $stream_obj->next_seq) {
>             #this is what causes the problem...
>         }
> }
>
> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tue 10/30/2007 1:10 PM
> To: snaphit at planet.nl
> Cc: Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every call.
>
> What happens if you create a new Bio::DB::GenBank instance each time
> within streamQuery() instead of using a cached instance?  Does the
> memory issue go away?
>
> I'll try to look into it when I can; if you could file a bug on this
> it would help track it:
>
> http://www.bioperl.org/wiki/Bugs
>
> chris
>
> On Oct 30, 2007, at 3:51 AM, <snaphit at planet.nl> wrote:
>
> > This doesn't seem to work. It still keeps using more memory. I
> > already tried it once and didn't seem to make a difference. But
> > gave it another try. But as I said, it doesn't solve the problem.
> >
> >
> > -----Original Message-----
> > From: Chris Fields [mailto:cjfields at uiuc.edu]
> > Sent: Mon 10/29/2007 5:06 PM
> > To: snaphit at planet.nl
> > Cc: Bioperl-l at lists.open-bio.org
> > Subject: Re: [Bioperl-l] get_Stream_by_gi: Memory going up every  
> call.
> >
> > It may be based on the mode (set by -retrievaltype) in which the
> > sequences are being retrieved and parsed.  The Bio::DB::WebDBSeqI
> > module has the documentation for this parameter.  If you are making
> > tons of calls to get_Seq*/get_Stream* methods it may lead to
> > substantial increases in memory until the child processes finish up
> > parsing each data stream.
> >
> > You can possibly add in a wait() in between sequence retrieval  
> calls,
> > or try setting the Bio::DB::GenBank instance to 'tempfile' or
> > 'io_string' (the former always worked faster for me):
> >
> > $self->{gb} = Bio::DB::GenBank->new(-retrievaltype => 'tempfile');
> >
> > chris
> >
> > On Oct 26, 2007, at 7:42 AM, Jelle86 wrote:
> >
> > > Ok I stripped a lot. And this is causing the problem:
> > >
> > > use Bio::DB::Genbank;
> > > sub new(){
> > >   my $invocant = shift;
> > >   my $class = ref($invocant) || $invocant;
> > >   my $self = {@_};
> > >   $self->{gb} = Bio::DB::GenBank->new();
> > >   bless $self, $class;
> > >   return $self;
> > > }
> > >
> > > sub streamQuery(){
> > >       my $self = shift;
> > >       my $stream_obj = $self->{gb}->get_Stream_by_gi($self-> 
> {ids});
> > >         while (my $seq_obj = $stream_obj->next_seq) {
> > >
> > >         }
> > > }
> > >
> > > Both subs (new and streamQuery) are called several times with a  
> new
> > > accessionlist.
> > > Removing the while loop, will use a bit less memory. But the  
> memory
> > > usage is
> > > still going up.
> > > --
> > > View this message in context: http://www.nabble.com/ 
> get_Stream_by_gi
> > > %3A-Memory-going-up-every-call.-tf4689188.html#a13426480
> > > Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> >
> >
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>
>

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign







From swapnatbhat at gmail.com  Wed Oct 31 21:34:38 2007
From: swapnatbhat at gmail.com (swapna26)
Date: Wed, 31 Oct 2007 14:34:38 -0700 (PDT)
Subject: [Bioperl-l]  BLAST output parsing
Message-ID: <13519112.post@talk.nabble.com>


Hi all,

I am new to bioperl.  I did BLAST search of ~4000 genes and I need to parse
it.  I did use -m 9 option to get a tabular information of the blast data. 
But it does not include the gene names or the names of the organisms of each
hit.  Are there any parsers that can do this job ??

I would really appreciate if anybody can help me with this.

Swapna
-- 
View this message in context: http://www.nabble.com/BLAST-output-parsing-tf4728082.html#a13519112
Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.