From jason.stajich at duke.edu Tue Nov 1 17:47:50 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 1 17:46:30 2005 Subject: [Bioperl-l] Genbank parser In-Reply-To: <865D7AB5-B2F4-4555-9365-62B881F9F8ED@bcm.tmc.edu> References: <865D7AB5-B2F4-4555-9365-62B881F9F8ED@bcm.tmc.edu> Message-ID: Bio::SeqIO parses genbank files. There is a spliced_seq method to splice CDS sequence out from a set of http://bioperl.org/Core/Latest/faq.html#Q5.5 See the HOWTOs for sequence introduction and feature and annotation introduction. http://bioperl.org/Core/Latest/modules.html and particularly the tutorial as well: http://bioperl.org/Core/Latest/bptutorial.html -jason On Oct 30, 2005, at 8:35 PM, Bingshan Li wrote: > Hi All, > > I am new to Bioperl and recently found it has a lot of useful > modules. I wrote a perl script to extract all protein sequences and > corresponding coding sequences from Genbank files. But I found some > bugs and it's hard to make sue my script is bug free after several > revision. I am wondering if there are some modules and specific > functions to use to fulfill my requirement. Does anybody have > similar code to share with? Most bugs come from multiple segments > of coding sequences and some cds sequences are on the minus strand. > > Thanks a lot! > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From bli1 at bcm.tmc.edu Tue Nov 1 19:00:39 2005 From: bli1 at bcm.tmc.edu (Bingshan Li) Date: Tue Nov 1 18:59:16 2005 Subject: [Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs? In-Reply-To: References: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> Message-ID: <4102B135-4AA9-4777-8069-7EB3A5EE745D@bcm.tmc.edu> Thanks, Jason, for this reply and the other for Ganbank parser. For Yn00, can we pass a slice of alignment to it so that I can calculate ka/ks for sliding windows? I ran PAML as a stand alone program but never used it in perl script. Thanks a lot! -bs On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote: > I suggest Codeml and YN00 - I assume you are only doing this for > pairwise comparisons and not along a tree? > > The dnastats module calculates Nei-Gojobori so it will be > different, but shouldn't be that different so something must be > wrong with your code or the module's method. Maybe you can post a > bug to bugzilla.open-bio.org with a clear example of where it is > going wrong and we'll take a look. > > I would just use YN00 for most pairwise - you can parse it with > Bio::Tools::Phylo::PAML and automate running it with > Bio::Tools::Run::Phylo::PAML::Yn00 > > > -jason > On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote: > > >> Hi all, >> >> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio >> but I found the result is very different from the output by yn00 >> in PAML 3.14. I applied "calc_KaKs_pair" function on two sequences >> to test it. The difference is pretty big (for one case it gave ka/ >> ks=1.35 while yn00 gave 0.37). Does anybody have same experience? >> Is there any other methods I can use to calculate ka/ks ratios? I >> will also use it to calculate ka/ks in sliding windows. >> >> Thanks a lot! >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > From jason.stajich at duke.edu Tue Nov 1 17:45:16 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 1 19:18:11 2005 Subject: [Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs? In-Reply-To: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> References: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> Message-ID: I suggest Codeml and YN00 - I assume you are only doing this for pairwise comparisons and not along a tree? The dnastats module calculates Nei-Gojobori so it will be different, but shouldn't be that different so something must be wrong with your code or the module's method. Maybe you can post a bug to bugzilla.open-bio.org with a clear example of where it is going wrong and we'll take a look. I would just use YN00 for most pairwise - you can parse it with Bio::Tools::Phylo::PAML and automate running it with Bio::Tools::Run::Phylo::PAML::Yn00 -jason On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote: > Hi all, > > I used Bio::Align::DNAStatistics module to calculate ka/ks ratio > but I found the result is very different from the output by yn00 in > PAML 3.14. I applied "calc_KaKs_pair" function on two sequences to > test it. The difference is pretty big (for one case it gave ka/ > ks=1.35 while yn00 gave 0.37). Does anybody have same experience? > Is there any other methods I can use to calculate ka/ks ratios? I > will also use it to calculate ka/ks in sliding windows. > > Thanks a lot! > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From torsten.seemann at infotech.monash.edu.au Tue Nov 1 18:08:04 2005 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Tue Nov 1 19:54:38 2005 Subject: [Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs? In-Reply-To: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> References: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> Message-ID: <1130886484.20485.22.camel@chauvel.csse.monash.edu.au> > I used Bio::Align::DNAStatistics module to calculate ka/ks ratio but > I found the result is very different from the output by yn00 in PAML > 3.14. I applied "calc_KaKs_pair" function on two sequences to test > it. The difference is pretty big (for one case it gave ka/ks=1.35 > while yn00 gave 0.37). Does anybody have same experience? Is there > any other methods I can use to calculate ka/ks ratios? I will also > use it to calculate ka/ks in sliding windows. I don't know anything about the details of those ratios, but I do notice that 1.35 = (1/2) / 0.37 if that helps. -- Torsten Seemann Victorian Bioinformatics Consortium From jason.stajich at duke.edu Tue Nov 1 19:08:28 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 1 20:26:07 2005 Subject: [Bioperl-l] Bio::Align::DNAStatistics ka/ks calculation bugs? In-Reply-To: <4102B135-4AA9-4777-8069-7EB3A5EE745D@bcm.tmc.edu> References: <732BF5F9-3ADE-4BEF-9B14-E0C3369B47B8@bcm.tmc.edu> <4102B135-4AA9-4777-8069-7EB3A5EE745D@bcm.tmc.edu> Message-ID: <905E7105-2D87-47BA-A4C0-8E8CFAC8E31A@duke.edu> That's right. see the PAML HOWTO - $dna_aln can be slices of an alignment. # set the alignment object $kaks_factory->alignment($dna_aln); # run the KaKs analysis my ($rc,$parser) = $kaks_factory->run(); my $result = $parser->next_result; my $MLmatrix = $result->get_MLmatrix(); On Nov 1, 2005, at 7:00 PM, Bingshan Li wrote: > Thanks, Jason, for this reply and the other for Ganbank parser. For > Yn00, can we pass a slice of alignment to it so that I can > calculate ka/ks for sliding windows? I ran PAML as a stand alone > program but never used it in perl script. > > Thanks a lot! > > -bs > > On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote: > > >> I suggest Codeml and YN00 - I assume you are only doing this for >> pairwise comparisons and not along a tree? >> >> The dnastats module calculates Nei-Gojobori so it will be >> different, but shouldn't be that different so something must be >> wrong with your code or the module's method. Maybe you can post a >> bug to bugzilla.open-bio.org with a clear example of where it is >> going wrong and we'll take a look. >> >> I would just use YN00 for most pairwise - you can parse it with >> Bio::Tools::Phylo::PAML and automate running it with >> Bio::Tools::Run::Phylo::PAML::Yn00 >> >> >> -jason >> On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote: >> >> >> >>> Hi all, >>> >>> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio >>> but I found the result is very different from the output by yn00 >>> in PAML 3.14. I applied "calc_KaKs_pair" function on two >>> sequences to test it. The difference is pretty big (for one case >>> it gave ka/ks=1.35 while yn00 gave 0.37). Does anybody have same >>> experience? Is there any other methods I can use to calculate ka/ >>> ks ratios? I will also use it to calculate ka/ks in sliding windows. >>> >>> Thanks a lot! >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >>> >> >> -- >> Jason Stajich >> Duke University >> http://www.duke.edu/~jes12 >> >> >> >> > > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From chen_li3 at yahoo.com Wed Nov 2 00:29:54 2005 From: chen_li3 at yahoo.com (chen li) Date: Wed Nov 2 00:35:11 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO Message-ID: <20051102052954.63512.qmail@web30801.mail.mud.yahoo.com> Hi folks, Here is one script copied from the Bio::SeqIO HOWTO: use Bio::SeqIO; my $usage = "getaccs.pl file format\n"; my $file = shift or die $usage; my $format = shift or die $usage; my $inseq = Bio::SeqIO->new('-file' => "<$file", '-format' => $format ); while (my $seq = $inseq->next_seq) { print $seq->accession_number,"\n"; } exit; I have a small file called mouse.fasta kept in the same directory. My question is that how does the script know to read in mouse.fasta? Where should I make a small modification in the script? Thanks, Li __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From bmoore at genetics.utah.edu Wed Nov 2 01:00:58 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Wed Nov 2 01:09:02 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO Message-ID: Li- You don't need to modify the script. It is written to accept the filename and format on the command line like this: perl getaccs.pl mouse.fasta fasta. Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of chen li > Sent: Tuesday, November 01, 2005 10:30 PM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] Bio::SeqIO HOWTO > > Hi folks, > > Here is one script copied from the Bio::SeqIO HOWTO: > > use Bio::SeqIO; > my $usage = "getaccs.pl file format\n"; > my $file = shift or die $usage; > my $format = shift or die $usage; > > my $inseq = Bio::SeqIO->new('-file' => "<$file", > '-format' => $format ); > while (my $seq = $inseq->next_seq) { > print $seq->accession_number,"\n"; > } > exit; > > > I have a small file called mouse.fasta kept in the > same directory. My question is that how does the > script know to read in mouse.fasta? Where should I > make a small modification in the script? > > Thanks, > > Li > > > > > > > > __________________________________ > Yahoo! FareChase: Search multiple travel sites in one click. > http://farechase.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From ewijaya at singnet.com.sg Tue Nov 1 20:49:08 2005 From: ewijaya at singnet.com.sg (Edward WIJAYA) Date: Wed Nov 2 02:45:35 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO In-Reply-To: <20051102052954.63512.qmail@web30801.mail.mud.yahoo.com> References: <20051102052954.63512.qmail@web30801.mail.mud.yahoo.com> Message-ID: On Wed, 02 Nov 2005 13:29:54 +0800, chen li wrote: > Hi folks, > Hi > I have a small file called mouse.fasta kept in the > same directory. My question is that how does the > script know to read in mouse.fasta? Where should I > make a small modification in the script? > http://search.cpan.org/src/BIRNEY/bioperl-1.4/Bio/Tools/GuessSeqFormat.pm It's in Bio::Tools::GuessSeqFormat. -- Regards, Edward WIJAYA SINGAPORE From brian_osborne at cognia.com Wed Nov 2 04:42:25 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Nov 2 05:00:19 2005 Subject: [Bioperl-l] noob Bio::DB::Biblio problem In-Reply-To: <1130768366.12915.37.camel@leona.gen.cam.ac.uk> Message-ID: Chihiro, What happens when you set the access mode to "soap" or "eutils" rather than to "biofetch"? Brian O. On 10/31/05 9:19 AM, "Chihiro Yamada" wrote: > Hiya folks, > > I'm trying to use the Bio::DB::Biblio::biofetch module to get references > by ID, but I'm having a problem... > > If I run this code... > > use Bio::Biblio; > my $biblio = new Bio::Biblio (-access => 'biofetch'); > my $ref = $biblio->get_by_id('15519282'); > > I get the error message: > > ------------- EXCEPTION ------------- > MSG: retrieval type pipeline unsupported > > STACK > Bio::DB::Biblio::biofetch::get_seq_stream > /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:237 > STACK > Bio::DB::DBFetch::get_Stream_by_id > /opt/csw/share/perl/site_perl/Bio/DB/DBFetch.pm:194 > STACK > Bio::DB::Biblio::biofetch::get_by_id > /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:153 > STACK toplevel bbt4.pl:7 > > -------------------------------------- > > I've tried this on 1.3 (on Solaris) and 1.5.1 (using OS X) and get the > same error message. > > Can anyone tell me what I'm doing wrong? > > Thanks > > Chihiro From t-nakazato at muj.biglobe.ne.jp Wed Nov 2 04:54:11 2005 From: t-nakazato at muj.biglobe.ne.jp (t-nakazato@muj.biglobe.ne.jp) Date: Wed Nov 2 05:32:24 2005 Subject: [Bioperl-l] noob Bio::DB::Biblio problem References: <1130768366.12915.37.camel@leona.gen.cam.ac.uk> Message-ID: <20051102185411.SODGC0A82742.C7EE0C8A@wpop.biglobe.ne.jp> Hi, If you don't need to use "biofetch" protocol, try "eutils". use Bio::Biblio; my $biblio = new Bio::Biblio (-access => 'eutils'); # biofetch -> eutils my $ref = $biblio->get_by_id('15519282'); And, you can write with perl one liner (on command line). perl -MBio::Biblio -le 'print Bio::Biblio->new(-access => "eutils")->get_by_id("1551982")' Takeru > Hiya folks, > > I'm trying to use the Bio::DB::Biblio::biofetch module to get references > by ID, but I'm having a problem... > > If I run this code... > > use Bio::Biblio; > my $biblio = new Bio::Biblio (-access => 'biofetch'); > my $ref = $biblio->get_by_id('15519282'); > > I get the error message: > > ------------- EXCEPTION ------------- > MSG: retrieval type pipeline unsupported > > STACK > Bio::DB::Biblio::biofetch::get_seq_stream /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:237 > STACK > Bio::DB::DBFetch::get_Stream_by_id /opt/csw/share/perl/site_perl/Bio/DB/DBFetch.pm:194 > STACK > Bio::DB::Biblio::biofetch::get_by_id /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:153 > STACK toplevel bbt4.pl:7 > > -------------------------------------- > > I've tried this on 1.3 (on Solaris) and 1.5.1 (using OS X) and get the > same error message. > > Can anyone tell me what I'm doing wrong? > > Thanks > > Chihiro > > -- > > ---------------------------------------------------------------------- > Chihiro Yamada. > FlyBase (Cambridge), http://www.FlyBase.org/ > Department of Genetics, > University of Cambridge, email: c.yamada@gen.cam.ac.uk > Downing Street, Tel : 01223-333963 > Cambridge, CB2 3EH, FAX : 01223-333992 > United Kingdom. Memes don't exist. Spread the Word. > ---------------------------------------------------------------------- > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From avilella at ub.edu Wed Nov 2 06:49:39 2005 From: avilella at ub.edu (Albert Vilella) Date: Wed Nov 2 07:05:19 2005 Subject: [Bioperl-l] PAML wrappers Message-ID: <1130932179.12062.3.camel@localhost.localdomain> Hi Sergios, (I forward your email to the bioperl mailing list) > i noticed there are wrappers for the ctl's of PAML's codeml. do u > have for baseml, too? do u have them tested on OSX? can u email them > to me, pls? zip them, preferably (no compression). > The wrappers you mention are part of bioperl-run. They should work under OSX having bioperl installed: Download http://bioperl.org/DIST/current_core_unstable.zip Download http://bioperl.org/DIST/current_run_unstable.zip unzip current_run_unstable.zip unzip current_core_unstable.zip export PERL5LIB="$HOME/bioperl-1.5.1:$HOME/bioperl-run-1.5.1" tar zxf paml3.14b.OSX_G5.tar.gz export PAMLDIR="$HOME/paml3.14/src" cd $PAMLDIR make ----- I believe that the codeml wrapper is the most tested and used, but the baseml wrapper has a problem right now with the input files: PAML's baseml is pickier than a hungry three year old in an expensive French bistro about the format of the sequence file and the tree file, so the example in the synopsis for bioperl-run-1.5.1/Bio/Tools/Run/Phylo/PAML/Baseml.pm is not working right now (at least for me). You will find more information on how to run PAML wrappers in the documentation. For example, in this howto: http://bioperl.org/HOWTOs/html/PAML.html Cheers, Albert. From daniel.lang at biologie.uni-freiburg.de Wed Nov 2 08:52:59 2005 From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang) Date: Wed Nov 2 09:19:41 2005 Subject: [Bioperl-l] Bio::MapIO::mapmaker Message-ID: <4368C4BB.8080304@biologie.uni-freiburg.de> Hi, I found something odd when working with Bio::MapIO::mapmaker (1.5.1 but also todays cvs version) ... Is it on purpose, that the parser "forgets" the last marker of a map? For example when parsing a map like: Map: mapname=THE_NAME_OF_MAP Markers Distance 1 bnl5.62a 35.3 cM coremarker 2 npi406 15.6 cM EST 3 npi439a 27.2 cM 4 dpg11 30.7 cM ssr 5 bnl7.21a 33 cM 6 bnl23b 8.6 cM coremarker 7 umc58 107.9 cM 8 npi605a 26.5 cM EST 9 npi120 19 cM ssr 10 npi615 19.5 cM coremarker 11 npi407 14 cM 12 npi241a 45.2 cM 13 bnl6.32 ---------- RflP marker n?13 is always left out when iterating over the map i.e. like this: #!/usr/bin/perl #test script to read mapmaker outputs use strict; use warnings; use Bio::MapIO; my $mapio = new Bio::MapIO(-format => "mapmaker", -file => $ARGV[0]); while (my $map = $mapio->next_map) { last unless $map->length; print $map->type ." ". $map->length ." " . $map->unique_id ."\n"; foreach my $marker ( $map->each_element ) { print $marker->name ."\t" .$marker->position->order ."\t", $marker->position->value , "\t", $marker->position->numeric ,"\n"; } } Output: ./readMap.pl test.map Genetic 382.5 1 bnl5.62a 1 35.3 35.3 npi406 2 50.9 50.9 npi439a 3 78.1 78.1 dpg11 4 108.8 108.8 bnl7.21a 5 141.8 141.8 bnl23b 6 150.4 150.4 umc58 7 258.3 258.3 npi605a 8 284.8 284.8 npi120 9 303.8 303.8 npi615 10 323.3 323.3 npi407 11 337.3 337.3 npi241a 12 382.5 382.5 Additionally, the iterator method Bio::MapIO::mapmaker::next_map doesn?t terminate correctly (Hence my test for the length of the map in the while loop). Thanks in advance! Daniel:) -- Daniel Lang University of Freiburg, Plant Biotechnology Schaenzlestr. 1, D-79104 Freiburg fax: +49 761 203 6945 phone: +49 761 203 6974 homepage: http://www.plant-biotech.net/ e-mail: daniel.lang@biologie.uni-freiburg.de ################################################# My software never has bugs. It just develops random features. ################################################# From brian_osborne at cognia.com Wed Nov 2 10:31:27 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Nov 2 10:30:35 2005 Subject: [Bioperl-l] Bio::MapIO::mapmaker In-Reply-To: <4368C4BB.8080304@biologie.uni-freiburg.de> Message-ID: Daniel, I've never used this module but this certainly doesn't sound right. Can you submit this as a bug so your observation isn't "lost"? Please attach your input file as well, I will look into it. Brian O. On 11/2/05 8:52 AM, "Daniel Lang" wrote: > Hi, > I found something odd when working with Bio::MapIO::mapmaker (1.5.1 but > also todays cvs version) ... > Is it on purpose, that the parser "forgets" the last marker of a map? > For example when parsing a map like: > Map: > mapname=THE_NAME_OF_MAP > Markers Distance > 1 bnl5.62a 35.3 cM coremarker > 2 npi406 15.6 cM EST > 3 npi439a 27.2 cM > 4 dpg11 30.7 cM ssr > 5 bnl7.21a 33 cM > 6 bnl23b 8.6 cM coremarker > 7 umc58 107.9 cM > 8 npi605a 26.5 cM EST > 9 npi120 19 cM ssr > 10 npi615 19.5 cM coremarker > 11 npi407 14 cM > 12 npi241a 45.2 cM > 13 bnl6.32 ---------- RflP > > marker n?13 is always left out when iterating over the map i.e. like this: > #!/usr/bin/perl > #test script to read mapmaker outputs > use strict; > use warnings; > use Bio::MapIO; > > my $mapio = new Bio::MapIO(-format => "mapmaker", > -file => $ARGV[0]); > while (my $map = $mapio->next_map) { > last unless $map->length; > print $map->type ." ". $map->length ." " . $map->unique_id ."\n"; > foreach my $marker ( $map->each_element ) { > print $marker->name ."\t" .$marker->position->order > ."\t", $marker->position->value , "\t", $marker->position->numeric ,"\n"; > } > } > Output: > ./readMap.pl test.map > Genetic 382.5 1 > bnl5.62a 1 35.3 35.3 > npi406 2 50.9 50.9 > npi439a 3 78.1 78.1 > dpg11 4 108.8 108.8 > bnl7.21a 5 141.8 141.8 > bnl23b 6 150.4 150.4 > umc58 7 258.3 258.3 > npi605a 8 284.8 284.8 > npi120 9 303.8 303.8 > npi615 10 323.3 323.3 > npi407 11 337.3 337.3 > npi241a 12 382.5 382.5 > > Additionally, the iterator method Bio::MapIO::mapmaker::next_map doesn?t > terminate correctly (Hence my test for the length of the map in the > while loop). > > Thanks in advance! > Daniel:) > From ajo11 at mole.bio.cam.ac.uk Wed Nov 2 11:22:43 2005 From: ajo11 at mole.bio.cam.ac.uk (Amanda O'Reilly) Date: Wed Nov 2 12:14:49 2005 Subject: [Bioperl-l] bioperl - swissprot GN lines Message-ID: <27cb312115521b38caea661a93e12f49@mole.bio.cam.ac.uk> Hello, I've found your bioperl posting [Bioperl-l] SwissProt/UniProt GN line format changed in which you say /I added the capability to parse this and a test to the main trunk. /I would be very grateful if you could let me know how I can access this capability. Sorry if I'm missing something obvious! Many thanks for any help, Amanda O'Reilly. From brian_osborne at cognia.com Wed Nov 2 12:43:58 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Nov 2 12:42:40 2005 Subject: [Bioperl-l] bioperl - swissprot GN lines In-Reply-To: <27cb312115521b38caea661a93e12f49@mole.bio.cam.ac.uk> Message-ID: Amanda, Most of the data in a Swissprot file, including the GN lines, is found in Annotation objects. This particular one has a tag of 'gene_name'. Take a look at the Feature-Annotation HOWTO for an explanation of how to extract these Annotations (http://bioperl.org/HOWTOs). Brian O. On 11/2/05 11:22 AM, "Amanda O'Reilly" wrote: > Hello, I've found your bioperl posting > [Bioperl-l] SwissProt/UniProt GN line format changed > > in which you say > > /I added the capability to parse this and a test to the main trunk. > > /I would be very grateful if you could let me know how I can access > this capability. > Sorry if I'm missing something obvious! > > Many thanks for any help, > Amanda O'Reilly. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Wed Nov 2 12:34:58 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Nov 2 13:39:01 2005 Subject: [Bioperl-l] bioperl - swissprot GN lines In-Reply-To: <27cb312115521b38caea661a93e12f49@mole.bio.cam.ac.uk> References: <27cb312115521b38caea661a93e12f49@mole.bio.cam.ac.uk> Message-ID: <13D6362E-F9D2-4EFA-AE25-72789845A78F@duke.edu> Did you try the bioperl-1.5.1 release? http://news.open-bio.org/archives/2005_10.html#000084 On Nov 2, 2005, at 11:22 AM, Amanda O'Reilly wrote: > Hello, I've found your bioperl posting > [Bioperl-l] SwissProt/UniProt GN line format changed bioperl.org/pipermail/bioperl-l/2004-July/016493.html> > in which you say > > /I added the capability to parse this and a test to the main trunk. > > /I would be very grateful if you could let me know how I can access > this capability. > Sorry if I'm missing something obvious! > > Many thanks for any help, > Amanda O'Reilly. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From bmoore at genetics.utah.edu Wed Nov 2 23:25:29 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Wed Nov 2 23:21:33 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO Message-ID: Li- The script is working correctly. You are giving it a fasta file and then asking it to print the accession number. While you and I can plainly see that the accession number NM_021308.1 is in the fasta header, bioperl makes no attempt to parse accession numbers from a fasta header. The reason for this is there is no uniformity in how fasta headers are written, so every fasta file could use a different header format and be valid. If you just want to see the script work correctly for learning purposes, change the line: print $seq->accession_number,"\n"; to this any or all of these lines: print $seq->alphabet,"\n"; print $seq->description,"\n"; print $seq->display_name,"\n"; print $seq->length,"\n"; print $seq->seq,"\n"; If you want the script to print the accession number, try downloading the full GenBank formatted sequence and run your script something like: perl getaccs.pl mouse.gb genbank Barry > -----Original Message----- > From: chen li [mailto:chen_li3@yahoo.com] > Sent: Wednesday, November 02, 2005 8:36 PM > To: Barry Moore > Subject: RE: [Bioperl-l] Bio::SeqIO HOWTO > > Barry, > > Thank you very much. > > Here are the results. 1) If I type "perl getaccs.pl" I > get this result "getaccs.pl File format" on the > screen. 2)If I type "perl getaccs.pl mouse.fasta > fasta" I get "unknow" on the screen. IT seems there > are no access no. printed out after the script is > executed. > > So what is the problem here? > > Li > > here is part of my file: > > >gi|10946609|ref|NM_021308.1| Mus musculus piwi like > homolog 2 (Drosophila) (Piwil2), mRNA > AGTGTGTGGGAGGAACGCAGGGGCTGGAATAGGAGGGAAAGGAGGTGGCTCCAGGAGAGAGCGAGAGAGG > GAGCGCTCGCATCGGGGCTCAGTGGCACCAGACCTAAAAAGAAATCTAGGCAAGGCTCCGGCACAGTCCA.. .. > .... > > --- Barry Moore wrote: > > > Li- > > > > You don't need to modify the script. It is written > > to accept the > > filename and format on the command line like this: > > perl getaccs.pl > > mouse.fasta fasta. > > > > Barry > > > > > -----Original Message----- > > > From: bioperl-l-bounces@portal.open-bio.org > > [mailto:bioperl-l- > > > bounces@portal.open-bio.org] On Behalf Of chen li > > > Sent: Tuesday, November 01, 2005 10:30 PM > > > To: bioperl-l@bioperl.org > > > Subject: [Bioperl-l] Bio::SeqIO HOWTO > > > > > > Hi folks, > > > > > > Here is one script copied from the Bio::SeqIO > > HOWTO: > > > > > > use Bio::SeqIO; > > > my $usage = "getaccs.pl file format\n"; > > > my $file = shift or die $usage; > > > my $format = shift or die $usage; > > > > > > my $inseq = Bio::SeqIO->new('-file' => > > "<$file", > > > '-format' => $format ); > > > while (my $seq = $inseq->next_seq) { > > > print $seq->accession_number,"\n"; > > > } > > > exit; > > > > > > > > > I have a small file called mouse.fasta kept in the > > > same directory. My question is that how does the > > > script know to read in mouse.fasta? Where should I > > > make a small modification in the script? > > > > > > Thanks, > > > > > > Li > > > > > > > > > > > > > > > > > > > > > > > > __________________________________ > > > Yahoo! FareChase: Search multiple travel sites in > > one click. > > > http://farechase.yahoo.com > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com From hlapp at gnf.org Thu Nov 3 01:48:02 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Nov 3 02:41:01 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO In-Reply-To: References: Message-ID: <1f0b7c7937e41d7f285fcccabb612c2a@gnf.org> $seq->display_id will give you the full composite ID after the greater-than character. It's trivial enough to split it with a regular expression to obtain only the part you're interested in, so for the reasons Barry mentions Bioperl doesn't do this for you. On Nov 2, 2005, at 8:25 PM, Barry Moore wrote: > Li- > > The script is working correctly. You are giving it a fasta file and > then asking it to print the accession number. While you and I can > plainly see that the accession number NM_021308.1 is in the fasta > header, bioperl makes no attempt to parse accession numbers from a > fasta > header. The reason for this is there is no uniformity in how fasta > headers are written, so every fasta file could use a different header > format and be valid. > > If you just want to see the script work correctly for learning > purposes, > change the line: > print $seq->accession_number,"\n"; > to this any or all of these lines: > print $seq->alphabet,"\n"; > print $seq->description,"\n"; > print $seq->display_name,"\n"; > print $seq->length,"\n"; > print $seq->seq,"\n"; > > If you want the script to print the accession number, try downloading > the full GenBank formatted sequence and run your script something like: > perl getaccs.pl mouse.gb genbank > > Barry > >> -----Original Message----- >> From: chen li [mailto:chen_li3@yahoo.com] >> Sent: Wednesday, November 02, 2005 8:36 PM >> To: Barry Moore >> Subject: RE: [Bioperl-l] Bio::SeqIO HOWTO >> >> Barry, >> >> Thank you very much. >> >> Here are the results. 1) If I type "perl getaccs.pl" I >> get this result "getaccs.pl File format" on the >> screen. 2)If I type "perl getaccs.pl mouse.fasta >> fasta" I get "unknow" on the screen. IT seems there >> are no access no. printed out after the script is >> executed. >> >> So what is the problem here? >> >> Li >> >> here is part of my file: >> >>> gi|10946609|ref|NM_021308.1| Mus musculus piwi like >> homolog 2 (Drosophila) (Piwil2), mRNA >> AGTGTGTGGGAGGAACGCAGGGGCTGGAATAGGAGGGAAAGGAGGTGGCTCCAGGAGAGAGCGAGAGAGG >> > GAGCGCTCGCATCGGGGCTCAGTGGCACCAGACCTAAAAAGAAATCTAGGCAAGGCTCCGGCACAGTCCA. > . > .. >> .... >> >> --- Barry Moore wrote: >> >>> Li- >>> >>> You don't need to modify the script. It is written >>> to accept the >>> filename and format on the command line like this: >>> perl getaccs.pl >>> mouse.fasta fasta. >>> >>> Barry >>> >>>> -----Original Message----- >>>> From: bioperl-l-bounces@portal.open-bio.org >>> [mailto:bioperl-l- >>>> bounces@portal.open-bio.org] On Behalf Of chen li >>>> Sent: Tuesday, November 01, 2005 10:30 PM >>>> To: bioperl-l@bioperl.org >>>> Subject: [Bioperl-l] Bio::SeqIO HOWTO >>>> >>>> Hi folks, >>>> >>>> Here is one script copied from the Bio::SeqIO >>> HOWTO: >>>> >>>> use Bio::SeqIO; >>>> my $usage = "getaccs.pl file format\n"; >>>> my $file = shift or die $usage; >>>> my $format = shift or die $usage; >>>> >>>> my $inseq = Bio::SeqIO->new('-file' => >>> "<$file", >>>> '-format' => $format ); >>>> while (my $seq = $inseq->next_seq) { >>>> print $seq->accession_number,"\n"; >>>> } >>>> exit; >>>> >>>> >>>> I have a small file called mouse.fasta kept in the >>>> same directory. My question is that how does the >>>> script know to read in mouse.fasta? Where should I >>>> make a small modification in the script? >>>> >>>> Thanks, >>>> >>>> Li >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> __________________________________ >>>> Yahoo! FareChase: Search multiple travel sites in >>> one click. >>>> http://farechase.yahoo.com >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l@portal.open-bio.org >>>> >>> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >> >> >> >> >> >> __________________________________ >> Yahoo! Mail - PC Magazine Editors' Choice 2005 >> http://mail.yahoo.com > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From benn at cenix-bioscience.com Thu Nov 3 11:34:53 2005 From: benn at cenix-bioscience.com (Neil Benn) Date: Thu Nov 3 11:33:30 2005 Subject: [Bioperl-l] Laboratory Automation Control using Perl Message-ID: <436A3C2D.8060201@cenix-bioscience.com> Hello, I am guest editing an issue of the Journal of the Association for Laboratory Automation which is focusing on the strengths/weaknesses and application examples of various computer languages in the field of automation control moving up the process chain to the level of interaction with DB systems (but not actual data interpretation, mining, etc). The common languages in this field are Python, C#, C++ however I would like to include some languages which are not commonly used in this field. Therefore I would like to discover if there are any such applications someone has written in Perl in this field. If you have any examples of such an application (I don't need the code or a working copy, just an description) please could you let me know. If you have done work in this area and would be willing to submit a technical article to the journal, even better - please contact me. Thanks for your time. Cheers, -- Neil Benn Senior Automation Engineer Cenix BioScience BioInnovations Zentrum Tatzberg 46 D-01307 Dresden Germany Tel : +49 (0)351 4173 154 e-mail : benn@cenix-bioscience.com Cenix Website : http://www.cenix-bioscience.com From hlapp at gnf.org Thu Nov 3 11:22:21 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Thu Nov 3 11:37:57 2005 Subject: [Bioperl-l] Bio::SeqIO HOWTO In-Reply-To: <20051103085625.99813.qmail@web30804.mail.mud.yahoo.com> References: <20051103085625.99813.qmail@web30804.mail.mud.yahoo.com> Message-ID: Sure, only fasta format is 5-10x less space and parses 3x faster. (You could also instruct the genbank parser to ignore most of the attributes except accession and sequence if that's all you need, and it will be much faster then too. See Bio::Seq::SeqBuilder.) -hilmar On Nov 3, 2005, at 12:56 AM, chen li wrote: > Thanks Hilmar. Both methods work for me now. It turns > out this script can correctly print out what is > expected if the input file is in genbank format but > not a fasta format. > > Li > > --- Hilmar Lapp wrote: > >> $seq->display_id will give you the full composite ID >> after the >> greater-than character. >> >> It's trivial enough to split it with a regular >> expression to obtain >> only the part you're interested in, so for the >> reasons Barry mentions >> Bioperl doesn't do this for you. >> >> >> On Nov 2, 2005, at 8:25 PM, Barry Moore wrote: >> >>> Li- >>> >>> The script is working correctly. You are giving >> it a fasta file and >>> then asking it to print the accession number. >> While you and I can >>> plainly see that the accession number NM_021308.1 >> is in the fasta >>> header, bioperl makes no attempt to parse >> accession numbers from a >>> fasta >>> header. The reason for this is there is no >> uniformity in how fasta >>> headers are written, so every fasta file could use >> a different header >>> format and be valid. >>> >>> If you just want to see the script work correctly >> for learning >>> purposes, >>> change the line: >>> print $seq->accession_number,"\n"; >>> to this any or all of these lines: >>> print $seq->alphabet,"\n"; >>> print $seq->description,"\n"; >>> print $seq->display_name,"\n"; >>> print $seq->length,"\n"; >>> print $seq->seq,"\n"; >>> >>> If you want the script to print the accession >> number, try downloading >>> the full GenBank formatted sequence and run your >> script something like: >>> perl getaccs.pl mouse.gb genbank >>> >>> Barry >>> >>>> -----Original Message----- >>>> From: chen li [mailto:chen_li3@yahoo.com] >>>> Sent: Wednesday, November 02, 2005 8:36 PM >>>> To: Barry Moore >>>> Subject: RE: [Bioperl-l] Bio::SeqIO HOWTO >>>> >>>> Barry, >>>> >>>> Thank you very much. >>>> >>>> Here are the results. 1) If I type "perl >> getaccs.pl" I >>>> get this result "getaccs.pl File format" on the >>>> screen. 2)If I type "perl getaccs.pl mouse.fasta >>>> fasta" I get "unknow" on the screen. IT seems >> there >>>> are no access no. printed out after the script is >>>> executed. >>>> >>>> So what is the problem here? >>>> >>>> Li >>>> >>>> here is part of my file: >>>> >>>>> gi|10946609|ref|NM_021308.1| Mus musculus piwi >> like >>>> homolog 2 (Drosophila) (Piwil2), mRNA >>>> >> > AGTGTGTGGGAGGAACGCAGGGGCTGGAATAGGAGGGAAAGGAGGTGGCTCCAGGAGAGAGCGAGAGAGG >>>> >>> >> > GAGCGCTCGCATCGGGGCTCAGTGGCACCAGACCTAAAAAGAAATCTAGGCAAGGCTCCGGCACAGTCCA. >> >>> . >>> .. >>>> .... >>>> >>>> --- Barry Moore wrote: >>>> >>>>> Li- >>>>> >>>>> You don't need to modify the script. It is >> written >>>>> to accept the >>>>> filename and format on the command line like >> this: >>>>> perl getaccs.pl >>>>> mouse.fasta fasta. >>>>> >>>>> Barry >>>>> >>>>>> -----Original Message----- >>>>>> From: bioperl-l-bounces@portal.open-bio.org >>>>> [mailto:bioperl-l- >>>>>> bounces@portal.open-bio.org] On Behalf Of chen >> li >>>>>> Sent: Tuesday, November 01, 2005 10:30 PM >>>>>> To: bioperl-l@bioperl.org >>>>>> Subject: [Bioperl-l] Bio::SeqIO HOWTO >>>>>> >>>>>> Hi folks, >>>>>> >>>>>> Here is one script copied from the Bio::SeqIO >>>>> HOWTO: >>>>>> >>>>>> use Bio::SeqIO; >>>>>> my $usage = "getaccs.pl file format\n"; >>>>>> my $file = shift or die $usage; >>>>>> my $format = shift or die $usage; >>>>>> >>>>>> my $inseq = Bio::SeqIO->new('-file' => >>>>> "<$file", >>>>>> '-format' => $format ); >>>>>> while (my $seq = $inseq->next_seq) { >>>>>> print $seq->accession_number,"\n"; >>>>>> } >>>>>> exit; >>>>>> >>>>>> >>>>>> I have a small file called mouse.fasta kept in >> the >>>>>> same directory. My question is that how does >> the >>>>>> script know to read in mouse.fasta? Where >> should I >>>>>> make a small modification in the script? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Li >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> __________________________________ >>>>>> Yahoo! FareChase: Search multiple travel sites >> in >>>>> one click. >>>>>> http://farechase.yahoo.com >>>>>> _______________________________________________ >>>>>> Bioperl-l mailing list >>>>>> Bioperl-l@portal.open-bio.org >>>>>> >>>>> >>>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>> >>>> >>>> >>>> >>>> >>>> __________________________________ >>>> Yahoo! Mail - PC Magazine Editors' Choice 2005 >>>> http://mail.yahoo.com >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >> -- >> > ------------------------------------------------------------- >> Hilmar Lapp email: lapp >> at gnf.org >> GNF, San Diego, Ca. 92121 phone: >> +1-858-812-1757 >> > ------------------------------------------------------------- >> >> > > > > > __________________________________ > Start your day with Yahoo! - Make it your home page! > http://www.yahoo.com/r/hs > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From bmoore at genetics.utah.edu Thu Nov 3 11:52:26 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Thu Nov 3 11:48:26 2005 Subject: [Bioperl-l] RE: :SeqIO HOWTO Message-ID: Li- If I understand you question correctly, you are asking if the variable that contains the sequence(s) ($inseq in your script) from you sequence file is a string (called a scalar in perl) as opposed to an array. The answer is "neither". The variable $inseq is a hash based Bio::SeqIO object that holds the details for reading sequences from your sequence file. One of the methods associated with that object is next_seq which returns then next sequence in you file. Actually it returns another hash based object - a Bio::Seq object which contains all the details about the next sequence in the file. That Bio::Seq object has a number of methods associated with it which allow you to retrieve details like display id and sequence. So while $inseq is neither a scalar nor an array, in terms of what it can do, it would be better to think of it in terms of an array because it can read a file with many sequences in it, and you can step through those sequences with next_seq like you would step through the elements in an array with a for each loop. Hope I answered the correct question. Barry P.S. Try to remember to reply-all so that your questions go to the list, and not only to me. That way others can contribute to the discussion as well. > -----Original Message----- > From: chen li [mailto:chen_li3@yahoo.com] > Sent: Thursday, November 03, 2005 2:05 AM > To: Barry Moore > Subject: Bio::SeqIO HOWTO > > Dear Dr. Moore, > > Thank you very much. > > You are right. The script works correctly only if the > input is in genbank format but not the fasta format. > > One more question: I guess the read-in sequence is a > string but not an array, am I right? > > Li > > > > __________________________________ > Yahoo! FareChase: Search multiple travel sites in one click. > http://farechase.yahoo.com From bmoore at genetics.utah.edu Thu Nov 3 12:10:59 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Thu Nov 3 12:06:57 2005 Subject: [Bioperl-l] RE: :SeqIO HOWTO Message-ID: Li- The HOWTOs are generally example based, and thus are not comprehensive documentation. The primary documentation for the details of any module is found in POD within that module. You can access that by running perldoc on the actual perl module (perldoc /usr/lib/perl5/site_perl/5.8.5/Bio/Seq.pm on my system) or browse through the module documentation online (for bioperl 1.4 currently) at http://doc.bioperl.org/releases/bioperl-1.4/. For instance, point you browser to http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html click on "Methods", choose Description under display_name, and you'll get: Title : display_name Usage : $string = $obj->display_name() Function: A string which is what should be displayed to the user the string should have no spaces (ideally, though a cautious user of this interface would not assumme this) and should be less than thirty characters (though again, double checking this is a good idea) This is aliased to display_id(). Returns : A scalar Barry > -----Original Message----- > From: chen li [mailto:chen_li3@yahoo.com] > Sent: Thursday, November 03, 2005 6:55 AM > To: Barry Moore > Subject: Bio::SeqIO HOWTO > > Dear Dr. Moore, > > One more question: which parts of the HOWTOs describe > the methods for > alphabet/description/display_name/length/seq? > > > print $seq->alphabet,"\n"; > > print $seq->description,"\n"; > > print $seq->display_name,"\n"; > > print $seq->length,"\n"; > > print $seq->seq,"\n"; > > > Li > > > > __________________________________ > Yahoo! FareChase: Search multiple travel sites in one click. > http://farechase.yahoo.com From brian_osborne at cognia.com Thu Nov 3 13:32:31 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Nov 3 13:31:13 2005 Subject: [Bioperl-l] RE: :SeqIO HOWTO In-Reply-To: Message-ID: Barry, That was a beautiful answer. You should write some HOWTOs! Brian O. On 11/3/05 11:52 AM, "Barry Moore" wrote: > Li- > > If I understand you question correctly, you are asking if the variable > that contains the sequence(s) ($inseq in your script) from you sequence > file is a string (called a scalar in perl) as opposed to an array. The > answer is "neither". The variable $inseq is a hash based Bio::SeqIO > object that holds the details for reading sequences from your sequence > file. One of the methods associated with that object is next_seq which > returns then next sequence in you file. Actually it returns another hash > based object - a Bio::Seq object which contains all the details about > the next sequence in the file. That Bio::Seq object has a number of > methods associated with it which allow you to retrieve details like > display id and sequence. So while $inseq is neither a scalar nor an > array, in terms of what it can do, it would be better to think of it in > terms of an array because it can read a file with many sequences in it, > and you can step through those sequences with next_seq like you would > step through the elements in an array with a for each loop. Hope I > answered the correct question. > > Barry > > P.S. Try to remember to reply-all so that your questions go to the > list, and not only to me. That way others can contribute to the > discussion as well. > >> -----Original Message----- >> From: chen li [mailto:chen_li3@yahoo.com] >> Sent: Thursday, November 03, 2005 2:05 AM >> To: Barry Moore >> Subject: Bio::SeqIO HOWTO >> >> Dear Dr. Moore, >> >> Thank you very much. >> >> You are right. The script works correctly only if the >> input is in genbank format but not the fasta format. >> >> One more question: I guess the read-in sequence is a >> string but not an array, am I right? >> >> Li >> >> >> >> __________________________________ >> Yahoo! FareChase: Search multiple travel sites in one click. >> http://farechase.yahoo.com > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From saldroubi at yahoo.com Thu Nov 3 13:34:49 2005 From: saldroubi at yahoo.com (Sam Al-Droubi) Date: Thu Nov 3 13:40:06 2005 Subject: [Bioperl-l] Tip: How to find promoter region Message-ID: <20051103183450.49111.qmail@web34302.mail.mud.yahoo.com> All, I started writing a program using bioperl to extract the promoter region given a gene seq or an accession number but then I found that someone has already done this. You can find this at http://biowulf.bu.edu/zlab/PromoSer/ I hope this helps others. Sincerely, Sam Al-Droubi, M.S. saldroubi@yahoo.com From resch at ncbi.nlm.nih.gov Thu Nov 3 13:56:08 2005 From: resch at ncbi.nlm.nih.gov (Resch, Alissa (NIH/NLM/NCBI)) Date: Thu Nov 3 14:07:31 2005 Subject: [Bioperl-l] Please remove my name from email list Message-ID: Hi there, Please remove my email from your list. My email box can no longer sustain the influx of mail. Thanks, Alissa Resch (resch@ncbi.nlm.nih.gov) From benn at cenix-bioscience.com Tue Nov 1 11:22:04 2005 From: benn at cenix-bioscience.com (Neil Benn) Date: Thu Nov 3 14:25:33 2005 Subject: [Bioperl-l] Laboratory Automation Control using Perl Message-ID: <4367962C.8000702@cenix-bioscience.com> Hello, I am guest editing an issue of the Journal of the Association for Laboratory Automation which is focusing on the strengths/weaknesses and application examples of various computer languages in the field of automation control moving up the process chain to the level of interaction with DB systems (but not actual data interpretation, mining, etc). The common languages in this field are Python, C#, C++ however I would like to include some languages which are not commonly used in this field. Therefore I would like to discover if there are any such applications someone has written in Perl in this field. If you have any examples of such an application (I don't need the code or a working copy, just an description) please could you let me know. If you have done work in this area and would be willing to submit a technical article to the journal, even better - please contact me. Finally, please could you respond to my email directly (benn@cenix-bioscience.com), I'm having problems joining the bio-perl list (the confirmation request e-mail won't come through). Thanks for your time. Cheers, Neil -- Neil Benn Senior Automation Engineer Cenix BioScience BioInnovations Zentrum Tatzberg 46 D-01307 Dresden Germany Tel : +49 (0)351 4173 154 e-mail : benn@cenix-bioscience.com Cenix Website : http://www.cenix-bioscience.com From equevill at infobiogen.fr Wed Nov 2 12:16:16 2005 From: equevill at infobiogen.fr (Emmanuel Quevillon) Date: Thu Nov 3 14:25:34 2005 Subject: [Bioperl-l] Bio::Tools::RepeatMasker typo? Message-ID: <4368F460.3070202@infobiogen.fr> Hi, I just played with RepeatMasker module to parse output and create GFF3. I noticed there is (I am not sure if it is a typo or it is wanted) mistyped line in function next_result() : my $rf = Bio::SeqFeature::Generic->new; $rf->seq_id ($query_name); $rf->score ($score); $rf->start ($query_start); $rf->end ($query_end); $rf->strand ($strand); $rf->source_tag ("RepeatMasker"); $rf->primary_tag ($repeat_class); my $rf2 = Bio::SeqFeature::Generic->new; $rf2->seq_id ($repeat_name); $rf2->score ($score); $rf2->start ($hit_start); $rf2->end ($hit_end); $rf2->strand ($strand); $rf2->source_tag ("RepeatMasker"); $rf->primary_tag ($repeat_class); <=========== Would not be $rf2 instead? Please let me know. Thanks Regards Emmanuel -------------- next part -------------- A non-text attachment was scrubbed... Name: equevill.vcf Type: text/x-vcard Size: 322 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20051102/01c19ef1/equevill-0001.vcf From kun.he at yale.edu Wed Nov 2 17:36:35 2005 From: kun.he at yale.edu (Kun He) Date: Thu Nov 3 14:25:36 2005 Subject: [Bioperl-l] Failed to load tigr xml files through Bio::Seq::tigr Message-ID: <43693F73.7030103@yale.edu> Dear all, I have just tried to use the Bio::Seq::tigr module (BioPerl 1.5.1) to import information from TIGR Rice version 3 XML format pseudochromosome data, but it always failed on the loading (initiating) procedure. " use strict; use Bio::SeqIO; my $file=shift; print $file,"\n"; my $io = Bio::SeqIO->new(-file => "<$file", -format => "tigr" ); " There are a lot kinds of errors thrown out, based on different XML files. Attached is a sample xml from tigr, who can kindly help me to try if you can load it by the tigr.pm module? Thanks a lot! Kun He -------------- next part -------------- A non-text attachment was scrubbed... Name: sample.xml Type: text/xml Size: 267587 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20051102/a5c6f2dc/sample-0001.xml From dag at sonsorol.org Thu Nov 3 14:25:05 2005 From: dag at sonsorol.org (Chris Dagdigian) Date: Thu Nov 3 14:25:37 2005 Subject: [Bioperl-l] Please remove my name from email list In-Reply-To: References: Message-ID: There are 1500+ people subscribed to the bioperl list and 1200+ more on the announce list. If we had to manually take care of user sub/unsub actions we'd never be able to actually get any other work done. Especially as EVERY SINGLE EMAIL sent through the mailing list contains explicit links on how to *manage your own* subscriptions. At the footer of EVERY email you will note the following: > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l Following that URL will take you to a page that will let you adjust your settings. You can even change your preferences to "digest" mode which will only send you one email per day. You need a password and if you don't have that handy you can just punch in your email address to get it sent to you. Besides the footer in EVERY email we send out, you can also find this data in the header fields: > List-Id: Bioperl Project Discussion List bio.org> > List-Unsubscribe: bioperl-l>, > > List-Archive: > List-Post: > List-Help: > List-Subscribe: bioperl-l>, > As the easily clickable link shows, besides the web management method you can also send an email to bioperl-l-request@bioperl.org with "unsubscribe" in the subject and the automated software will try to do the right thing. And finally, when subscribing to the list you also received explicit instructions on how to do this. Generally speaking, the volunteers who run the site and the mailing lists are only needed to manually intervene in cases where someone has lost access to an email account. For every other situation the 'self serve' methods are best. -c On Nov 3, 2005, at 1:56 PM, Resch, Alissa ((NIH/NLM/NCBI)) wrote: > > Hi there, > > Please remove my email from your list. My email box can no longer > sustain the influx of mail. > Thanks, > Alissa Resch > (resch@ncbi.nlm.nih.gov) From reneeh at stanford.edu Thu Nov 3 17:09:48 2005 From: reneeh at stanford.edu (Renee Halbrook) Date: Thu Nov 3 17:22:16 2005 Subject: [Bioperl-l] Blast -- data streams? In-Reply-To: <200511031929.jA3JTW8U007951@portal.open-bio.org> References: <200511031929.jA3JTW8U007951@portal.open-bio.org> Message-ID: <1131055788.436a8aacc152b@webmail.stanford.edu> Hi, I notice that the Blast web package in bioperl uses a lot of file i/o, reading and writing temporary files. On a couple of systems I am working with, the problem seems to be that these temp files build up, and need to be deleted using a chron job. My question is, is there any reason to use file io, rather than working directly with data streams? Thanks for any feedback, Renee Renee Halbrook Bioinformatics Programmer The Carnegie Institution of Washington Department of Plant Biology 260 Panama Street Stanford, CA 94305 From jason.stajich at duke.edu Thu Nov 3 19:03:29 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Nov 3 19:02:04 2005 Subject: [Bioperl-l] Blast -- data streams? In-Reply-To: <1131055788.436a8aacc152b@webmail.stanford.edu> References: <200511031929.jA3JTW8U007951@portal.open-bio.org> <1131055788.436a8aacc152b@webmail.stanford.edu> Message-ID: <33B715BB-D606-4889-83DD-7B9B30F0CB36@duke.edu> It does work with streams, nothing in the parsers assumes that it needs to be a file. You pass in -fh to provide a filehandle and - file for a file name. open($fh, "blastp -d nr -i qfile E=1e-5 |") || die $!; my $in = Bio::SearchIO->new(-fh => $fh, -format=> 'blast'); .... If you are talking about the the blast wrapper, Tools::StandAloneBlast, it creates tempfiles which are either removed when the object is destroyed or on the subsequence submit using the File::Temp module. I will reiterate what I've said in the past, Tools::StandAloneBlast could DEFINITELY be improved and needs people to adopt it.... -jason On Nov 3, 2005, at 5:09 PM, Renee Halbrook wrote: > Hi, > I notice that the Blast web package in bioperl uses a lot of file i/o, > reading and writing temporary files. > On a couple of systems I am working with, the problem seems to be > that these > temp files build up, and need to be deleted using a chron job. > My question is, is there any reason to use file io, rather than > working > directly with data streams? > > > Thanks for any feedback, > Renee > > > Renee Halbrook > Bioinformatics Programmer > The Carnegie Institution of Washington > Department of Plant Biology > 260 Panama Street > Stanford, CA 94305 > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From chen_li3 at yahoo.com Thu Nov 3 20:50:43 2005 From: chen_li3 at yahoo.com (chen li) Date: Thu Nov 3 20:55:59 2005 Subject: [Bioperl-l] RE: :SeqIO HOWTO In-Reply-To: Message-ID: <20051104015043.95208.qmail@web30808.mail.mud.yahoo.com> Dear Dr. Moore, Thank you very much. It helps me a lot. Li --- Barry Moore wrote: > Li- > > The HOWTOs are generally example based, and thus are > not comprehensive > documentation. The primary documentation for the > details of any module > is found in POD within that module. You can access > that by running > perldoc on the actual perl module (perldoc > /usr/lib/perl5/site_perl/5.8.5/Bio/Seq.pm on my > system) or browse > through the module documentation online (for bioperl > 1.4 currently) at > http://doc.bioperl.org/releases/bioperl-1.4/. > > For instance, point you browser to > http://doc.bioperl.org/releases/bioperl-1.4/Bio/Seq.html > click on > "Methods", choose Description under display_name, > and you'll get: > > Title : display_name > Usage : $string = $obj->display_name() > Function: A string which is what should be > displayed to the user > the string should have no spaces > (ideally, though a cautious > user of this interface would not assumme > this) and should be > less than thirty characters (though > again, double checking > this is a good idea) > > This is aliased to display_id(). > Returns : A scalar > > Barry > > > -----Original Message----- > > From: chen li [mailto:chen_li3@yahoo.com] > > Sent: Thursday, November 03, 2005 6:55 AM > > To: Barry Moore > > Subject: Bio::SeqIO HOWTO > > > > Dear Dr. Moore, > > > > One more question: which parts of the HOWTOs > describe > > the methods for > > alphabet/description/display_name/length/seq? > > > > > print $seq->alphabet,"\n"; > > > print $seq->description,"\n"; > > > print $seq->display_name,"\n"; > > > print $seq->length,"\n"; > > > print $seq->seq,"\n"; > > > > > > Li > > > > > > > > __________________________________ > > Yahoo! FareChase: Search multiple travel sites in > one click. > > http://farechase.yahoo.com > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From s_waechter at gmx.net Fri Nov 4 06:43:20 2005 From: s_waechter at gmx.net (=?ISO-8859-1?Q?Stefan_W=E4chter?=) Date: Fri Nov 4 06:41:54 2005 Subject: [Bioperl-l] Need help: RemoteBlast Problem Message-ID: <436B4958.5070104@gmx.net> Hi, I wrote a Perl script a year ago. It use a few bioperl modules, one of them is RemoteBlast. This script worked fine until the beginning of september :-) . Read the articles in this news group I found out, that there happened some changes at the NCBI. Ok. So I installed bioperl-1.5.1 yesterday and run the script. First, it seemed to work fine, but suddenly it broke with this message: ------------- EXCEPTION ----------- MSG: no data for midline Features flanking this part of subject sequence: STACK Bio::SearchIO::blast::next_result /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1172 STACK main::RemoteBlast ./cDNAComparer.pl:1223 STACK main::runAnalyse ./cDNAComparer.pl:373 STACK toplevel ./cDNAComparer.pl:1411 -------------------------------------- When I blast the Sequence directly at NCBI I found in the result page the line that seems to cause this break: >gi|61216116|ref|NG_001019.4| Geo Download subject sequence spanning the HSP Homo sapiens immunoglobulin heavy locus (IGH@) on chromosome 14 Length=1279711 Features flanking this part of subject sequence: 498 bp at 5' side: immunoglobulin heavy constant gamma 3 (G3m marker), membr... 21702 bp at 3' side: CDS Score = 1235 bits (623), Expect = 0.0 Identities = 641/646 (99%), Gaps = 1/646 (0%) Strand=Plus/Plus Query 69 GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 128 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1057788 GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 1057847 Query 129 GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 188 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1057848 GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 1057907 Query 189 CAGCACCACCCCTTGGCTGCCTGCCTACACNTGCTGGATTCTCGGGTGGAACTCGACCCG 248 What can I do to fix this problem ? Any ideas ? Cheers Stefan From govind.chandra at bbsrc.ac.uk Fri Nov 4 08:42:15 2005 From: govind.chandra at bbsrc.ac.uk (Govind Chandra) Date: Fri Nov 4 08:48:16 2005 Subject: [Bioperl-l] Multiple tags of same name in a Bio::SeqFeature::Generic object Message-ID: <1131111735.5063.14.camel@jic51958.jic.bbsrc.ac.uk> Hi, I wish to assign multiple tags of the same name in a Bio::SeqFeature::Generic object. What I am doing below does not work. I did not expect it to. What I get is: FT /db_xref="InterPro:IPR001957" If I pass a reference to an array to a single db_xref tag, that does not work either. I get: FT /db_xref="ARRAY(0x841da94)" If I pick up a feature from an embl file (rather than build my own) which has multiple db_xref tags and add it to my sequence using add_SeqFeature I do get multiple db_xref tags in the output. So I conclude that I am not building the Bio::SeqFeature::Generic object right. Could someone help me with this please. I am using BioPerl 1.4.0. Thanks Govind Govind Chandra Microbiology John Innes Centre Norwich UK. ### begin script ### use Bio::SeqIO; use Bio::Seq; use Bio::SeqFeature::Generic; $seq="agaagcgcaccgcacccgcgagcgccttcgccgcgggccctttcg"; $seqout=Bio::SeqIO->new('-fh' => \*STDOUT, '-format' => 'embl'); $seqobj=Bio::Seq->new('-seq' => $seq); #@xrefs=("GOA:Q8FUL7","HSSP:1J1V","InterPro:IPR001957"); $feature=Bio::SeqFeature::Generic->new(-start => 10, -end => 20, -strand => 1, -primary => 'RBS', -tag => { # db_xref=> \@xrefs db_xref => "GOA:Q8FUL7", db_xref => "HSSP:1J1V", db_xref => "InterPro:IPR001957" } ); $seqobj->add_SeqFeature($feature); $seqout->write_seq($seqobj); ### end script ### From chen_li3 at yahoo.com Fri Nov 4 09:54:47 2005 From: chen_li3 at yahoo.com (chen li) Date: Fri Nov 4 10:00:00 2005 Subject: [Bioperl-l] PPM and repository Message-ID: <20051104145448.75146.qmail@web30805.mail.mud.yahoo.com> Dear all, I use ActivePerl under windows XP. I would like PPM to search a specific and new added repository instead of the default one. I follow the commands and add a new repository as following: rep add Bioperl http://bioperl.org/DIST After that I check and make sure the new repository is on the list. Then I inactivate others except the new added one. I type on the command line: search Bioperl. I get Bioperl module show up. But to my surprise PPM always check the default one which comes from ActiveState. So my question: which repository does PPM really search now? Why does PPM always search the default one even it is inactivated? Thanks, Li __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From jason.stajich at duke.edu Fri Nov 4 10:02:35 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 4 10:01:18 2005 Subject: [Bioperl-l] Need help: RemoteBlast Problem In-Reply-To: <436B4958.5070104@gmx.net> References: <436B4958.5070104@gmx.net> Message-ID: <73479E1E-61F1-48BD-9898-C112FB461599@duke.edu> You can request the XML format and it should work fine. my $remote_blastxml = Bio::Tools::Run::RemoteBlast->new ('-verbose' => $v, '-prog' => $prog, '-data' => $db, '-readmethod' => 'xml', # this tells the parser to use blastxml format for parsing '-expect' => $e_val, ); $remote_blastxml->retrieve_parameter('FORMAT_TYPE', 'XML'); # this tells NCBI to send you XML back There is code in the test file t/RemoteBlast.t test which does this as an example. As I think I posted to the mailing list when we were making these changes to support more of the API - I think in Aug or Sept. NCBI has said, they reserves the right to make the HTML & text output from the CGI unparseable so they can insert all the fancy links.... When/ if this has happened we will need to just disable HTML and plain text parsing all together with this module and force everything to use XML. Someone else can do this, I do not intend to maintain this module (I've been saying this for years and yet I'm still working on it...) as I don't use it and people can use blastcl3 to achieve the same things. Can someone help out and make sure this documentation and information makes it to the RemoteBlast module and the FAQ? -jason On Nov 4, 2005, at 6:43 AM, Stefan W?chter wrote: > Hi, > > I wrote a Perl script a year ago. It use a few bioperl modules, one of > them is RemoteBlast. This script worked fine until the beginning of > september :-) . > Read the articles in this news group I found out, that there happened > some changes at the NCBI. Ok. > So I installed bioperl-1.5.1 yesterday and run the script. First, it > seemed to work fine, but suddenly it broke with this message: > > ------------- EXCEPTION ----------- > MSG: no data for midline Features flanking this part of subject > sequence: > STACK Bio::SearchIO::blast::next_result > /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1172 > STACK main::RemoteBlast ./cDNAComparer.pl:1223 > STACK main::runAnalyse ./cDNAComparer.pl:373 > STACK toplevel ./cDNAComparer.pl:1411 > > -------------------------------------- > > When I blast the Sequence directly at NCBI I found in the result page > the line that seems to cause this break: > > >> gi|61216116|ref|NG_001019.4| > query.fcgi? >> cmd=Retrieve&db=Nucleotide&list_uids=61216116&dopt=GenBank> Geo >> > db=geo&term=61216116%5Bgi%5D>Download subject sequence spanning >> the HSP > db=nr&na=1&gnl=ref%7CNG_001019.4% >> 7C&gi=61216116&RID=1131096982-21134-187861614975.BLASTQ3&QUERY_NUMBER >> =1&segs=1057787-1058431,1159074-1159718,1085947-1086591,1182734-11833 >> 78,1201786-1202430,1057611-1057679,1085771-1085839,1182558-1182626,12 >> 01610-1201678,1158898-1158963> Homo sapiens immunoglobulin heavy >> locus (IGH@) on chromosome >> > 14 > Length=1279711 > > Features flanking this part of subject sequence: > 498 bp at 5' side: immunoglobulin heavy constant gamma 3 (G3m > marker), membr... val=61216116&db=Nucleotide&from=1051799&to=1057290&view=gbwithparts> > 21702 bp at 3' side: CDS viewer.fcgi? > val=61216116&db=Nucleotide&from=1080134&to=1081731&view=gbwithparts> > > Score = 1235 bits (623), Expect = 0.0 > Identities = 641/646 (99%), Gaps = 1/646 (0%) > Strand=Plus/Plus > > Query 69 > GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 128 > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > Sbjct 1057788 > GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 1057847 > > Query 129 > GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 188 > > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| > Sbjct 1057848 > GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 1057907 > > Query 189 > CAGCACCACCCCTTGGCTGCCTGCCTACACNTGCTGGATTCTCGGGTGGAACTCGACCCG 248 > > > What can I do to fix this problem ? Any ideas ? > > Cheers > Stefan > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From hlapp at gmx.net Fri Nov 4 11:03:00 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri Nov 4 11:02:03 2005 Subject: [Bioperl-l] Multiple tags of same name in a Bio::SeqFeature::Generic object In-Reply-To: <1131111735.5063.14.camel@jic51958.jic.bbsrc.ac.uk> References: <1131111735.5063.14.camel@jic51958.jic.bbsrc.ac.uk> Message-ID: <7d78b8b18c45dbc24fcc1488ac1e168f@gmx.net> You add values to a tag by calling the feature's add_tag_value() method: $feature->add_tag_value('dbxref',"blah:X362376"); On Nov 4, 2005, at 5:42 AM, Govind Chandra wrote: > Hi, > > I wish to assign multiple tags of the same name in a > Bio::SeqFeature::Generic object. What I am doing below does not work. I > did not expect it to. What I get is: > > FT /db_xref="InterPro:IPR001957" > > If I pass a reference to an array to a single db_xref tag, that does > not > work either. I get: > > FT /db_xref="ARRAY(0x841da94)" > > If I pick up a feature from an embl file (rather than build my own) > which has multiple db_xref tags and add it to my sequence using > add_SeqFeature I do get multiple db_xref tags in the output. So I > conclude that I am not building the Bio::SeqFeature::Generic object > right. > > Could someone help me with this please. I am using BioPerl 1.4.0. > > Thanks > > Govind > > Govind Chandra > Microbiology > John Innes Centre > Norwich UK. > > > > ### begin script ### > use Bio::SeqIO; > use Bio::Seq; > use Bio::SeqFeature::Generic; > > $seq="agaagcgcaccgcacccgcgagcgccttcgccgcgggccctttcg"; > > $seqout=Bio::SeqIO->new('-fh' => \*STDOUT, '-format' => 'embl'); > > $seqobj=Bio::Seq->new('-seq' => $seq); > > #@xrefs=("GOA:Q8FUL7","HSSP:1J1V","InterPro:IPR001957"); > > $feature=Bio::SeqFeature::Generic->new(-start => 10, > -end => 20, > -strand => 1, > -primary => 'RBS', > -tag => { > # db_xref=> \@xrefs > db_xref => "GOA:Q8FUL7", > db_xref => "HSSP:1J1V", > db_xref => "InterPro:IPR001957" > } > ); > $seqobj->add_SeqFeature($feature); > $seqout->write_seq($seqobj); > > ### end script ### > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From s_waechter at gmx.net Fri Nov 4 05:07:51 2005 From: s_waechter at gmx.net (=?ISO-8859-1?Q?Stefan_W=E4chter?=) Date: Fri Nov 4 11:17:16 2005 Subject: [Bioperl-l] Need help: RemoteBlast Problem Message-ID: <436B32F7.1020005@gmx.net> Hi, I wrote a Perl script a year ago. It use a few bioperl modules, one of them is RemoteBlast. This script worked fine until the beginning of september :-) . Read the articles in this news group I found out, that there happened some changes at the NCBI. Ok. So I installed bioperl-1.5.1 yesterday and run the script. First, it seemed to work fine, but suddenly it broke with this message: ------------- EXCEPTION ----------- MSG: no data for midline Features flanking this part of subject sequence: STACK Bio::SearchIO::blast::next_result /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1172 STACK main::RemoteBlast ./cDNAComparer.pl:1223 STACK main::runAnalyse ./cDNAComparer.pl:373 STACK toplevel ./cDNAComparer.pl:1411 -------------------------------------- When I blast the Sequence directly at NCBI I found in the result page the line that seems to cause this break: >gi|61216116|ref|NG_001019.4| Geo Download subject sequence spanning the HSP Homo sapiens immunoglobulin heavy locus (IGH@) on chromosome 14 Length=1279711 Features flanking this part of subject sequence: 498 bp at 5' side: immunoglobulin heavy constant gamma 3 (G3m marker), membr... 21702 bp at 3' side: CDS Score = 1235 bits (623), Expect = 0.0 Identities = 641/646 (99%), Gaps = 1/646 (0%) Strand=Plus/Plus Query 69 GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 128 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1057788 GCCCGCAGCCAGCCAGCCTCCATTCCGGGCACTCCCGTGAACTCCTGACATGAGGAATGA 1057847 Query 129 GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 188 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1057848 GGTTGTTCTGATTTCAAGCAAAGAACGCTGCTCTCTGGCTCCTGGGAACAGTCTCGGTGC 1057907 Query 189 CAGCACCACCCCTTGGCTGCCTGCCTACACNTGCTGGATTCTCGGGTGGAACTCGACCCG 248 What can I do to fix this problem ? Any ideas ? Cheers Stefan -------------- next part -------------- Skipped content of type multipart/related From jason.stajich at duke.edu Fri Nov 4 11:19:48 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 4 11:18:24 2005 Subject: [Bioperl-l] Bio::Tools::RepeatMasker typo? In-Reply-To: <4368F460.3070202@infobiogen.fr> References: <4368F460.3070202@infobiogen.fr> Message-ID: Nice - thanks for seeing/reporting that. Fixed in CVS now. No reason that this can't just be two new calls though, I'm condensing the code a little. My commit diff is here: http://portal.open-bio.org/pipermail/bioperl-guts-l/2005-November/ 020113.html - jason On Nov 2, 2005, at 12:16 PM, Emmanuel Quevillon wrote: > Hi, > > I just played with RepeatMasker module to parse output and create > GFF3. > I noticed there is (I am not sure if it is a typo or it is wanted) > mistyped line in > function next_result() : > > my $rf = Bio::SeqFeature::Generic->new; > $rf->seq_id ($query_name); > $rf->score ($score); > $rf->start ($query_start); > $rf->end ($query_end); > $rf->strand ($strand); > $rf->source_tag ("RepeatMasker"); > $rf->primary_tag ($repeat_class); > my $rf2 = Bio::SeqFeature::Generic->new; > $rf2->seq_id ($repeat_name); > $rf2->score ($score); > $rf2->start ($hit_start); > $rf2->end ($hit_end); > $rf2->strand ($strand); > $rf2->source_tag ("RepeatMasker"); $rf- > >primary_tag ($repeat_class); <=========== Would not be > $rf2 instead? > > Please let me know. > > Thanks > > Regards > > Emmanuel > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jason.stajich at duke.edu Fri Nov 4 11:30:39 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 4 11:29:12 2005 Subject: [Bioperl-l] Failed to load tigr xml files through Bio::Seq::tigr In-Reply-To: <43693F73.7030103@yale.edu> References: <43693F73.7030103@yale.edu> Message-ID: Josh will have to chime in.... I don't know that Bio::SeqIO::tigr can parse all the different flavors from TIGR, but I believe it was written particularly for the rice data and maybe not for the version 3. Can you figure out what is different in the version 3 over previous version of the TIGR format? If I remember correctly the module was written with regexps instead of an XML parser so I think it is pretty brittle to changes. We may want to try and re-write it with XML::SAX or another XML parser - I have written tigrxml for a different TIGR XML flavor in this way. But we need someone to volunteer to help do this sort of thing.... In this case I think you need to submit a bug rather than posting the huge file to the mailing list. http://bugzilla.open-bio.org -jason On Nov 2, 2005, at 5:36 PM, Kun He wrote: > Dear all, > > I have just tried to use the Bio::Seq::tigr module (BioPerl 1.5.1) > to import information from TIGR Rice version 3 XML format > pseudochromosome data, but it always failed on the loading > (initiating) procedure. > > " > use strict; > use Bio::SeqIO; > > my $file=shift; > > print $file,"\n"; > my $io = Bio::SeqIO->new(-file => "<$file", -format => "tigr" ); > " > > There are a lot kinds of errors thrown out, based on different XML > files. Attached is a sample xml from tigr, who can kindly help me > to try if you can load it by the tigr.pm module? Thanks a lot! > > Kun He > [snip out XML, save bits!] -- Jason Stajich Duke University http://www.duke.edu/~jes12 From papadop at uga.edu Fri Nov 4 10:08:52 2005 From: papadop at uga.edu (Chris Papadopoulos) Date: Fri Nov 4 11:38:15 2005 Subject: [Bioperl-l] Bioperl-ext (staden::read) install issues Message-ID: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> Hi all, Running bioperl 1.4 on Mac OS 10.4.2. Installed the Inline modules, copied .h files to /usr/local/include/ io_lib/ Here's the directory, probably has more than it needs (just got frustrated and dumped 'em all): papadop:/usr/local/include/io_lib>ls Read.h compression.h open_trace_file.h tar_format.h abi.h config.h os.h traceType.h acconfig.h error.h plain.h translate.h alf.h expFileIO.h scf.h xalloc.h array.h fpoint.h scf_extras.h ztr.h calc_crc.h mach-io.h seqIOABI.h compress.h misc.h seqIOCTF.h For brevity's sake, please refer to the message dated Thu Apr 1 13:02:01 EST 2004 from Barry Moore entitled: [Bioperl-l] Trouble installing bioperl-ext / Bio::SeqIO::staden::read I'm having the exact same problem and my make output is virtually identical. I specified the location of IOLIB_LIB and IOLIB_INC for Makefile.PL as suggested. I would appreciate anyone's help here. Thanks, Chris Papadopoulos From cy200 at gen.cam.ac.uk Fri Nov 4 11:20:10 2005 From: cy200 at gen.cam.ac.uk (Chihiro Yamada) Date: Fri Nov 4 11:39:57 2005 Subject: [Bioperl-l] noob Bio::DB::Biblio problem In-Reply-To: References: Message-ID: <1131121210.15569.28.camel@leona.gen.cam.ac.uk> On Wed, 2005-11-02 at 04:42 -0500, Brian Osborne wrote: > Chihiro, > > What happens when you set the access mode to "soap" or "eutils" rather than > to "biofetch"? and On Wed, 2005-11-02 at 18:54 +0900, t-nakazato@muj.biglobe.ne.jp wrote: > If you don't need to use "biofetch" protocol, try "eutils". > > use Bio::Biblio; > my $biblio = new Bio::Biblio (-access => 'eutils'); # biofetch -> > eutils > my $ref = $biblio->get_by_id('15519282'); > > -- Thanks guys, Ah, so I guess, soap and eutils are newer modules. I can get them to work on my mac (Bioperl 1.5.1) But not on the Sun Boxes running 1.3. (Which I don't have root access to) I'll hassle my sysadmin to install a newer version. From the doc it looks like we'll need 1.5 - is that right? Incidentally, is either method (soap or eutils) 'better' than the other? Cheers, Chihiro P.S. nice to hear from you Brian! c;y -------------------------------------- > Brian O. > > > On 10/31/05 9:19 AM, "Chihiro Yamada" wrote: > > > Hiya folks, > > > > I'm trying to use the Bio::DB::Biblio::biofetch module to get references > > by ID, but I'm having a problem... > > > > If I run this code... > > > > use Bio::Biblio; > > my $biblio = new Bio::Biblio (-access => 'biofetch'); > > my $ref = $biblio->get_by_id('15519282'); > > > > I get the error message: > > > > ------------- EXCEPTION ------------- > > MSG: retrieval type pipeline unsupported > > > > STACK > > Bio::DB::Biblio::biofetch::get_seq_stream > > /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:237 > > STACK > > Bio::DB::DBFetch::get_Stream_by_id > > /opt/csw/share/perl/site_perl/Bio/DB/DBFetch.pm:194 > > STACK > > Bio::DB::Biblio::biofetch::get_by_id > > /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:153 > > STACK toplevel bbt4.pl:7 > > > > -------------------------------------- > > > > I've tried this on 1.3 (on Solaris) and 1.5.1 (using OS X) and get the > > same error message. > > > > Can anyone tell me what I'm doing wrong? > > > > Thanks > > > > Chihiro > > -- ---------------------------------------------------------------------- Chihiro Yamada. FlyBase (Cambridge), http://www.FlyBase.org/ Department of Genetics, University of Cambridge, email: c.yamada@gen.cam.ac.uk Downing Street, Tel : 01223-333963 Cambridge, CB2 3EH, FAX : 01223-333992 United Kingdom. Memes don't exist. Spread the Word. ---------------------------------------------------------------------- From jason.stajich at duke.edu Fri Nov 4 10:05:39 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 4 12:41:06 2005 Subject: [Bioperl-l] Multiple tags of same name in a Bio::SeqFeature::Generic object In-Reply-To: <1131111735.5063.14.camel@jic51958.jic.bbsrc.ac.uk> References: <1131111735.5063.14.camel@jic51958.jic.bbsrc.ac.uk> Message-ID: I think you need to do it in multiple steps per value. The 1.5.1 code will accept an array of values but I suspect that 1.4.0 only accepted one at a time Does this work for you? $feature->add_tag_value('db_xref', "InterPro:IPR001957"); $feature->add_tag_value('db_xref', "EMBL:AC123456"); On Nov 4, 2005, at 8:42 AM, Govind Chandra wrote: > Hi, > > I wish to assign multiple tags of the same name in a > Bio::SeqFeature::Generic object. What I am doing below does not > work. I > did not expect it to. What I get is: > > FT /db_xref="InterPro:IPR001957" > > If I pass a reference to an array to a single db_xref tag, that > does not > work either. I get: > > FT /db_xref="ARRAY(0x841da94)" > > If I pick up a feature from an embl file (rather than build my own) > which has multiple db_xref tags and add it to my sequence using > add_SeqFeature I do get multiple db_xref tags in the output. So I > conclude that I am not building the Bio::SeqFeature::Generic object > right. > > Could someone help me with this please. I am using BioPerl 1.4.0. > > Thanks > > Govind > > Govind Chandra > Microbiology > John Innes Centre > Norwich UK. > > > > ### begin script ### > use Bio::SeqIO; > use Bio::Seq; > use Bio::SeqFeature::Generic; > > $seq="agaagcgcaccgcacccgcgagcgccttcgccgcgggccctttcg"; > > $seqout=Bio::SeqIO->new('-fh' => \*STDOUT, '-format' => 'embl'); > > $seqobj=Bio::Seq->new('-seq' => $seq); > > #@xrefs=("GOA:Q8FUL7","HSSP:1J1V","InterPro:IPR001957"); > > $feature=Bio::SeqFeature::Generic->new(-start => 10, > -end => 20, > -strand => 1, > -primary => 'RBS', > -tag => { > # db_xref=> \@xrefs > db_xref => "GOA:Q8FUL7", > db_xref => "HSSP:1J1V", > db_xref => "InterPro:IPR001957" > } > ); > $seqobj->add_SeqFeature($feature); > $seqout->write_seq($seqobj); > > ### end script ### > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From senger at ebi.ac.uk Fri Nov 4 12:27:32 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri Nov 4 12:41:30 2005 Subject: [Bioperl-l] noob Bio::DB::Biblio problem Message-ID: > What happens when you set the access mode to "soap" > By default, it will go to the MEDLINE database running at EBI, using Web Service protocol. The protocol itself is hidden, but this implementtaion has more methods than the others - for example you can get also a list of available attributes that can be used in the search. The details about this module is best to find by running scripts/biblio/biblio.PLS -h > Ah, so I guess, soap and eutils are newer modules > Actually, soap is the oldest one, this was the first module for fetching biblio information. Cheers, Martin -- Martin Senger email: martin.senger@gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From bli1 at bcm.tmc.edu Fri Nov 4 14:18:05 2005 From: bli1 at bcm.tmc.edu (Bingshan Li) Date: Fri Nov 4 14:39:09 2005 Subject: [Bioperl-l] Bio::PopGen modules performance Message-ID: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> Hi all, I used Bio::PopGen modules to calculate various statistics such as Tajima's D, Pi and so on. For single data, the performance is fine. But to get a sense of significance, I simulated the data using Hudson's "ms" program to generate 10000 simulated populations. When I used Bio::PopGen modules on the 10000 samples, it takes long time (finished 600 samples in about 10 hours, population size about 200, segregating size about 500). If I have a set of data, say 100, for each data I need 10000 simulated populations, I do not think it is doable. I am wondering if it makes sense for these modules or I can increase the performance by optimization of my code. I think 10000 simulations are typical for population genetics analysis. Does any body have experiences with this issue and can anyone give me any suggestions about the performance? Thanks a lot! --bs From jason.stajich at duke.edu Fri Nov 4 15:35:48 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 4 15:34:29 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> References: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> Message-ID: My guess is it has more to do with the object creation/teardown than the actual code calculating the statistics. I'm not entirely sure how we solve this as I chose to use a rich objects so that you can pass lots of different kinds of data in. I wrote simple methods to calc Tajima's D, Fu & Li's D, etc just from the simple counts - see the XX_counts method for more information. For example, for Tajima's D, you can call tajima_D_counts with the # samples, # sites, and pi to just get back D. But of course to calculate pi you need to pass in a population object to the pi method so it doesn't really solve it for you. Maybe we can figure out a way to simplify it, but I embraced the object-oriented here to support a flexible design, but I didn't realize the speed was going to be so bad. You can certainly use Kevin Thornton's msstats which is going to be bazillion (approx.) times faster than the bioperl object code. http://molpopgen.org/software/libsequence_html/libsequence.htm search down for msstats I am hoping someone will have a magic Perl insight on how to do OO better one day - and may that be a day before Perl6! On Nov 4, 2005, at 2:18 PM, Bingshan Li wrote: > Hi all, > > I used Bio::PopGen modules to calculate various statistics such as > Tajima's D, Pi and so on. For single data, the performance is fine. > But to get a sense of significance, I simulated the data using > Hudson's "ms" program to generate 10000 simulated populations. When > I used Bio::PopGen modules on the 10000 samples, it takes long time > (finished 600 samples in about 10 hours, population size about 200, > segregating size about 500). If I have a set of data, say 100, for > each data I need 10000 simulated populations, I do not think it is > doable. I am wondering if it makes sense for these modules or I can > increase the performance by optimization of my code. I think 10000 > simulations are typical for population genetics analysis. Does any > body have experiences with this issue and can anyone give me any > suggestions about the performance? > > Thanks a lot! > > --bs > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From avilella at ub.edu Fri Nov 4 16:29:45 2005 From: avilella at ub.edu (Albert Vilella) Date: Fri Nov 4 16:46:01 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: References: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> Message-ID: <1131139785.7997.12.camel@localhost.localdomain> If your datasets are annotations inside large syntenic regions (MBp-GBp scale) and you are interested in sliding windows/Multiresolution analysis... you may be interested in trying VariScan: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15814564&query_hl=1 otherwise, for "gene-like" sequences (Kbp-MBp scale), Kevin's libsequence+analyse is a fantastic tool, and I believe the best choice. Cheers, Albert. El dv 04 de 11 del 2005 a les 15:35 -0500, en/na Jason Stajich va escriure: > My guess is it has more to do with the object creation/teardown than > the actual code calculating the statistics. I'm not entirely sure > how we solve this as I chose to use a rich objects so that you can > pass lots of different kinds of data in. > > I wrote simple methods to calc Tajima's D, Fu & Li's D, etc just from > the simple counts - see the XX_counts method for more information. > > For example, for Tajima's D, you can call tajima_D_counts with the # > samples, # sites, and pi to just get back D. But of course to > calculate pi you need to pass in a population object to the pi method > so it doesn't really solve it for you. Maybe we can figure out a way > to simplify it, but I embraced the object-oriented here to support a > flexible design, but I didn't realize the speed was going to be so bad. > > > You can certainly use Kevin Thornton's msstats which is going to be > bazillion (approx.) times faster than the bioperl object code. > http://molpopgen.org/software/libsequence_html/libsequence.htm > search down for msstats > > I am hoping someone will have a magic Perl insight on how to do OO > better one day - and may that be a day before Perl6! > > > > On Nov 4, 2005, at 2:18 PM, Bingshan Li wrote: > > > Hi all, > > > > I used Bio::PopGen modules to calculate various statistics such as > > Tajima's D, Pi and so on. For single data, the performance is fine. > > But to get a sense of significance, I simulated the data using > > Hudson's "ms" program to generate 10000 simulated populations. When > > I used Bio::PopGen modules on the 10000 samples, it takes long time > > (finished 600 samples in about 10 hours, population size about 200, > > segregating size about 500). If I have a set of data, say 100, for > > each data I need 10000 simulated populations, I do not think it is > > doable. I am wondering if it makes sense for these modules or I can > > increase the performance by optimization of my code. I think 10000 > > simulations are typical for population genetics analysis. Does any > > body have experiences with this issue and can anyone give me any > > suggestions about the performance? > > > > Thanks a lot! > > > > --bs > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Fri Nov 4 17:41:34 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Fri Nov 4 17:37:30 2005 Subject: [Bioperl-l] PPM and repository Message-ID: Li- I've noticed a similar annoyance with ppm. If you have bioperl1-1.4 listed from two different repositories how do you know which is from which as repositories are listed in search results. However, I was always able to just turn off unwanted repositories and have things work as expected, so I'm not real sure what to tell you there. You could delete repositories completely, but be careful deleteing the ActiveState reps as I did that and couldn't get them back correctly. Sorry I'm not more help. Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of chen li > Sent: Friday, November 04, 2005 7:55 AM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] PPM and repository > > Dear all, > > I use ActivePerl under windows XP. I would like PPM to > search a specific and new added repository instead of > the default one. I follow the commands and add a new > repository as following: > > rep add Bioperl http://bioperl.org/DIST > > After that I check and make sure the new repository is > on the list. Then I inactivate others except the new > added one. I type on the command line: > search Bioperl. I get Bioperl module show up. But to > my surprise PPM always check the default one which > comes from ActiveState. > > So my question: which repository does PPM really > search now? Why does PPM always search the default one > even it is inactivated? > > Thanks, > > Li > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Fri Nov 4 17:29:59 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Fri Nov 4 17:37:57 2005 Subject: [Bioperl-l] install binary bioperl-1.4 on windows Message-ID: Anders- http://bioperl.org/Core/Latest/INSTALL.WIN Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of Anders Stegmann > Sent: Friday, October 28, 2005 8:34 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] install binary bioperl-1.4 on windows > > Hi BioPerl! > > I have downloaded the binary windows BioPerl-1.4 version > unzipped it and run perl Makefile.Pl > > It tells me everything looks good and I should be able to use it after > typing: make install > > but I get: 'make' is not recognized as an internal or external command, > operable program of batch file > > I guess I can't use make, but what then? I have tried a lot of different > commands with the same result > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jay at jays.net Fri Nov 4 17:15:44 2005 From: jay at jays.net (Jay Hannah) Date: Fri Nov 4 18:10:36 2005 Subject: [Bioperl-l] Fwd: "Volunteers needed" Message-ID: > Volunteers needed > Bioperl is run by volunteers from all over the world, with many types > of backgrounds. Any contributions of Perl code, html, documentation > writing or code testing are very welcome. Contact > bioperl-l@bioperl.org for more information. Hello -- I've been a Perl/database hacker for 10 years, and am trying to find out how best I can help genetics research. I saw your request above, so am throwing my name into your hat if you want to try throwing me into a project or twelve. Hoping I can help, Jay Hannah Omaha, NE Omaha Perl Mongers (http://omaha.pm.org) From jay at jays.net Fri Nov 4 17:10:07 2005 From: jay at jays.net (Jay Hannah) Date: Fri Nov 4 18:10:37 2005 Subject: [Bioperl-l] Re: "Volunteers needed" In-Reply-To: <33755cc4bcf41ee481f0935fbe1b5a96@jays.net> References: <33755cc4bcf41ee481f0935fbe1b5a96@jays.net> Message-ID: <41a3b2dfef86d1a554eaa6edc4b99c62@jays.net> > Volunteers needed > Bioperl is run by volunteers from all over the world, with many types > of backgrounds. Any contributions of Perl code, html, documentation > writing or code testing are very welcome. Contact > bioperl-l@bioperl.org for more information. Hello -- I've been a Perl/database hacker for 10 years, and am trying to find out how best I can help genetics research. I saw your request above, so am throwing my name into your hat if you want to try throwing me into a project or twelve. Hoping I can help, Jay Hannah Omaha, NE Omaha Perl Mongers (http://omaha.pm.org) From bli1 at bcm.tmc.edu Fri Nov 4 18:35:15 2005 From: bli1 at bcm.tmc.edu (Bingshan Li) Date: Fri Nov 4 18:33:48 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: <1131139785.7997.12.camel@localhost.localdomain> References: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> <1131139785.7997.12.camel@localhost.localdomain> Message-ID: <2A930325-8272-4AA2-96E0-48C8025ED54D@bcm.tmc.edu> Hi Jason and Albert, Thanks for the quick response. Actually the data are gene-like sequences so I decide to implement a C++ code or perl code myself for calculating various statistics. I haven't touched C++ programming for a long time. So I want to to try perl first and hope it works fine. As Jason pointed out, I may only need to calculate pi value (by my code, not Bioperl to increase speed) and pass it to XX_count() functions. I believe that the performance issue is not the calculation at all. It takes most of time to construct various objects, and in most of the functions, various objects are accessed to do the final calculation. I mean it takes a detour to get the final destination. Bioperl is very useful and convenient for small data set. But for larger data set, code must be optimized as performance instead of reusability is more important. Thanks and have a nice weekend! ;-) --bs On Nov 4, 2005, at 3:29 PM, Albert Vilella wrote: > If your datasets are annotations inside large syntenic regions (MBp- > GBp > scale) and you are interested in sliding windows/Multiresolution > analysis... > > > you may be interested in trying VariScan: > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? > cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15814564&query_hl=1 > > > otherwise, for "gene-like" sequences (Kbp-MBp scale), Kevin's > libsequence+analyse is a fantastic tool, and I believe the best > choice. > > Cheers, > > Albert. > > El dv 04 de 11 del 2005 a les 15:35 -0500, en/na Jason Stajich va > escriure: > >> My guess is it has more to do with the object creation/teardown than >> the actual code calculating the statistics. I'm not entirely sure >> how we solve this as I chose to use a rich objects so that you can >> pass lots of different kinds of data in. >> >> I wrote simple methods to calc Tajima's D, Fu & Li's D, etc just from >> the simple counts - see the XX_counts method for more information. >> >> For example, for Tajima's D, you can call tajima_D_counts with the # >> samples, # sites, and pi to just get back D. But of course to >> calculate pi you need to pass in a population object to the pi method >> so it doesn't really solve it for you. Maybe we can figure out a way >> to simplify it, but I embraced the object-oriented here to support a >> flexible design, but I didn't realize the speed was going to be so >> bad. >> >> >> You can certainly use Kevin Thornton's msstats which is going to be >> bazillion (approx.) times faster than the bioperl object code. >> http://molpopgen.org/software/libsequence_html/libsequence.htm >> search down for msstats >> >> I am hoping someone will have a magic Perl insight on how to do OO >> better one day - and may that be a day before Perl6! >> >> >> >> On Nov 4, 2005, at 2:18 PM, Bingshan Li wrote: >> >> >>> Hi all, >>> >>> I used Bio::PopGen modules to calculate various statistics such as >>> Tajima's D, Pi and so on. For single data, the performance is fine. >>> But to get a sense of significance, I simulated the data using >>> Hudson's "ms" program to generate 10000 simulated populations. When >>> I used Bio::PopGen modules on the 10000 samples, it takes long time >>> (finished 600 samples in about 10 hours, population size about 200, >>> segregating size about 500). If I have a set of data, say 100, for >>> each data I need 10000 simulated populations, I do not think it is >>> doable. I am wondering if it makes sense for these modules or I can >>> increase the performance by optimization of my code. I think 10000 >>> simulations are typical for population genetics analysis. Does any >>> body have experiences with this issue and can anyone give me any >>> suggestions about the performance? >>> >>> Thanks a lot! >>> >>> --bs >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> >> -- >> Jason Stajich >> Duke University >> http://www.duke.edu/~jes12 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > From birney at ebi.ac.uk Sat Nov 5 05:50:03 2005 From: birney at ebi.ac.uk (Ewan Birney) Date: Sat Nov 5 06:08:28 2005 Subject: [Bioperl-l] Re: "Volunteers needed" In-Reply-To: <41a3b2dfef86d1a554eaa6edc4b99c62@jays.net> References: <33755cc4bcf41ee481f0935fbe1b5a96@jays.net> <41a3b2dfef86d1a554eaa6edc4b99c62@jays.net> Message-ID: <436C8E5B.9040904@ebi.ac.uk> Jay Hannah wrote: >> Volunteers needed >> Bioperl is run by volunteers from all over the world, with many types >> of backgrounds. Any contributions of Perl code, html, documentation >> writing or code testing are very welcome. Contact >> bioperl-l@bioperl.org for more information. > > > Hello -- > > I've been a Perl/database hacker for 10 years, and am trying to find out > how best I can help genetics research. I saw your request above, so am > throwing my name into your hat if you want to try throwing me into a > project or twelve. > welcome on board - have you tried out BioPerl? It is a rather large project and definitely there are some un-cared for areas that need some TLC. I guess Jason or Aaron might have some ideas, but a good starting place is to download bioperl, go make test and also look at the start of the tutorial. I have no doubt that you'll spot some sub-optimal things on teh way Once that's done I'm not 100% sure where is a good place to start: DB access of some other internet accessible sequence databases? > Hoping I can help, > > Jay Hannah > Omaha, NE > Omaha Perl Mongers (http://omaha.pm.org) > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jay at jays.net Sat Nov 5 12:08:32 2005 From: jay at jays.net (Jay Hannah) Date: Sat Nov 5 12:25:30 2005 Subject: [Bioperl-l] Re: "Volunteers needed" In-Reply-To: <436C8E5B.9040904@ebi.ac.uk> References: <33755cc4bcf41ee481f0935fbe1b5a96@jays.net> <41a3b2dfef86d1a554eaa6edc4b99c62@jays.net> <436C8E5B.9040904@ebi.ac.uk> Message-ID: <481e94f3e11e4a3253e83f83c7458b86@jays.net> On Nov 5, 2005, at 4:50 AM, Ewan Birney wrote: > welcome on board - have you tried out BioPerl? It is a rather large > project > and definitely there are some un-cared for areas that need some TLC. > > I guess Jason or Aaron might have some ideas, but a good starting > place is > to download bioperl, go make test and also look at the start of the > tutorial. > I have no doubt that you'll spot some sub-optimal things on teh way > > Once that's done I'm not 100% sure where is a good place to start: DB > access > of some other internet accessible sequence databases? I suspect I may be good at wrestling/smoothing installs, test scripts, POD, etc. I have access to Mac OS X, 3 flavors of Linux, and AIX. I'm no porting guru, but I'm strong in general Perl, test scripts, CPAN installs, web/Internet coding, databases, Apache, Linux, etc. If those skills are needed in the Bioperl community I'd be happy to take a stab at submitting various patches or tackling whatever. The other side of my equation is that I'm thoroughly ignorant in biology and genetics. For 10 years I've been data crunching / web portaling / e-commercing for companies that have nothing to do with this new "hobby." I am, however, committed to learning if I can find a niche somewhere in which I can help, no matter how small the contribution. I've picked up a few books and am consuming those as time allows. Turns out genetics and biology are complicated. Who knew? -grin- It would be fantastic if I could find a local lab that could use my help (Omaha, NE USA). Luckily my skills telecommute fairly easily, so if any scientist genius type anywhere wants some slave labor I'd happily do their bidding under their wing. Programming, databases, and Internet interaction are my forte. Unfortunately I'm guessing my lack of bio skills render my programming skills unusable for much of the work going on...? Anyway, I'm just very motivated to help someone doing genetic research for the greater good. It would be a great feeling to know that maybe someday my labor may help produce something that will help people. I've been working for money for 10 years now, and am attempting a shift in focus. Part time. -grin- I hope I can help. Jay Hannah Omaha, NE mobile: 402-578-3976 From chen_li3 at yahoo.com Sat Nov 5 20:20:49 2005 From: chen_li3 at yahoo.com (chen li) Date: Sat Nov 5 20:19:27 2005 Subject: [Bioperl-l] bioperl-db and MySQL Message-ID: <20051106012049.54727.qmail@web30801.mail.mud.yahoo.com> Hello everyone, I want to install bioperl-db on my windows XP with ActivePerl. I read the HOWTOs about installing( http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/HOWTO-MySQL.html). But I failed to do the nmake test. Then I read the HOWTOs again, which points out that install will fail if the DBD:: and DBI::Mysql modules cannot be found. On my PC MySQL, Perl, and Bioperl-db are kept in different directory. I use PPM to install DBD::Mysql and DBI::Mysql. I install MySQL using binary code. My question: Where should I keep the Bioperl-db including bioperl-schema so that installation will succeed? Thanks, Li __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From jason.stajich at duke.edu Sun Nov 6 13:07:51 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sun Nov 6 13:06:23 2005 Subject: [Bioperl-l] Bioperl-ext (staden::read) install issues In-Reply-To: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> References: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> Message-ID: <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> In os.h did you change #include to #include "config.h" This made a difference for me. Make sure the the compile commands are actually point to the right include path. i.e. make sure this is correct: -IPATH/TO/IOLIB/INCLUDE/io_lib in the gcc stmt below (for your system) gcc -c -I/home/jes12/src/bioperl/bioperl-ext-1.5.1/Bio/SeqIO/staden - IPATH/TO/IOLIB/INCLUDE/io_lib -D_REENTRANT -D_GNU_SOURCE -DDEBUGGING - fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE - D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wp,- D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 -mtune=pentium4 - fasynchronous-unwind-tables -DVERSION=\"1.51\" -DXS_VERSION=\"1.51 \" -fPIC "-I/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE" read.c There appears to be some complaints from Inline::C about version numbers not matching and not being parseable. I just changed things to "1.50" instead of "1.5.1" and made sure that in read.pm the code looks like this: use Inline (C => 'DATA', VERSION => '1.51', NAME => 'Bio::SeqIO::staden::read', instead of this: use Inline (C => 'DATA', VERSION => '0.1', NAME => 'Bio::SeqIO::staden::read', And further down I made this change $VERSION = 1.51; instead of $VERSION = 1.5; All this to say the ext stuff needs some more TLC to work on different platforms and be more generally installable. -jason On Nov 4, 2005, at 10:08 AM, Chris Papadopoulos wrote: > Hi all, > Running bioperl 1.4 on Mac OS 10.4.2. > Installed the Inline modules, copied .h files to /usr/local/include/ > io_lib/ > Here's the directory, probably has more than it needs (just got > frustrated and dumped 'em all): > papadop:/usr/local/include/io_lib>ls > Read.h compression.h open_trace_file.h tar_format.h > abi.h config.h os.h traceType.h > acconfig.h error.h plain.h translate.h > alf.h expFileIO.h scf.h xalloc.h > array.h fpoint.h scf_extras.h ztr.h > calc_crc.h mach-io.h seqIOABI.h > compress.h misc.h seqIOCTF.h > > For brevity's sake, please refer to the message dated Thu Apr 1 > 13:02:01 EST 2004 from Barry Moore entitled: > [Bioperl-l] Trouble installing bioperl-ext / Bio::SeqIO::staden::read > > I'm having the exact same problem and my make output is virtually > identical. I specified the location of IOLIB_LIB and IOLIB_INC for > Makefile.PL as suggested. > > I would appreciate anyone's help here. > Thanks, > Chris Papadopoulos > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From bobfreemanma at speakeasy.net Sun Nov 6 13:43:41 2005 From: bobfreemanma at speakeasy.net (Bob Freeman) Date: Sun Nov 6 14:10:16 2005 Subject: [Bioperl-l] Bioperl-ext (staden::read) install issues In-Reply-To: <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> References: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> Message-ID: Jason, I remember reading a past posting about the possibility of commenting out the EVAL statement in Bio::SeqIO.pm (lines 315-317): sub BEGIN { # eval { require Bio::SeqIO::staden::read; }; } It certainly does eliminate the runtime error thrown by Perl about Bio::SeqIO::staden::read not being installed correctly. Any comments on whether or not this should be done? Bob At 1:07 PM -0500 11/6/05, Jason Stajich wrote: >In os.h did you change >#include > >to >#include "config.h" > >This made a difference for me. >Make sure the the compile commands are actually point to the right >include path. >i.e. make sure this is correct: -IPATH/TO/IOLIB/INCLUDE/io_lib in >the gcc stmt below (for your system) > >gcc -c -I/home/jes12/src/bioperl/bioperl-ext-1.5.1/Bio/SeqIO/staden >-IPATH/TO/IOLIB/INCLUDE/io_lib -D_REENTRANT -D_GNU_SOURCE >-DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include >-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 >-g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 >-mtune=pentium4 -fasynchronous-unwind-tables -DVERSION=\"1.51\" >-DXS_VERSION=\"1.51\" -fPIC >"-I/usr/lib/perl5/5.8.6/i386-linux-thread-multi/CORE" read.c > > >There appears to be some complaints from Inline::C about version >numbers not matching and not being parseable. I just changed things >to "1.50" instead of "1.5.1" and made sure that in read.pm >the code looks like this: > use Inline (C => 'DATA', > VERSION => '1.51', > NAME => 'Bio::SeqIO::staden::read', > >instead of this: > use Inline (C => 'DATA', > VERSION => '0.1', > NAME => 'Bio::SeqIO::staden::read', > >And further down I made this change >$VERSION = 1.51; > >instead of >$VERSION = 1.5; > > >All this to say the ext stuff needs some more TLC to work on >different platforms and be more generally installable. > >-jason > >On Nov 4, 2005, at 10:08 AM, Chris Papadopoulos wrote: > >>Hi all, >>Running bioperl 1.4 on Mac OS 10.4.2. >>Installed the Inline modules, copied .h files to /usr/local/include/io_lib/ >>Here's the directory, probably has more than it needs (just got >>frustrated and dumped 'em all): >>papadop:/usr/local/include/io_lib>ls >>Read.h compression.h open_trace_file.h tar_format.h >>abi.h config.h os.h traceType.h >>acconfig.h error.h plain.h translate.h >>alf.h expFileIO.h scf.h xalloc.h >>array.h fpoint.h scf_extras.h ztr.h >>calc_crc.h mach-io.h seqIOABI.h >>compress.h misc.h seqIOCTF.h >> >>For brevity's sake, please refer to the message dated Thu Apr 1 >>13:02:01 EST 2004 from Barry Moore entitled: >>[Bioperl-l] Trouble installing bioperl-ext / Bio::SeqIO::staden::read >> >>I'm having the exact same problem and my make output is virtually >>identical. I specified the location of IOLIB_LIB and IOLIB_INC for >>Makefile.PL as suggested. >> >>I would appreciate anyone's help here. >>Thanks, >>Chris Papadopoulos >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > >-- >Jason Stajich >Duke University >http://www.duke.edu/~jes12 > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ----------------------------------------------------- Bob Freeman, Ph.D. Bioinformatics consultant 90 Worcester St., #4 Boston, MA 02118 617/699.7057, vox From jason.stajich at duke.edu Sun Nov 6 17:26:54 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sun Nov 6 17:25:27 2005 Subject: [Bioperl-l] Bioperl-ext (staden::read) install issues In-Reply-To: References: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> Message-ID: <714919DF-DA88-483A-998E-1AE9E9083ADB@duke.edu> On Nov 6, 2005, at 1:43 PM, Bob Freeman wrote: > Jason, > > I remember reading a past posting about the possibility of > commenting out the EVAL statement in Bio::SeqIO.pm (lines 315-317): > > sub BEGIN { > # eval { require Bio::SeqIO::staden::read; }; > } > > It certainly does eliminate the runtime error thrown by Perl about > Bio::SeqIO::staden::read not being installed correctly. Any > comments on whether or not this should be done? > I don't really have any knowledgeable comments about it -- disabling the eval hasn't been necessary for me with or without staden::read installed. Someone who has been bitten by this will have to chime in. > Bob > > At 1:07 PM -0500 11/6/05, Jason Stajich wrote: >> In os.h did you change >> #include >> >> to >> #include "config.h" >> >> This made a difference for me. >> Make sure the the compile commands are actually point to the right >> include path. >> i.e. make sure this is correct: -IPATH/TO/IOLIB/INCLUDE/io_lib in >> the gcc stmt below (for your system) >> >> gcc -c -I/home/jes12/src/bioperl/bioperl-ext-1.5.1/Bio/SeqIO/ >> staden -IPATH/TO/IOLIB/INCLUDE/io_lib -D_REENTRANT -D_GNU_SOURCE - >> DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include - >> D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 - >> g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 - >> mtune=pentium4 -fasynchronous-unwind-tables -DVERSION=\"1.51\" - >> DXS_VERSION=\"1.51\" -fPIC "-I/usr/lib/perl5/5.8.6/i386-linux- >> thread-multi/CORE" read.c >> >> >> There appears to be some complaints from Inline::C about version >> numbers not matching and not being parseable. I just changed >> things to "1.50" instead of "1.5.1" and made sure that in read.pm >> the code looks like this: >> use Inline (C => 'DATA', >> VERSION => '1.51', >> NAME => 'Bio::SeqIO::staden::read', >> >> instead of this: >> use Inline (C => 'DATA', >> VERSION => '0.1', >> NAME => 'Bio::SeqIO::staden::read', >> >> And further down I made this change >> $VERSION = 1.51; >> >> instead of >> $VERSION = 1.5; >> >> >> All this to say the ext stuff needs some more TLC to work on >> different platforms and be more generally installable. >> >> -jason >> >> On Nov 4, 2005, at 10:08 AM, Chris Papadopoulos wrote: >>> Hi all, >>> Running bioperl 1.4 on Mac OS 10.4.2. >>> Installed the Inline modules, copied .h files to /usr/local/ >>> include/io_lib/ >>> Here's the directory, probably has more than it needs (just got >>> frustrated and dumped 'em all): >>> papadop:/usr/local/include/io_lib>ls >>> Read.h compression.h open_trace_file.h tar_format.h >>> abi.h config.h os.h traceType.h >>> acconfig.h error.h plain.h translate.h >>> alf.h expFileIO.h scf.h xalloc.h >>> array.h fpoint.h scf_extras.h ztr.h >>> calc_crc.h mach-io.h seqIOABI.h >>> compress.h misc.h seqIOCTF.h >>> >>> For brevity's sake, please refer to the message dated Thu Apr 1 >>> 13:02:01 EST 2004 from Barry Moore entitled: >>> [Bioperl-l] Trouble installing bioperl-ext / >>> Bio::SeqIO::staden::read >>> >>> I'm having the exact same problem and my make output is virtually >>> identical. I specified the location of IOLIB_LIB and IOLIB_INC >>> for Makefile.PL as suggested. >>> >>> I would appreciate anyone's help here. >>> Thanks, >>> Chris Papadopoulos >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> Jason Stajich >> Duke University >> http://www.duke.edu/~jes12 >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > -- > > ----------------------------------------------------- > Bob Freeman, Ph.D. > Bioinformatics consultant > 90 Worcester St., #4 > Boston, MA 02118 > 617/699.7057, vox > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From bmoore at genetics.utah.edu Mon Nov 7 09:53:43 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Mon Nov 7 09:49:37 2005 Subject: [Bioperl-l] Re: "Volunteers needed" Message-ID: Jay- Jason Stajich, who has been one of the lead developers in bioperl for many years now, mentioned last week that: "Tools::StandAloneBlast could DEFINITELY be improved and needs people to adopt it...." Now what the hell is Tools::StandAloneBlast? Blast (and it's relatives wu-blast and fasta) are probably the most frequently used algorithms in bioinformatics. They take a nucleic acid or protein sequence as input and searches for similar sequences in a large database of sequences. Tools::StandAloneBlast is the module that provides the bioperl interface to a locally running copy of the NCBI Blast tool. NCBI (National Center for Biotechnology Information) has written one version of Blast, and they also maintain a comprehensive database of nucleic acid and protein sequences and sequence related information. Check out the education section of the NCBI website (http://www.ncbi.nlm.nih.gov/Education/) and the Blast handbook http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.610). Install a copy of Blast, install the nr sequence database and get Tools::StandAloneBlast running on one of your machines, and start poking around that code to see if it can use some improving. BTW, In Europe, EBI (European Bioinformatics Institue and the Ensembl project fills a similar niche but from a different angle. It would be worth becoming familiar with their tools as well because their API is often more programmer friendly. Barry P.S. Write a script to use bioperl to blast search the following sequence against a local copy of the nr database and decide what protein it is from and why this protein was your friend last Friday night. MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of Jay Hannah > Sent: Saturday, November 05, 2005 10:09 AM > To: bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Re: "Volunteers needed" > > > On Nov 5, 2005, at 4:50 AM, Ewan Birney wrote: > > welcome on board - have you tried out BioPerl? It is a rather large > > project > > and definitely there are some un-cared for areas that need some TLC. > > > > I guess Jason or Aaron might have some ideas, but a good starting > > place is > > to download bioperl, go make test and also look at the start of the > > tutorial. > > I have no doubt that you'll spot some sub-optimal things on teh way > > > > Once that's done I'm not 100% sure where is a good place to start: DB > > access > > of some other internet accessible sequence databases? > > I suspect I may be good at wrestling/smoothing installs, test scripts, > POD, etc. I have access to Mac OS X, 3 flavors of Linux, and AIX. I'm > no porting guru, but I'm strong in general Perl, test scripts, CPAN > installs, web/Internet coding, databases, Apache, Linux, etc. If those > skills are needed in the Bioperl community I'd be happy to take a stab > at submitting various patches or tackling whatever. > > The other side of my equation is that I'm thoroughly ignorant in > biology and genetics. For 10 years I've been data crunching / web > portaling / e-commercing for companies that have nothing to do with > this new "hobby." I am, however, committed to learning if I can find a > niche somewhere in which I can help, no matter how small the > contribution. I've picked up a few books and am consuming those as time > allows. Turns out genetics and biology are complicated. Who knew? > -grin- > > It would be fantastic if I could find a local lab that could use my > help (Omaha, NE USA). Luckily my skills telecommute fairly easily, so > if any scientist genius type anywhere wants some slave labor I'd > happily do their bidding under their wing. > > Programming, databases, and Internet interaction are my forte. > Unfortunately I'm guessing my lack of bio skills render my programming > skills unusable for much of the work going on...? > > Anyway, I'm just very motivated to help someone doing genetic research > for the greater good. It would be a great feeling to know that maybe > someday my labor may help produce something that will help people. I've > been working for money for 10 years now, and am attempting a shift in > focus. Part time. -grin- > > I hope I can help. > > Jay Hannah > Omaha, NE > mobile: 402-578-3976 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Mon Nov 7 10:39:22 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Nov 7 12:26:16 2005 Subject: [Bioperl-l] Re: "Volunteers needed" In-Reply-To: References: Message-ID: <1CB22038-20A5-4A44-B017-8A5E1BDD20DC@duke.edu> Course I must not have actually posted the proper name in my email, it's real name is Bio::Tools::Run::StandAloneBlast - don't want that to throw Jay for a loop at the get-go.... There are certainly things that we can use just plain-old perl help on if you aren't comfortable with the bioinformatics and biology concepts. I will post some more information this week about efforts on a new Bioperl website which will help aid the efforts in tracking TO-DO projects and a cleaner and simpler website interface. I'll be looking for volunteers to help with the new site content and migrating (and editing) the text from the existing site. Part of the new site will be a wiki which will allow tracking and commenting on particular sub-projects that need help. I've started collecting my thoughts on what we need to work on and will post the URL where others can contribute to the list. I hope this sort of work will help direct people towards the projects that need help. Best, -jason On Nov 7, 2005, at 9:53 AM, Barry Moore wrote: > Jay- > > Jason Stajich, who has been one of the lead developers in bioperl for > many years now, mentioned last week that: > > "Tools::StandAloneBlast could DEFINITELY be improved and needs people > to adopt it...." > > Now what the hell is Tools::StandAloneBlast? Blast (and it's > relatives > wu-blast and fasta) are probably the most frequently used > algorithms in > bioinformatics. They take a nucleic acid or protein sequence as input > and searches for similar sequences in a large database of sequences. > Tools::StandAloneBlast is the module that provides the bioperl > interface > to a locally running copy of the NCBI Blast tool. NCBI (National > Center > for Biotechnology Information) has written one version of Blast, and > they also maintain a comprehensive database of nucleic acid and > protein > sequences and sequence related information. Check out the education > section of the NCBI website (http://www.ncbi.nlm.nih.gov/ > Education/) and > the Blast handbook > http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.chapter.610). > Install a copy of Blast, install the nr sequence database and get > Tools::StandAloneBlast running on one of your machines, and start > poking > around that code to see if it can use some improving. > > BTW, In Europe, EBI (European Bioinformatics Institue and the Ensembl > project fills a similar niche but from a different angle. It would be > worth becoming familiar with their tools as well because their API is > often more programmer friendly. > > Barry > > P.S. Write a script to use bioperl to blast search the following > sequence against a local copy of the nr database and decide what > protein > it is from and why this protein was your friend last Friday night. > MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA > >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >> bounces@portal.open-bio.org] On Behalf Of Jay Hannah >> Sent: Saturday, November 05, 2005 10:09 AM >> To: bioperl-l@bioperl.org >> Subject: Re: [Bioperl-l] Re: "Volunteers needed" >> >> >> On Nov 5, 2005, at 4:50 AM, Ewan Birney wrote: >>> welcome on board - have you tried out BioPerl? It is a rather large >>> project >>> and definitely there are some un-cared for areas that need some TLC. >>> >>> I guess Jason or Aaron might have some ideas, but a good starting >>> place is >>> to download bioperl, go make test and also look at the start of the >>> tutorial. >>> I have no doubt that you'll spot some sub-optimal things on teh way >>> >>> Once that's done I'm not 100% sure where is a good place to start: > DB >>> access >>> of some other internet accessible sequence databases? >> >> I suspect I may be good at wrestling/smoothing installs, test >> scripts, >> POD, etc. I have access to Mac OS X, 3 flavors of Linux, and AIX. I'm >> no porting guru, but I'm strong in general Perl, test scripts, CPAN >> installs, web/Internet coding, databases, Apache, Linux, etc. If >> those >> skills are needed in the Bioperl community I'd be happy to take a >> stab >> at submitting various patches or tackling whatever. >> >> The other side of my equation is that I'm thoroughly ignorant in >> biology and genetics. For 10 years I've been data crunching / web >> portaling / e-commercing for companies that have nothing to do with >> this new "hobby." I am, however, committed to learning if I can >> find a >> niche somewhere in which I can help, no matter how small the >> contribution. I've picked up a few books and am consuming those as > time >> allows. Turns out genetics and biology are complicated. Who knew? >> -grin- >> >> It would be fantastic if I could find a local lab that could use my >> help (Omaha, NE USA). Luckily my skills telecommute fairly easily, so >> if any scientist genius type anywhere wants some slave labor I'd >> happily do their bidding under their wing. >> >> Programming, databases, and Internet interaction are my forte. >> Unfortunately I'm guessing my lack of bio skills render my >> programming >> skills unusable for much of the work going on...? >> >> Anyway, I'm just very motivated to help someone doing genetic >> research >> for the greater good. It would be a great feeling to know that maybe >> someday my labor may help produce something that will help people. > I've >> been working for money for 10 years now, and am attempting a shift in >> focus. Part time. -grin- >> >> I hope I can help. >> >> Jay Hannah >> Omaha, NE >> mobile: 402-578-3976 >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From kt234 at cornell.edu Sun Nov 6 22:34:55 2005 From: kt234 at cornell.edu (Kevin Thornton) Date: Mon Nov 7 16:36:21 2005 Subject: [Bioperl-l] Bio::PopGen modules performance Message-ID: <8D2B558D-306A-49A2-9FBC-C20329A9ED14@cornell.edu> Hi-- First, thanks to Jason and Albert for the plug. This thread brings up something I've been meaning to post to this list for a while now. Recent versions of libsequence now contain definitions for all the data types and functions necessary to do coalescent simulations with recombination. The efficiency is quite good, easily on par with "ms", with a few extra nuts and bolts thrown in there that can lead to improved efficiency over ms. Also, the resulting data structure (i.e. the ancestral recombination graph), can be accessed directly, and/or mutations can be thrown down on them, and objects are returned that are compatible with the summary- statistic calculation factories already in the library. Here's where bioperl may come in. I have attempted to create a python wrapper for the library (using boost::python), with the ultimate goal of mentioning or submitting it to biopython. Unfortunately, there appears to be some limitations to boost::python that will prevent a full python interface to libsequence from appearing any time soon. However, the code is all there for someone who's motivated to provide perl wrappers. It is my understanding that a direct perl interface to a C++ API is not possible, or at least not easy. If I'm wrong here, I'd be interested in hearing more about it. However, some basic binaries could be provided which perl could call. While this would be a pain in that it wouldn't be self- contained perl, it would be quite fast, and potentially quite flexible. If this sounds interesting to anybody, I'd be willing to discuss this further. --Kevin _________________________ Kevin Thornton Molecular Biology and Genetics Cornell University http://www.molpopgen.org From equevill at infobiogen.fr Mon Nov 7 04:45:48 2005 From: equevill at infobiogen.fr (Emmanuel Quevillon) Date: Mon Nov 7 16:36:22 2005 Subject: [Bioperl-l] Bio::SeqFeature::Annotated too much varaibles Message-ID: <436F224C.5070103@infobiogen.fr> Hi, I already sent this small bug few months ago but nobody answered me nor corrected the bug. I get the bioperl-live on friday and checked Bio::SeqFeature::Annotated module. The problem still remains uncorrected in '_initialize' subroutine : ... *my* *(* $start, $end, $strand, $frame, $phase, $score, $name, $id, $annot, $location, <========= $id should not be here, it shift all the followin values (check below) $display_name, ##deprecate $seq_id, $type,$source *)* = $self->_rearrange*(**[**qw**(*START END STRAND FRAME PHASE SCORE NAME ANNOTATION LOCATION DISPLAY_NAME SEQ_ID TYPE SOURCE *)**]*, @args*)*; ... I wrote a simple test to illustrate it : #!/usr/local/bin/perl -w use lib '/home/tuco/tmp/src/bioperl-live/'; use Bio::SeqFeature::Annotated; $sfa = Bio::SeqFeature::Annotated->new( -start => 1, -end => 5, -strand => "+", -frame => 2, -phase => 2, -score => 12, -display_name => 'test.annot', -seq_id => 'test.displayname' ); print "Name:",$sfa->name, " \nAnnotation:", $sfa->annotation(), " \nLOC:", $sfa->location(), "\nSeq_ID:", $sfa->seq_id(), "\n"; Here is the results with the cvs module : tuco@euphorbe SeqFeature>perl ~/test.pl ------------- EXCEPTION ------------- MSG: object test.annot pretends to be a location but does not implement Bio::LocationI STACK Bio::SeqFeature::Annotated::location /home/tuco/tmp/src/bioperl-live//Bio/SeqFeature/Annotated.pm:792 STACK Bio::SeqFeature::Annotated::_initialize /home/tuco/tmp/src/bioperl-live//Bio/SeqFeature/Annotated.pm:152 STACK Bio::SeqFeature::Annotated::new /home/tuco/tmp/src/bioperl-live//Bio/SeqFeature/Annotated.pm:117 STACK toplevel /home/tuco/test.pl:6 -------------------------------------- tuco@euphorbe SeqFeature> Where you can see I did not set any location. If I remove '$id' from _initialize : tuco@euphorbe SeqFeature>perl ~/test.pl Name: <============ another problem (below) Annotation:Bio::Annotation::Collection=HASH(0x81910a0) LOC:Bio::Location::Simple=HASH(0x8168b14) Seq_ID:test.displayname tuco@euphorbe SeqFeature> No problems. Another problem is when the name is set, : *defined* $name && $self->name*(*$name || $display_name*)*; How can the name be set if only $name is tested? Maybe would be better if this line was : *defined* ($name || $display_name) && $self->name*(*$name || $display_name*)*; In this case : tuco@euphorbe SeqFeature>perl ~/test.pl Name:test.annot Annotation:Bio::Annotation::Collection=HASH(0x8190fa4) LOC:Bio::Location::Simple=HASH(0x8168aa0) Seq_ID:test.displayname tuco@euphorbe SeqFeature> The name is correctly set by using -name or -display_name . Maybe a warning might be thrown when -dsiaply_name is used to force user to use -name? Sorry to bother you with that. Please could you correct this? Thanks Regards Emmanuel -------------- next part -------------- A non-text attachment was scrubbed... Name: equevill.vcf Type: text/x-vcard Size: 322 bytes Desc: not available Url : http://portal.open-bio.org/pipermail/bioperl-l/attachments/20051107/5e6b1579/equevill.vcf From j.huxley-jones at postgrad.manchester.ac.uk Mon Nov 7 06:43:00 2005 From: j.huxley-jones at postgrad.manchester.ac.uk (Julie Huxley - Jones) Date: Mon Nov 7 16:36:24 2005 Subject: [Bioperl-l] Install Bioperl Errors Message-ID: <770F58EF-0438-4F8F-9861-248F983F0132@postgrad.manchester.ac.uk> Dear Sir / Madam I was wondering if you could help. I have tried to install bioperl 1.4 onto my apple OSX system and have come across some errors. I attach a file containing the history of the installation. Could you help me with the errors in make test as a few of the segments did not install. I have errors using make install as at the end of the script there is a permission error although I have root access. Please can you tell me whether the errors in make test can be overcome and whether I need to be in my home directory or bioperl-1.4 directory to perform the make install etc / any reason why the last error occurred. ? Thanks Julie Huxley - Jones Wellcome Trust Centre for Cell-Matrix Research Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road Manchester M13 9PT Tel +44 161 275 6616 Tel +44 161 275 1566 Fax +44 161 275 5082 -------------- next part -------------- Skipped content of type multipart/mixed From anst at kvl.dk Mon Nov 7 10:14:03 2005 From: anst at kvl.dk (Anders Stegmann) Date: Mon Nov 7 16:36:25 2005 Subject: [Bioperl-l] yeast gene prediction tools Message-ID: Hi! I need a gene prediction tool(s) for predicting genes in a S. cere genome sequence. what tool(s) should I use? I mean, predicting genes from sequence alone. Anders. From jason.stajich at duke.edu Mon Nov 7 16:50:43 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Nov 7 16:49:16 2005 Subject: [Bioperl-l] Bio::SeqFeature::Annotated too much varaibles In-Reply-To: <436F224C.5070103@infobiogen.fr> References: <436F224C.5070103@infobiogen.fr> Message-ID: <993F5A18-A6F7-40C9-BE66-97F22A619712@duke.edu> On Nov 7, 2005, at 4:45 AM, Emmanuel Quevillon wrote: > Hi, > > I already sent this small bug few months ago but nobody answered me > nor corrected the bug. > I get the bioperl-live on friday and checked > Bio::SeqFeature::Annotated module. > The problem still remains uncorrected in '_initialize' subroutine : > That's why they should be submitted to bugzilla.open-bio.org - if you can submit a patch to bugzilla it will get fixed a lot faster this time I hope. $ cvs diff -Nau Bio/SeqFeature/Annotated.pm Thanks for reporting it - I'm sorry it slipped through the cracks, shows how much this module is used/tested in the tests.... Maybe someone will be willing to add some tests for it. I assume there is a good reason to be using it over Bio::SeqFeature::Generic? -jason -- Jason Stajich Duke University http://www.duke.edu/~jes12 From papadop at uga.edu Mon Nov 7 16:24:07 2005 From: papadop at uga.edu (Chris Papadopoulos) Date: Mon Nov 7 18:36:45 2005 Subject: [Bioperl-l] Bioperl-ext (staden::read) install issues In-Reply-To: <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> References: <2C73F23D-D120-4098-8AF6-FBCCEB9FACF8@uga.edu> <1141F011-E552-4EAE-89B3-1A4C43F930B3@duke.edu> Message-ID: <14367A97-7249-49B0-B751-99C1EDDA31FD@uga.edu> Thanks for the info. make clean, make and make install went OK but make test failed. bptutorial.pl was also looking for the t/ files. I'm looking for how CATFILE gets set in Bio::Root::IO.pm. I don't want to follow the entire trail but it's probably something more experienced folks would know. Worse case scenario, I just cp the files from the bioperl-ext source directory. Just need to know where to. Thanks again, Chris Papadopoulos [Just as an aside, I really wish I kept notes on the whole process of bioperl and friends on OS 10.4. There were some minutiae that the online install tips didn't go over. Maybe if I'm feeling particularly masochistic after finals. I'll try to throw it on an older box I have. Folks on Darwin would benefit...] On Nov 6, 2005, at 1:07 PM, Jason Stajich wrote: > In os.h did you change > #include > > to > #include "config.h" > > This made a difference for me. > Make sure the the compile commands are actually point to the right > include path. > i.e. make sure this is correct: -IPATH/TO/IOLIB/INCLUDE/io_lib in > the gcc stmt below (for your system) > > gcc -c -I/home/jes12/src/bioperl/bioperl-ext-1.5.1/Bio/SeqIO/ > staden -IPATH/TO/IOLIB/INCLUDE/io_lib -D_REENTRANT -D_GNU_SOURCE - > DDEBUGGING -fno-strict-aliasing -pipe -I/usr/local/include - > D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 - > g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m32 -march=i386 - > mtune=pentium4 -fasynchronous-unwind-tables -DVERSION=\"1.51\" - > DXS_VERSION=\"1.51\" -fPIC "-I/usr/lib/perl5/5.8.6/i386-linux- > thread-multi/CORE" read.c > > > There appears to be some complaints from Inline::C about version > numbers not matching and not being parseable. I just changed > things to "1.50" instead of "1.5.1" and made sure that in read.pm > the code looks like this: > use Inline (C => 'DATA', > VERSION => '1.51', > NAME => 'Bio::SeqIO::staden::read', > > instead of this: > use Inline (C => 'DATA', > VERSION => '0.1', > NAME => 'Bio::SeqIO::staden::read', > > And further down I made this change > $VERSION = 1.51; > > instead of > $VERSION = 1.5; > > > All this to say the ext stuff needs some more TLC to work on > different platforms and be more generally installable. > > -jason From brian_osborne at cognia.com Mon Nov 7 19:11:21 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Mon Nov 7 19:15:16 2005 Subject: [Bioperl-l] Install Bioperl Errors In-Reply-To: <770F58EF-0438-4F8F-9861-248F983F0132@postgrad.manchester.ac.uk> Message-ID: Julie, Failed 7/179 test scripts, 96.09% okay. 1/8127 subtests failed, 99.99% okay. make: *** [test_dynamic] Error 2 [pc071090:~/bioperl-1.4] juliehux% make install Warning: You do not have permissions to install into //usr/bin at /System/Library/Perl/5.8.6/ExtUtils/Install.pm line 114. This means you don?t have permission to install the Bioperl scripts into /usr/bin, it appears that the rest of Bioperl was installed successfully. In order to connect to remote databases such as Genbank or EMBL you?ll need to install LWP and HTTP::Request, most Bioperlers would consider these Perl modules essential. Do, as root: >perl ?e shell ?MCPAN Then: cpan>install LWP And cpan>install HTTP::Request Brian O. On 11/7/05 6:43 AM, "Julie Huxley - Jones" wrote: > Dear Sir / Madam > > I was wondering if you could help. I have tried to install bioperl 1.4 onto my > apple OSX system and have come across some errors. I attach a file containing > the history of the installation. > > Could you help me with the errors in make test as a few of the segments did > not install. I have errors using make install as at the end of the script > there is a permission error although I have root access. > > Please can you tell me whether the errors in make test can be overcome and > whether I need to be in my home directory or bioperl-1.4 directory to perform > the make install etc / any reason why the last error occurred. > > > > > > > Thanks > > > > Julie Huxley - Jones > > Wellcome Trust Centre for Cell-Matrix Research > > Faculty of Life Sciences > > University of Manchester > > Michael Smith Building > > Oxford Road > > Manchester > > M13 9PT > > > > Tel??+44 161 275 6616 > > Tel +44 161 275 1566 > > Fax +44 161 275 5082 > > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From papadop at uga.edu Mon Nov 7 17:11:08 2005 From: papadop at uga.edu (Chris Papadopoulos) Date: Mon Nov 7 20:25:24 2005 Subject: [Bioperl-l] Install Bioperl Errors In-Reply-To: <770F58EF-0438-4F8F-9861-248F983F0132@postgrad.manchester.ac.uk> References: <770F58EF-0438-4F8F-9861-248F983F0132@postgrad.manchester.ac.uk> Message-ID: <5D8F7072-3910-4FC8-BFF8-12C124C0C69B@uga.edu> Hi Julie Try 'sudo make install' for starters. Chris On Nov 7, 2005, at 6:43 AM, Julie Huxley - Jones wrote: > Dear Sir / Madam > > I was wondering if you could help. I have tried to install bioperl > 1.4 onto my apple OSX system and have come across some errors. I > attach a file containing the history of the installation. > > Could you help me with the errors in make test as a few of the > segments did not install. I have errors using make install as at > the end of the script there is a permission error although I have > root access. > > Please can you tell me whether the errors in make test can be > overcome and whether I need to be in my home directory or > bioperl-1.4 directory to perform the make install etc / any reason > why the last error occurred. > > > > > > Thanks > > Julie Huxley - Jones > Wellcome Trust Centre for Cell-Matrix Research > Faculty of Life Sciences > University of Manchester > Michael Smith Building > Oxford Road > Manchester > M13 9PT > > Tel +44 161 275 6616 > Tel +44 161 275 1566 > Fax +44 161 275 5082 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From avilella at ub.edu Tue Nov 8 01:43:00 2005 From: avilella at ub.edu (Albert Vilella) Date: Tue Nov 8 01:41:53 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: <8D2B558D-306A-49A2-9FBC-C20329A9ED14@cornell.edu> References: <8D2B558D-306A-49A2-9FBC-C20329A9ED14@cornell.edu> Message-ID: <1131432181.8091.25.camel@localhost.localdomain> I would say that one way to have a Bioperl wrapper would be to have a document in libsequence explaining how to call each binaries, with which options. For example: ms-like-binary --option1 --option2 --option3 [...] does-something-cool-binary --option1 --option2 [...] or with config files, along the lines of programs like PAML .ctl files. This is definitively a fantastic wrapper to implement, Cheers, Albert. > This thread brings up something I've been meaning to post to this > list for a while now. Recent versions of libsequence now contain > definitions for all the data types and functions necessary to do > coalescent simulations with recombination. The efficiency is quite > good, easily on par with "ms", with a few extra nuts and bolts thrown > in there that can lead to improved efficiency over ms. Also, the > resulting data structure (i.e. the ancestral recombination graph), > can be accessed directly, and/or mutations can be thrown down on > them, and objects are returned that are compatible with the summary- > statistic calculation factories already in the library. > > Here's where bioperl may come in. I have attempted to create a > python wrapper for the library (using boost::python), with the > ultimate goal of mentioning or submitting it to biopython. > Unfortunately, there appears to be some limitations to boost::python > that will prevent a full python interface to libsequence from > appearing any time soon. However, the code is all there for someone > who's motivated to provide perl wrappers. It is my understanding > that a direct perl interface to a C++ API is not possible, or at > least not easy. If I'm wrong here, I'd be interested in hearing more > about it. However, some basic binaries could be provided which perl > could call. While this would be a pain in that it wouldn't be self- > contained perl, it would be quite fast, and potentially quite flexible. > If this sounds interesting to anybody, I'd be willing to discuss this > further. > > --Kevin > _________________________ > Kevin Thornton > Molecular Biology and Genetics > Cornell University > http://www.molpopgen.org From kt234 at cornell.edu Tue Nov 8 08:05:34 2005 From: kt234 at cornell.edu (Kevin Thornton) Date: Tue Nov 8 08:04:06 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: <1131432181.8091.25.camel@localhost.localdomain> References: <8D2B558D-306A-49A2-9FBC-C20329A9ED14@cornell.edu> <1131432181.8091.25.camel@localhost.localdomain> Message-ID: <524D30E3-E0EB-4C09-8ABA-262A2359D42E@cornell.edu> That is possible. Although, like bioperl, the actual programs that people may need/want do not exist yet. The examples/ subdirectory in the libsequence source package contains two example programs, ms-- and msbeta. The former is a basic simulation with recombination, and the latter a simulation with recombination where the shape of the genetic map on the sequence is described by a Beta(a,b) density sitting on top of the sequence. For both programs, the demographic model is the standard continuous approximation of a large Wright- Fisher population. One thing that would be quite quick to do is to document those a little better at the top of their source files. --Kevin On Nov 8, 2005, at 1:43 AM, Albert Vilella wrote: > I would say that one way to have a Bioperl wrapper would be to have a > document in libsequence explaining how to call each binaries, with > which > options. For example: > > ms-like-binary --option1 > --option2 > --option3 > [...] > > does-something-cool-binary --option1 > --option2 > [...] > > or with config files, along the lines of programs like PAML .ctl > files. > > This is definitively a fantastic wrapper to implement, > > Cheers, > > Albert. > >> This thread brings up something I've been meaning to post to this >> list for a while now. Recent versions of libsequence now contain >> definitions for all the data types and functions necessary to do >> coalescent simulations with recombination. The efficiency is quite >> good, easily on par with "ms", with a few extra nuts and bolts thrown >> in there that can lead to improved efficiency over ms. Also, the >> resulting data structure (i.e. the ancestral recombination graph), >> can be accessed directly, and/or mutations can be thrown down on >> them, and objects are returned that are compatible with the summary- >> statistic calculation factories already in the library. >> >> Here's where bioperl may come in. I have attempted to create a >> python wrapper for the library (using boost::python), with the >> ultimate goal of mentioning or submitting it to biopython. >> Unfortunately, there appears to be some limitations to boost::python >> that will prevent a full python interface to libsequence from >> appearing any time soon. However, the code is all there for someone >> who's motivated to provide perl wrappers. It is my understanding >> that a direct perl interface to a C++ API is not possible, or at >> least not easy. If I'm wrong here, I'd be interested in hearing more >> about it. However, some basic binaries could be provided which perl >> could call. While this would be a pain in that it wouldn't be self- >> contained perl, it would be quite fast, and potentially quite >> flexible. > >> If this sounds interesting to anybody, I'd be willing to discuss this >> further. >> >> --Kevin >> _________________________ >> Kevin Thornton >> Molecular Biology and Genetics >> Cornell University >> http://www.molpopgen.org _________________________ Kevin Thornton Molecular Biology and Genetics Cornell University http://www.molpopgen.org From fgarret at ub.edu Tue Nov 8 09:17:37 2005 From: fgarret at ub.edu (Filipe Garrett) Date: Tue Nov 8 09:31:59 2005 Subject: [Bioperl-l] GFF to GTF Message-ID: <4370B381.4020600@ub.edu> Hi all, I'm currently trying to use a software called Projector to predict genes. As input it needs two sequences and the anotation of one of them in GTF. As the info in GTF is included in the GFF I was thinking of getting a way to convert the GFF files into GTF. I thought of using the Bioperl module for GFF to parse the GFF and write the GTF fields to an output. Does anyone knows if there's any script already made? Or of a simple way to do it? Thanks in advance FG From avilella at gmail.com Tue Nov 8 08:11:50 2005 From: avilella at gmail.com (Albert Vilella) Date: Tue Nov 8 13:58:23 2005 Subject: [Bioperl-l] Bio::PopGen modules performance In-Reply-To: <524D30E3-E0EB-4C09-8ABA-262A2359D42E@cornell.edu> References: <8D2B558D-306A-49A2-9FBC-C20329A9ED14@cornell.edu> <1131432181.8091.25.camel@localhost.localdomain> <524D30E3-E0EB-4C09-8ABA-262A2359D42E@cornell.edu> Message-ID: <1131455510.7883.3.camel@localhost.localdomain> El dt 08 de 11 del 2005 a les 08:05 -0500, en/na Kevin Thornton va escriure: > That is possible. Although, like bioperl, the actual programs that > people may need/want do not exist yet. The examples/ subdirectory in > the libsequence source package contains two example programs, ms-- > and msbeta. The former is a basic simulation with recombination, and > the latter a simulation with recombination where the shape of the > genetic map on the sequence is described by a Beta(a,b) density > sitting on top of the sequence. For both programs, the demographic > model is the standard continuous approximation of a large Wright- > Fisher population. One thing that would be quite quick to do is to > document those a little better at the top of their source files. Yes, that sounds good. If you want I can open a bugzilla ticket with the generic subject "libsequence wrapper" and then add this first approximation as a first item to achieve. Bests, Albert. > > --Kevin > On Nov 8, 2005, at 1:43 AM, Albert Vilella wrote: > > > I would say that one way to have a Bioperl wrapper would be to have a > > document in libsequence explaining how to call each binaries, with > > which > > options. For example: > > > > ms-like-binary --option1 > > --option2 > > --option3 > > [...] > > > > does-something-cool-binary --option1 > > --option2 > > [...] > > > > or with config files, along the lines of programs like PAML .ctl > > files. > > > > This is definitively a fantastic wrapper to implement, > > > > Cheers, > > > > Albert. > > > >> This thread brings up something I've been meaning to post to this > >> list for a while now. Recent versions of libsequence now contain > >> definitions for all the data types and functions necessary to do > >> coalescent simulations with recombination. The efficiency is quite > >> good, easily on par with "ms", with a few extra nuts and bolts thrown > >> in there that can lead to improved efficiency over ms. Also, the > >> resulting data structure (i.e. the ancestral recombination graph), > >> can be accessed directly, and/or mutations can be thrown down on > >> them, and objects are returned that are compatible with the summary- > >> statistic calculation factories already in the library. > >> > >> Here's where bioperl may come in. I have attempted to create a > >> python wrapper for the library (using boost::python), with the > >> ultimate goal of mentioning or submitting it to biopython. > >> Unfortunately, there appears to be some limitations to boost::python > >> that will prevent a full python interface to libsequence from > >> appearing any time soon. However, the code is all there for someone > >> who's motivated to provide perl wrappers. It is my understanding > >> that a direct perl interface to a C++ API is not possible, or at > >> least not easy. If I'm wrong here, I'd be interested in hearing more > >> about it. However, some basic binaries could be provided which perl > >> could call. While this would be a pain in that it wouldn't be self- > >> contained perl, it would be quite fast, and potentially quite > >> flexible. > > > >> If this sounds interesting to anybody, I'd be willing to discuss this > >> further. > >> > >> --Kevin > >> _________________________ > >> Kevin Thornton > >> Molecular Biology and Genetics > >> Cornell University > >> http://www.molpopgen.org > > _________________________ > Kevin Thornton > Molecular Biology and Genetics > Cornell University > http://www.molpopgen.org > > From kellert at ohsu.edu Tue Nov 8 14:49:56 2005 From: kellert at ohsu.edu (Thomas J Keller) Date: Tue Nov 8 14:57:47 2005 Subject: [Bioperl-l] more GD woes Message-ID: <355E936E-475B-45C0-AC67-1FA65C5160D5@ohsu.edu> Greetings, I never can get GD to work. It is very frustrating. Here's the error I'm getting running the example 1 script from the Graphics HowTo folder: Can't locate object method "png" via package "GD::Image" at /Library/ Perl/5.8.6/Bio/Graphics/Panel.pm line 930, <> line 9. I believe I have everything needed: $ perl -MGD -e 'print $GD::VERSION'; 2.30 $ ls -l /sw/lib | grep libgd* -rwxr-xr-x 1 root admin 255244 May 25 09:57 libgd.1.8.dylib lrwxr-xr-x 1 root admin 15 Oct 25 12:20 libgd.1.dylib -> libgd.1.8.dylib -rwxr-xr-x 1 root admin 445384 May 16 03:01 libgd.2.0.0.dylib lrwxr-xr-x 1 root admin 17 Sep 28 17:26 libgd.2.dylib -> libgd.2.0.0.dylib -rw-r--r-- 1 root admin 227144 May 25 09:57 libgd.a lrwxr-xr-x 1 root admin 13 Oct 25 12:27 libgd.dylib -> libgd.1.dylib -rwxr-xr-x 1 root admin 20740724 May 22 11:17 libgeos.2.1.1.dylib lrwxr-xr-x 1 root admin 19 Oct 14 11:21 libgeos.2.dylib -> libgeos.2.1.1.dylib $ locate Image.pm /Library/Perl/5.8.6/darwin-thread-multi-2level/GD/Image.pm /Library/Perl/5.8.6/darwin-thread-multi-2level/Template/Plugin/GD/ Image.pm I'm thinking the left hand doesn't know what the right hand is doing. I.e., one or more of these interconnected files is not finding something it needs. But I'll be damned if I know how to find out which, much less how to fix it. Thanks for any suggestions. Tom Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert@ohsu.edu 503-494-2442 From lstein at cshl.edu Tue Nov 8 15:05:34 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Tue Nov 8 15:23:36 2005 Subject: [Bioperl-l] Bad bug in Bio::DB::GFF Message-ID: <200511081505.34593.lstein@cshl.edu> Hi Folks, It looks like I broke Bio::DB::GFF's handling of gff3 format files just prior to the release. The new version is in bioperl-live. The files to update are: Bio/DB/GFF.pm Bio/DB/GFF/Adaptor/memory.pm Lincoln -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse@cshl.edu From lstein at cshl.edu Tue Nov 8 15:03:29 2005 From: lstein at cshl.edu (Lincoln Stein) Date: Tue Nov 8 15:23:42 2005 Subject: [Bioperl-l] more GD woes In-Reply-To: <355E936E-475B-45C0-AC67-1FA65C5160D5@ohsu.edu> References: <355E936E-475B-45C0-AC67-1FA65C5160D5@ohsu.edu> Message-ID: <200511081503.29975.lstein@cshl.edu> When you compiled GD and libgd, did you include PNG support? If not, this would explain your problem. For what it's worth, the ActiveState build of GD works fine. Lincoln On Tuesday 08 November 2005 02:49 pm, Thomas J Keller wrote: > Greetings, > I never can get GD to work. It is very frustrating. > Here's the error I'm getting running the example 1 script from the > Graphics HowTo folder: > Can't locate object method "png" via package "GD::Image" at /Library/ > Perl/5.8.6/Bio/Graphics/Panel.pm line 930, <> line 9. > > I believe I have everything needed: > $ perl -MGD -e 'print $GD::VERSION'; > 2.30 > > $ ls -l /sw/lib | grep libgd* > -rwxr-xr-x 1 root admin 255244 May 25 09:57 libgd.1.8.dylib > lrwxr-xr-x 1 root admin 15 Oct 25 12:20 libgd.1.dylib -> > libgd.1.8.dylib > -rwxr-xr-x 1 root admin 445384 May 16 03:01 libgd.2.0.0.dylib > lrwxr-xr-x 1 root admin 17 Sep 28 17:26 libgd.2.dylib -> > libgd.2.0.0.dylib > -rw-r--r-- 1 root admin 227144 May 25 09:57 libgd.a > lrwxr-xr-x 1 root admin 13 Oct 25 12:27 libgd.dylib -> > libgd.1.dylib > -rwxr-xr-x 1 root admin 20740724 May 22 11:17 libgeos.2.1.1.dylib > lrwxr-xr-x 1 root admin 19 Oct 14 11:21 libgeos.2.dylib -> > libgeos.2.1.1.dylib > > $ locate Image.pm > /Library/Perl/5.8.6/darwin-thread-multi-2level/GD/Image.pm > /Library/Perl/5.8.6/darwin-thread-multi-2level/Template/Plugin/GD/ > Image.pm > > I'm thinking the left hand doesn't know what the right hand is doing. > I.e., one or more of these interconnected files is not finding > something it needs. But I'll be damned if I know how to find out > which, much less how to fix it. > > Thanks for any suggestions. > > Tom > > Tom Keller, Ph.D. > http://www.ohsu.edu/research/core > kellert@ohsu.edu > 503-494-2442 > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT michelse@cshl.edu From bli1 at bcm.tmc.edu Tue Nov 8 17:11:09 2005 From: bli1 at bcm.tmc.edu (Bingshan Li) Date: Tue Nov 8 17:09:34 2005 Subject: [Bioperl-l] Fay and Wu's H test In-Reply-To: <1131139785.7997.12.camel@localhost.localdomain> References: <93038EE8-C99D-4432-B287-264E67E1456D@bcm.tmc.edu> <1131139785.7997.12.camel@localhost.localdomain> Message-ID: <499BE7A1-CD11-418D-B3AE-DA62ADA7A120@bcm.tmc.edu> Hi all, I am wondering if there is an implementation of Fay and Wu's H test for population genetics. I did not find this function in Bio::PopGen modules. Does anybody have one or could somebody implement this function in Bioperl? Sorry I am not familiar with the objects in Bioperl. Thanks a lot! All the best, --bs From stephan.rosecker at ish.de Wed Nov 9 09:19:00 2005 From: stephan.rosecker at ish.de (stephan) Date: Wed Nov 9 10:19:42 2005 Subject: [Bioperl-l] Problems to get secondary accessions from an object Message-ID: <43720554.2030701@ish.de> Hi, I have problems to get the secondary_accessions from an seq object. E.G $inx = Bio::Index::Swissprot->new($Index_File_Name); $prot = $inx->fetch( $accarray[ $_[0] ] ); #"$accarray[ $_[0]" is an array of accessions print "Description: " . $prot->description . "\n"; print "Accessions: " .$sec . "\n"; print "Species: " . $prot->species->binomial() . "\n"; print "Length: " . $prot->length . "\n"; #this looks good @a = $prot->get_secondary_accessions; #@a is empty! Seems that $prot is not a reference to a rich:seq object or somthing other is wrong. Hope that someone can help me. regards stephan From MEC at stowers-institute.org Wed Nov 9 10:48:10 2005 From: MEC at stowers-institute.org (Cook, Malcolm) Date: Wed Nov 9 11:02:02 2005 Subject: [Bioperl-l] GFF to GTF Message-ID: GFF as a format has a variety of versions. AFAIK, GTF is GFF 2.1 or 2.5 The main differences have to do with format and semantics of GFF's column 9, the inclusion of sequence data itself in the file, and version reference 1 & 2 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml 2.1 http://genes.cs.wustl.edu/GTF21.html 2.5 ref? 3 http://song.sourceforge.net/gff3.shtml What is your source of GFF? It is possible that your GFF annotation already is GTF. What version is it? Look in the file. There may be a '##gff-version' directive in it. Or, if you see that column 9 looks like 'gene_id "381.000"; transcript_id "381.000.1";' (c.f. gff 2.1 docs) then it probably already is in GTF. If it is NOT already GTF (GFF 2.1 or 2.5), then you must provide example expected input and output to see if we (I) can help further. Cheers, Malcolm Cook - mec@stowers-institute.org - 816-926-4449 Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, MO USA -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Filipe Garrett Sent: Tuesday, November 08, 2005 8:18 AM To: Bioperl Subject: [Bioperl-l] GFF to GTF Hi all, I'm currently trying to use a software called Projector to predict genes. As input it needs two sequences and the anotation of one of them in GTF. As the info in GTF is included in the GFF I was thinking of getting a way to convert the GFF files into GTF. I thought of using the Bioperl module for GFF to parse the GFF and write the GTF fields to an output. Does anyone knows if there's any script already made? Or of a simple way to do it? Thanks in advance FG _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From brian_osborne at cognia.com Wed Nov 9 11:20:01 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Wed Nov 9 11:24:55 2005 Subject: [Bioperl-l] Problems to get secondary accessions from an object In-Reply-To: <43720554.2030701@ish.de> Message-ID: Stephan, Your code looks correct - are you sure that your sequences have secondary accessions? The bioperl-live code retrieves these accessions correctly, my script is below. Brian O. #!/usr/bin/perl use strict; $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File"; $ENV{BIOPERL_INDEX} = "."; use Bio::Index::Swissprot; my @accs = qw(P09651 P12942 P13798 P58428); my $file_name = "multiple.sw"; my $inx = Bio::Index::Swissprot->new(-filename => $file_name . ".idx", -write_flag => 1); $inx->id_parser(\&get_id); $inx->make_index($file_name); for my $acc (@accs) { my $seq = $inx->fetch($acc); print $seq->seq(),"\n"; my @seconds = $seq->get_secondary_accessions; print "@seconds\n"; } sub get_id { my $line = shift; $line =~ /AC\s+([A-Z]\d+);/; $1; } On 11/9/05 9:19 AM, "stephan" wrote: > Hi, > > I have problems to get the secondary_accessions from an seq object. > > E.G > > $inx = Bio::Index::Swissprot->new($Index_File_Name); > $prot = $inx->fetch( $accarray[ $_[0] ] ); > #"$accarray[ $_[0]" is an array of accessions > > print "Description: " . $prot->description . "\n"; > print "Accessions: " .$sec . "\n"; > print "Species: " . $prot->species->binomial() . "\n"; > print "Length: " . $prot->length . "\n"; > #this looks good > > @a = $prot->get_secondary_accessions; > #@a is empty! > > Seems that $prot is not a reference to a rich:seq object or somthing > other is wrong. > > Hope that someone can help me. > > regards > stephan > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From stephan.rosecker at ish.de Wed Nov 9 12:04:36 2005 From: stephan.rosecker at ish.de (stephan) Date: Wed Nov 9 12:03:04 2005 Subject: [Bioperl-l] Problems to get secondary accessions from an object In-Reply-To: References: Message-ID: <43722C24.9060303@ish.de> Brian, thanks for your answer. Yes, I'am sure - my test sequence file (below) contains only one sequence. I'm using bioperl 1.4 - I assume that "bioperl-live code" is the newest code. I will test it. A test with SeqIO works: #!/xprog/perl/perl-5.9.1_inst/bin/perl use lib "perl5"; use Bio::SeqIO; my $seqio_object = Bio::SeqIO->new(-file => "s.swiss" ); my $seq_object = $seqio_object->next_seq; my @acc = $seq_object->get_secondary_accessions; print $acc[0]."\n"; print $acc[1]."\n"; print $acc[2]."\n"; regards stephan s.swiss: ID 128U_DROME STANDARD; PRT; 368 AA. AC Q9M641; P32234; AAR2D2; AAC3PO; DT 01-OCT-1993 (Rel. 27, Created) DT 01-OCT-1993 (Rel. 27, Last sequence update) DT 01-FEB-1996 (Rel. 33, Last annotation update) DE GTP-binding protein 128UP. GN 128UP OR GTP-BP. OS Drosophila melanogaster (Fruit fly). OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; OC Ephydroidea; Drosophilidae; Drosophila. OX NCBI_TaxID=7227; RN [1] RP SEQUENCE FROM N.A. RC STRAIN=Oregon-R; RX MEDLINE=94166747; PubMed=8121394; RA Sommer K.A., Petersen G., Bautz E.K.F.; RT "The gene upstream of DmRP128 codes for a novel GTP-binding protein RT of Drosophila melanogaster."; RL Mol. Gen. Genet. 242:391-398(1994). CC -!- SIMILARITY: Belongs to the GTP1 / OBG family. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X71866; CAA50701.1; -. DR PIR; S42582; S42582. DR FlyBase; FBgn0010339; 128up. DR GO; GO:0005525; F:GTP binding; IDA. DR InterPro; IPR006074; GTP1/OBG_dom. DR InterPro; IPR006073; GTP1_OBG. DR InterPro; IPR006169; GTP1_OBG_sub. DR InterPro; IPR005225; Small_GTP. DR InterPro; IPR004095; TGS_dom. DR Pfam; PF01018; GTP1_OBG; 1. DR Pfam; PF02824; TGS; 1. DR PRINTS; PR00326; GTP1OBG. DR TIGRFAMs; TIGR00231; small_GTP; 1. DR PROSITE; PS00905; GTP1_OBG; 1. KW GTP-binding. FT NP_BIND 71 78 GTP (By similarity). FT NP_BIND 117 121 GTP (By similarity). FT NP_BIND 248 251 GTP (By similarity). SQ SEQUENCE 368 AA; 41129 MW; 07C592292BA12A6E CRC64; MITILEKISA IESEMARTQK NKATSAHLGL LKANVAKLRR ELISPKGGGG GTGEAGFEVA KTGDARVGFV GFPSVGKSTL LSNLAGVYSE VAAYEFTTLT TVPGCIKYKG AKIQLLDLPG IIEGAKDGKG RGRQVIAVAR TCNLIFMVLD CLKPLGHKKL LEHELEGFGI RLNKKPPNIY YKRKDKGGIN LNSMVPQSEL DTDLVKTILS EYKIHNADIT LRYDATSDDL IDVIEGNRIY IPCIYLLNKI DQISIEELDV IYKIPHCVPI SAHHHWNFDD LLELMWEYLR LQRIYTKPKG QLPDYNSPVV LHNERTSIED FCNKLHRSIA KEFKYALVWG SSVKHQPQKV GIEHVLNDED VVQIVKKV // Brian Osborne schrieb: > Stephan, > > Your code looks correct - are you sure that your sequences have secondary > accessions? The bioperl-live code retrieves these accessions correctly, my > script is below. > > Brian O. > > #!/usr/bin/perl > > use strict; > $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File"; > $ENV{BIOPERL_INDEX} = "."; > use Bio::Index::Swissprot; > > my @accs = qw(P09651 > P12942 > P13798 > P58428); > my $file_name = "multiple.sw"; > my $inx = Bio::Index::Swissprot->new(-filename => $file_name . ".idx", > -write_flag => 1); > $inx->id_parser(\&get_id); > $inx->make_index($file_name); > > for my $acc (@accs) { > my $seq = $inx->fetch($acc); > print $seq->seq(),"\n"; > my @seconds = $seq->get_secondary_accessions; > print "@seconds\n"; > } > > sub get_id { > my $line = shift; > $line =~ /AC\s+([A-Z]\d+);/; > $1; > } > > > > > On 11/9/05 9:19 AM, "stephan" wrote: > > >>Hi, >> >>I have problems to get the secondary_accessions from an seq object. >> >>E.G >> >>$inx = Bio::Index::Swissprot->new($Index_File_Name); >>$prot = $inx->fetch( $accarray[ $_[0] ] ); >>#"$accarray[ $_[0]" is an array of accessions >> >>print "Description: " . $prot->description . "\n"; >>print "Accessions: " .$sec . "\n"; >>print "Species: " . $prot->species->binomial() . "\n"; >>print "Length: " . $prot->length . "\n"; >>#this looks good >> >>@a = $prot->get_secondary_accessions; >>#@a is empty! >> >>Seems that $prot is not a reference to a rich:seq object or somthing >>other is wrong. >> >>Hope that someone can help me. >> >>regards >>stephan >> >> >>_______________________________________________ >>Bioperl-l mailing list >>Bioperl-l@portal.open-bio.org >>http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From MEC at stowers-institute.org Wed Nov 9 13:20:46 2005 From: MEC at stowers-institute.org (Cook, Malcolm) Date: Wed Nov 9 13:19:29 2005 Subject: [Bioperl-l] GFF to GTF Message-ID: So, Projector is supposedly expecting GTF format at documented http://www.fruitfly.org/flyannot/format.html#GTF I know your problem is 'solved' in one form or another for getting flybase data in/out from UCSC/Ensembl/GBrowse, but the details elude me. I wonder if you can't simply avail yourself of UCSC's having done this already? For instance, the following 'GTF' is extactable from their site (http://genome.ucsc.edu/cgi-bin/hgTables?db=dm2) at region chr4:22000-24000 chr4 dm2_flyBaseGene CDS 22338 22528 0.000000 - 2 gene_id "CG32013-RA"; transcript_id "CG32013-RA"; chr4 dm2_flyBaseGene exon 22335 22528 0.000000 - . gene_id "CG32013-RA"; transcript_id "CG32013-RA"; chr4 dm2_flyBaseGene CDS 22617 23205 0.000000 - 0 gene_id "CG32013-RA"; transcript_id "CG32013-RA"; chr4 dm2_flyBaseGene start_codon 23203 23205 0.000000 - . gene_id "CG32013-RA"; transcript_id "CG32013-RA"; chr4 dm2_flyBaseGene exon 22617 23205 0.000000 - . gene_id "CG32013-RA"; transcript_id "CG32013-RA"; Though it is perhaps not quite 'right' becuase missing from it is stop_codon and the exon_ids... Also, there is some form of GFF converstion included in bioperl's 'process_gadfly. good luck --Malcolm -----Original Message----- From: Filipe Garrett [mailto:fgarret@ub.edu] Sent: Wednesday, November 09, 2005 11:05 AM To: Cook, Malcolm; Bioperl Subject: Re: [Bioperl-l] GFF to GTF Cook, Malcolm wrote: >GFF as a format has a variety of versions. AFAIK, GTF is GFF 2.1 or 2.5 > >The main differences have to do with format and semantics of GFF's >column 9, the inclusion of sequence data itself in the file, and > >version reference >1 & 2 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml >2.1 http://genes.cs.wustl.edu/GTF21.html >2.5 ref? >3 http://song.sourceforge.net/gff3.shtml > >What is your source of GFF? It is possible that your GFF annotation >already is GTF. What version is it? Look in the file. There may be a >'##gff-version' directive in it. Or, if you see that column 9 looks >like 'gene_id "381.000"; transcript_id "381.000.1";' (c.f. gff 2.1 docs) >then it probably already is in GTF. > >If it is NOT already GTF (GFF 2.1 or 2.5), then you must provide example >expected input and output to see if we (I) can help further. > >Cheers, > >Malcolm Cook - mec@stowers-institute.org - 816-926-4449 >Database Applications Manager - Bioinformatics >Stowers Institute for Medical Research - Kansas City, MO USA > > > >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Filipe >Garrett >Sent: Tuesday, November 08, 2005 8:18 AM >To: Bioperl >Subject: [Bioperl-l] GFF to GTF > > >Hi all, > >I'm currently trying to use a software called Projector to predict >genes. As input it needs two sequences and the anotation of one of them >in GTF. As the info in GTF is included in the GFF I was thinking of >getting a way to convert the GFF files into GTF. I thought of using the >Bioperl module for GFF to parse the GFF and write the GTF fields to an >output. > >Does anyone knows if there's any script already made? Or of a simple way > >to do it? > >Thanks in advance > >FG >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > Hi all, I'm using GFF v3 from FlyBase. I attached an example of input and how the output should come out.. Thanks in adv. FG From sdavis2 at mail.nih.gov Wed Nov 9 13:17:36 2005 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Wed Nov 9 13:27:00 2005 Subject: [Bioperl-l] Location mapping question Message-ID: I think I have seen code to do this kind of thing--hence this email--but I may be mistaken. I have oligo sequences mapped to mRNAs by blat and have blat alignments to the genome. Is there a way to quickly align the oligos to the genome given this information using a bioperl module. (Like I said, I just can't seem to find it). Thanks, Sean From jason.stajich at duke.edu Wed Nov 9 13:36:56 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Nov 9 13:35:25 2005 Subject: [Bioperl-l] Location mapping question In-Reply-To: References: Message-ID: <64BC0C82-4940-48FE-9928-BD2C081ED2DE@duke.edu> Try: Bio::Coordinate::GeneMapper. To see it in action: here is a script which maps protein domain/FASTP hits back to the Genome. http://fungal.genome.duke.edu/~jes12/software/scripts/ map2genome.perl.txt The downside is this can be a little slow. -jason On Nov 9, 2005, at 1:17 PM, Sean Davis wrote: > I think I have seen code to do this kind of thing--hence this > email--but I > may be mistaken. I have oligo sequences mapped to mRNAs by blat > and have > blat alignments to the genome. Is there a way to quickly align the > oligos > to the genome given this information using a bioperl module. (Like > I said, > I just can't seem to find it). > > Thanks, > Sean > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jason.stajich at duke.edu Wed Nov 9 14:37:54 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Nov 9 14:36:24 2005 Subject: [Bioperl-l] working on new Bioperl website Message-ID: I just wanted to make you aware that we are working on a new Bioperl website and to solicit interested experts to help in the content We are undertaking this to use some more modern technologies than just vi for building HTML for a website. We are moving towards using a mixture or static pages, Wiki, and blogging software. I am planning to announce the site in early December after a lot of the content on the static pages is updated and moved to the new wiki. Ideally, I'd like to see a regular postings on the blog site summarizing the mailing list traffic, and perhaps additional summaries of major commits to the repository. This would require someone to volunteer for a shift at the blogging helm - I would like to gauge the interest of whether or not a) summaries are useful b) you (or someone you know) would be willing to help in the summaries. Aaron Mackey did a few of these ages ago for the O'Reilly site, but I know it took some time. http://www.oreillynet.com/weblogs/author/1067 The static content on the current Bioperl page will be migrated (and updated) to a Wiki site that can be more easily updated and commented upon. We're using the MediaWiki software that runs wikipedia.org. We will continue to use bugzilla to track bugs, but maybe a tighter integration of the bugs with the wiki so we can help keep a history of how things are fixed and what is needed to be worked on. If you are interested in volunteering to help with the content or design of the new site, please get in touch and I can point you to the prototype's URL. Things are still preliminary and I'd like to start with a well organized site at the beginning before asking for everyone to contribute to it. We'll announce the new site when enough content has migrated that it can be useful and we can transition all the static files from the old server to the new one. The wiki doesn't quite solve the problem of a threaded discussion about a problem and there has also been at least one request for a bulletin-board/forum software like phpBB . The idea of maintaining and answering questions on a web forum AND a mailing list is not appealing to me but perhaps it can be a useful way to organize the FAQ capture other things that are hard to sort through on the mailing list. I think there ought to be some feedback from the community on what you would like, but I also expect the decision will come down to (like most of the open-source solutions) who is willing to do the work. In the end I do not expect the mailing list to go away, but perhaps a subset of conversations may be held on the forum site. Starting a BB/forum site is just an idea, if you have opinions, please share them so we might make the most informed decision about how to proceed with better documentation and efficient coordination of software developers. (Chris Dagdigian has been of course instrumental in getting the initial software installed - proper kudos will go out when things are officially announced). -jason -- Jason Stajich Duke University http://www.duke.edu/~jes12 From stephan.rosecker at ish.de Wed Nov 9 14:51:30 2005 From: stephan.rosecker at ish.de (stephan) Date: Wed Nov 9 15:50:02 2005 Subject: [Bioperl-l] RE:Problems to get secondary accessions from an object Message-ID: <43725342.3080908@ish.de> Hi, I found a trace. The problem is that after I add anotations to the object, the rich-features are disappeared. snippet: #prot is the seq object sub setProtAnnotations($$) { my $prot = $_[0]; my $col = new Bio::Annotation::Collection; my $sv = new Bio::Annotation::SimpleValue(-value => &getSimpleFam( $_[1] ) ); $col->add_Annotation( 'family', $sv ); $sv = new Bio::Annotation::SimpleValue(-value => &getWeight( $_[0] ) ); $col->add_Annotation( 'weight', $sv ); $sv = new Bio::Annotation::SimpleValue(-value => $link . $prot->accession_number() ); $col->add_Annotation( 'link', $sv ); $sv = new Bio::Annotation::SimpleValue(-value => &getEval( $_[1] ) ); $col->add_Annotation( 'e-val', $sv ); $sv = new Bio::Annotation::SimpleValue( -value => $_[0]->seq() ); $col->add_Annotation( 'sequence', $sv ); $prot->annotation($col);} sub getProtAnnotation($$) { my $ano = $_[0]->annotation(); my @an = $ano->get_Annotations( $_[1] ); my $erg = $an[0]->value();} sub setProtAnnotation($$$) { my $prot = $_[0]; my $ano = $prot->annotation(); my @an = $ano->get_Annotations( $_[1] ); my $erg = $an[0]->value( $_[2] );} sub getEval($) { my $report = $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); my $hit = $report->next_hit(); my $hsp = $hit->next_domain(); my $eval = $hsp->evalue();} sub getSimpleFam($) { my $report = $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); my $hit = $report->next_hit(); my $fam = $hit->name();} >Hi, >> >> I have problems to get the secondary_accessions from an seq object. >> >> E.G >> >> $inx = Bio::Index::Swissprot->new($Index_File_Name); >> $prot = $inx->fetch( $accarray[ $_[0] ] ); >> #"$accarray[ $_[0]" is an array of accessions >> >> print "Description: " . $prot->description . "\n"; >> print "Accessions: " .$sec . "\n"; >> print "Species: " . $prot->species->binomial() . "\n"; >> print "Length: " . $prot->length . "\n"; >> #this looks good >> >> @a = $prot->get_secondary_accessions; >> #@a is empty! >> >> Seems that $prot is not a reference to a rich:seq object or somthing >> other is wrong. >> >> Hope that someone can help me. >> >> regards >> stephan >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l From MEC at stowers-institute.org Wed Nov 9 16:50:56 2005 From: MEC at stowers-institute.org (Cook, Malcolm) Date: Wed Nov 9 17:04:44 2005 Subject: [Bioperl-l] Location mapping question Message-ID: Hows this strategy: assuming the 'maf' alignments produced by blat (gfClient) are legible to Bio::AlignIO (are they?) and you get your $mRNA2genome and $oligo2mRNA alignments in this 'maf' format (can you?) you can then read them into memory with Bio::AlignIO (which purports to read 'maf' format) and then step over the Bio::LocatableSequence $oligo_sequence in the oligo2mRNA alignment(s) using bioperl's $oligo_sequence ->column_from_residue_number to get each oligos start and end positions in the mRNA alignment and $oligo2mRNA->location_from_column to translate the start and end position into a coordiante on the mRNA then use the same technique to map these positions through the mRNA2genome alignment into genomic coordinates Shouldn't be too hard. I've done something like it to map insertion mutations to reference sequences (though not depending on 'maf' format as interlingua). Cheers, Malcolm Cook - mec@stowers-institute.org - 816-926-4449 Database Applications Manager - Bioinformatics Stowers Institute for Medical Research - Kansas City, MO USA -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Sean Davis Sent: Wednesday, November 09, 2005 12:18 PM To: Bioperl Subject: [Bioperl-l] Location mapping question I think I have seen code to do this kind of thing--hence this email--but I may be mistaken. I have oligo sequences mapped to mRNAs by blat and have blat alignments to the genome. Is there a way to quickly align the oligos to the genome given this information using a bioperl module. (Like I said, I just can't seem to find it). Thanks, Sean _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From Guido.Dieterich at gbf.de Tue Nov 8 06:26:41 2005 From: Guido.Dieterich at gbf.de (Guido Dieterich) Date: Wed Nov 9 20:17:28 2005 Subject: [Bioperl-l] load in biosql a genome genbank file Message-ID: <1131449201.8302.222.camel@sb289.gbf-braunschweig.de> Hi is it possible to load into biosql a complete bacterial genome genbank file from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ Best regards Guido From fgarret at ub.edu Wed Nov 9 12:05:00 2005 From: fgarret at ub.edu (Filipe Garrett) Date: Wed Nov 9 20:17:31 2005 Subject: [Bioperl-l] GFF to GTF In-Reply-To: References: Message-ID: <43722C3C.5070400@ub.edu> Cook, Malcolm wrote: >GFF as a format has a variety of versions. AFAIK, GTF is GFF 2.1 or 2.5 > >The main differences have to do with format and semantics of GFF's >column 9, the inclusion of sequence data itself in the file, and > >version reference >1 & 2 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml >2.1 http://genes.cs.wustl.edu/GTF21.html >2.5 ref? >3 http://song.sourceforge.net/gff3.shtml > >What is your source of GFF? It is possible that your GFF annotation >already is GTF. What version is it? Look in the file. There may be a >'##gff-version' directive in it. Or, if you see that column 9 looks >like 'gene_id "381.000"; transcript_id "381.000.1";' (c.f. gff 2.1 docs) >then it probably already is in GTF. > >If it is NOT already GTF (GFF 2.1 or 2.5), then you must provide example >expected input and output to see if we (I) can help further. > >Cheers, > >Malcolm Cook - mec@stowers-institute.org - 816-926-4449 >Database Applications Manager - Bioinformatics >Stowers Institute for Medical Research - Kansas City, MO USA > > > >-----Original Message----- >From: bioperl-l-bounces@portal.open-bio.org >[mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Filipe >Garrett >Sent: Tuesday, November 08, 2005 8:18 AM >To: Bioperl >Subject: [Bioperl-l] GFF to GTF > > >Hi all, > >I'm currently trying to use a software called Projector to predict >genes. As input it needs two sequences and the anotation of one of them >in GTF. As the info in GTF is included in the GFF I was thinking of >getting a way to convert the GFF files into GTF. I thought of using the >Bioperl module for GFF to parse the GFF and write the GTF fields to an >output. > >Does anyone knows if there's any script already made? Or of a simple way > >to do it? > >Thanks in advance > >FG >_______________________________________________ >Bioperl-l mailing list >Bioperl-l@portal.open-bio.org >http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > Hi all, I'm using GFF v3 from FlyBase. I attached an example of input and how the output should come out.. Thanks in adv. FG -------------- next part -------------- ##gff-version 3 ##sequence-region 4 1 1281640 #organism dmel #source FlyBase Chado DB r4.2.1 #date 20050807 # 4 . chromosome 1 1281640 . . . ID=4 4 . BAC 1 137841 . + . ID=BACR05L22-hsp;Name=BACR05L22 4 . scaffold 1 173874 . + . ID=AE003845;Dbxref=Gadfly:AE003845.4;dbxref_2nd=Gadfly:AE003845 4 . chromosome_arm 1 1281640 . . . ID=4;species=Drosophila_melanogaster 4 . repeat_region 2 347 . + . ID=:5142029 4 . transposable_element 2 611 . + . ID=TE62890;Name=ninja-Dsim-like{}4829;Dbxref=FlyBase:FBti0062890,Gadfly:TE62890;synonym=ninja-Dsim-like{}4829 4 . repeat_region 348 611 . + . ID=:5142030 4 sim4:na_transcript_dmel_r31 match 638 1719 . - . ID=:5141589 4 . transposable_element 638 1719 . - . ID=TE20395;Name=baggins{}1471;Dbxref=FlyBase:FBti0020395,Gadfly:TE20395;cyto_range=102A1-102A1;gbunit=AE003845;synonym=baggins{}1471,TE20395;synonym_2nd=baggins{}1471 4 . repeat_region 638 1723 . - . ID=:5142087 4 HDP match 661 4308 . - . ID=:5141724 4 . oligo 1483 1507 . - . ID=146637_at_149-hsp:196344;Name=146637_at_149 4 . oligo 1505 1529 . - . ID=146637_at_127-hsp:196343;Name=146637_at_127 4 . repeat_region 2022 2162 . + . ID=:5142031 4 . transposable_element 2022 2162 . + . ID=TE62886;Name=HMS-Beagle2{}4825;Dbxref=FlyBase:FBti0062886,Gadfly:TE62886;synonym=HMS-Beagle2{}4825 4 . transposable_element 2217 2505 . + . ID=TE62758;Name=gypsy{}4697;Dbxref=FlyBase:FBti0062758,Gadfly:TE62758;synonym=gypsy{}4697 4 . repeat_region 2496 2738 . - . ID=:5142088 4 . transposable_element 2506 4343 . - . ID=TE20396;Name=Rt1c{}1472;Dbxref=FlyBase:FBti0020396,Gadfly:TE20396;cyto_range=102A1-102A1;gbunit=AE003845;synonym=Rt1c{}1472,TE20396;synonym_2nd=Rt1c{}1472 4 sim4:na_transcript_dmel_r31 match 2554 4264 . - . ID=:5141588 4 . repeat_region 3692 4348 . - . ID=:5142089 4 . transposable_element 4364 13761 . - . ID=TE20400;Name=1360{}1476;Dbxref=FlyBase:FBti0020400,Gadfly:TE20400;cyto_range=102A1-102A1;gbunit=AE003845;synonym=1360{}1476,TE20400;synonym_2nd=1360{}1476 4 . repeat_region 4364 4611 . - . ID=:5142090 4 . transcription_start_site 4629 4630 . - . ID=:5140416 4 sim4:na_transcript_dmel_r31 match 4886 11664 . + . ID=:5141326 4 . repeat_region 4886 13244 . + . ID=:5142032 4 . transposable_element 4886 13244 . + . ID=TE59758;Name=GATE{}1697;Dbxref=FlyBase:FBti0059758,Gadfly:TE59758;synonym=GATE{}1697 4 . transcription_start_site 5031 5032 . + . ID=:5140355 4 sim4:na_dbEST.same.dmel match_part 5175 5627 . - . ID=8868228;Name=GH01459.5prime;Parent=88682278868229 4 sim4:na_dbEST.same.dmel match 5175 5627 . - . ID=88682278868229;Name=GH01459.5prime 4 . transcription_start_site 5996 5997 . - . ID=:5140417 4 . transcription_start_site 6231 6232 . + . ID=:5140356 4 sim4:na_dbEST.diff.dmel match_part 6312 6760 . + . ID=8868204;Name=EK241115.5prime;Parent=88682038868205 4 sim4:na_dbEST.diff.dmel match 6312 6760 . + . ID=88682038868205;Name=EK241115.5prime 4 HDP match 6597 6928 . + . ID=:5141702 4 sim4:na_dbEST.diff.dmel match_part 7095 7378 . + . ID=8868207;Name=CK00114.5prime.contig;Parent=88682068868208 4 sim4:na_dbEST.diff.dmel match 7095 7378 . + . ID=88682068868208;Name=CK00114.5prime.contig 4 sim4:na_dbEST.same.dmel match_part 7236 7740 . - . ID=8868231;Name=RH16086.5prime;Parent=88682308868232 4 sim4:na_dbEST.same.dmel match 7236 7740 . - . ID=88682308868232;Name=RH16086.5prime 4 sim4:na_dbEST.diff.dmel match_part 7431 7763 . + . ID=8868209;Name=CK00114.5prime.contig;Parent=88682068868208 4 HDP match 9305 10028 . - . ID=:5141722 4 . chromosome_band 9362 32056 . + . ID=band-101F1;cyto_range=101F1 4 sim4:na_dbEST.diff.dmel match_part 9485 9981 . - . ID=8868215;Name=SD08831.3prime;Parent=88682148868216 4 sim4:na_dbEST.diff.dmel match 9485 9981 . - . ID=88682148868216;Name=SD08831.3prime 4 sim4:na_dbEST.same.dmel match_part 9486 10040 . + . ID=8868234;Name=RH12136.5prime;Parent=88682338868235 4 sim4:na_dbEST.same.dmel match 9486 10040 . + . ID=88682338868235;Name=RH12136.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10058 . + . ID=8868237;Name=RH08968.5prime;Parent=88682368868238 4 sim4:na_dbEST.same.dmel match 9486 10058 . + . ID=88682368868238;Name=RH08968.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10105 . + . ID=8868240;Name=RH48040.5prime;Parent=88682398868241 4 sim4:na_dbEST.same.dmel match 9486 10105 . + . ID=88682398868241;Name=RH48040.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10133 . + . ID=8868243;Name=RH44242.5prime;Parent=88682428868244 4 sim4:na_dbEST.same.dmel match 9486 10133 . + . ID=88682428868244;Name=RH44242.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10134 . + . ID=8868246;Name=RH73307.5prime;Parent=88682459173144 4 sim4:na_dbEST.same.dmel match 9486 10134 . + . ID=88682459173144;Name=RH73307.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10149 . + . ID=9173146;Name=RH25961.5prime;Parent=91731459173147 4 sim4:na_dbEST.same.dmel match 9486 10149 . + . ID=91731459173147;Name=RH25961.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10169 . + . ID=9173149;Name=RH58061.5prime;Parent=91731489173150 4 sim4:na_dbEST.same.dmel match 9486 10169 . + . ID=91731489173150;Name=RH58061.5prime 4 sim4:na_dbEST.same.dmel match_part 9486 10189 . + . ID=9173152;Name=RH59867.5prime;Parent=91731519173153 4 sim4:na_dbEST.same.dmel match 9486 10189 . + . ID=91731519173153;Name=RH59867.5prime 4 sim4:na_dbEST.diff.dmel match_part 9885 10421 . + . ID=8868211;Name=SD22832.5prime;Parent=88682108868212 4 sim4:na_dbEST.diff.dmel match 9885 10421 . + . ID=88682108868212;Name=SD22832.5prime 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102383;Name=RH02591.5prime;Parent=101023829377562 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173155;Name=RH02741.5prime;Parent=91731549173156 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102379;Name=RH03564.5prime;Parent=101023789375809 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102399;Name=RH03774.5prime;Parent=101023989377570 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173160;Name=RH11163.5prime;Parent=91731599173161 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102371;Name=RH11216.5prime;Parent=101023709375805 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=9173165;Name=RH12703.5prime;Parent=91731649173166 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102391;Name=RH14480.5prime;Parent=101023909377554 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102375;Name=RH14757.5prime;Parent=101023749377558 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102407;Name=RH38788.5prime;Parent=101024069377578 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102415;Name=RH43241.5prime;Parent=101024149377586 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102411;Name=RH62973.5prime;Parent=101024109377582 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102403;Name=RH68715.5prime;Parent=101024029377574 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102387;Name=RH69115.5prime;Parent=101023869375816 4 sim4:na_dbEST.same.dmel match_part 9976 10009 . + . ID=10102395;Name=RH74065.5prime;Parent=101023949377566 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023829377562;Name=RH02591.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731549173156;Name=RH02741.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023789375809;Name=RH03564.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023989377570;Name=RH03774.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731599173161;Name=RH11163.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023709375805;Name=RH11216.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=91731649173166;Name=RH12703.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023909377554;Name=RH14480.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023749377558;Name=RH14757.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024069377578;Name=RH38788.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024149377586;Name=RH43241.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024109377582;Name=RH62973.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101024029377574;Name=RH68715.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023869375816;Name=RH69115.5prime 4 sim4:na_dbEST.same.dmel match 9976 10009 . + . ID=101023949377566;Name=RH74065.5prime 4 sim4:na_dbEST.same.dmel match_part 9976 10015 . - . ID=10102420;Name=RH16541.5prime;Parent=101024189375793 4 sim4:na_dbEST.same.dmel match 9976 10015 . - . ID=101024189375793;Name=RH16541.5prime 4 HDP match 10103 10417 . - . ID=:5141721 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102384;Name=RH02591.5prime;Parent=101023829377562 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173157;Name=RH02741.5prime;Parent=91731549173156 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102380;Name=RH03564.5prime;Parent=101023789375809 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102400;Name=RH03774.5prime;Parent=101023989377570 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173162;Name=RH11163.5prime;Parent=91731599173161 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102372;Name=RH11216.5prime;Parent=101023709375805 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=9173167;Name=RH12703.5prime;Parent=91731649173166 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102392;Name=RH14480.5prime;Parent=101023909377554 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102376;Name=RH14757.5prime;Parent=101023749377558 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102408;Name=RH38788.5prime;Parent=101024069377578 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102416;Name=RH43241.5prime;Parent=101024149377586 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102412;Name=RH62973.5prime;Parent=101024109377582 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102404;Name=RH68715.5prime;Parent=101024029377574 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102388;Name=RH69115.5prime;Parent=101023869375816 4 sim4:na_dbEST.same.dmel match_part 10108 10421 . + . ID=10102396;Name=RH74065.5prime;Parent=101023949377566 4 sim4:na_dbEST.same.dmel match_part 10114 10380 . - . ID=10102419;Name=RH16541.5prime;Parent=101024189375793 4 HDP match 10431 10936 . - . ID=:5141720 4 sim4:na_dbEST.diff.dmel match_part 10436 10499 . + . ID=8868213;Name=SD22832.5prime;Parent=88682108868212 4 sim4:na_dbEST.same.dmel match_part 10436 10514 . + . ID=9173158;Name=RH02741.5prime;Parent=91731549173156 4 sim4:na_dbEST.same.dmel match_part 10436 10623 . + . ID=9173163;Name=RH11163.5prime;Parent=91731599173161 4 sim4:na_dbEST.same.dmel match_part 10436 10624 . + . ID=9173168;Name=RH12703.5prime;Parent=91731649173166 4 sim4:na_dbEST.same.dmel match_part 10436 10636 . + . ID=10102373;Name=RH11216.5prime;Parent=101023709375805 4 sim4:na_dbEST.same.dmel match_part 10436 10638 . + . ID=10102377;Name=RH14757.5prime;Parent=101023749377558 4 sim4:na_dbEST.same.dmel match_part 10436 10639 . + . ID=10102381;Name=RH03564.5prime;Parent=101023789375809 4 sim4:na_dbEST.same.dmel match_part 10436 10669 . + . ID=10102385;Name=RH02591.5prime;Parent=101023829377562 4 sim4:na_dbEST.same.dmel match_part 10436 10675 . + . ID=10102393;Name=RH14480.5prime;Parent=101023909377554 4 sim4:na_dbEST.same.dmel match_part 10436 10675 . + . ID=10102389;Name=RH69115.5prime;Parent=101023869375816 4 sim4:na_dbEST.same.dmel match_part 10436 10734 . + . ID=10102397;Name=RH74065.5prime;Parent=101023949377566 4 sim4:na_dbEST.same.dmel match_part 10436 10739 . + . ID=10102401;Name=RH03774.5prime;Parent=101023989377570 4 sim4:na_dbEST.same.dmel match_part 10436 10774 . + . ID=10102405;Name=RH68715.5prime;Parent=101024029377574 4 sim4:na_dbEST.same.dmel match_part 10436 10775 . + . ID=10102409;Name=RH38788.5prime;Parent=101024069377578 4 sim4:na_dbEST.same.dmel match_part 10436 10777 . + . ID=10102413;Name=RH62973.5prime;Parent=101024109377582 4 sim4:na_dbEST.same.dmel match_part 10436 10779 . + . ID=10102417;Name=RH43241.5prime;Parent=101024149377586 4 HDP match 10968 12911 . - . ID=:5141719 4 HDP match 11351 12705 . - . ID=:5141723 4 sim4:na_dbEST.diff.dmel match_part 11561 12128 . - . ID=8868218;Name=SD14867.5prime;Parent=88682178868219 4 sim4:na_dbEST.diff.dmel match 11561 12128 . - . ID=88682178868219;Name=SD14867.5prime 4 sim4:na_transcript_dmel_r31 match 11691 12255 . - . ID=:5141587 4 . transposable_element 11691 12255 . - . ID=TE20398;Name=GATE{}1474;Dbxref=FlyBase:FBti0020398,Gadfly:TE20398;cyto_range=102A1-102A1;gbunit=AE003845;synonym=TE20398;synonym_2nd=GATE{}1474 4 sim4:na_dbEST.same.dmel match_part 12036 12645 . - . ID=10102426;Name=RH67006.5prime;Parent=101024259371916 4 sim4:na_dbEST.same.dmel match 12036 12645 . - . ID=101024259371916;Name=RH67006.5prime 4 sim4:na_dbEST.same.dmel match_part 12065 12680 . + . ID=10102422;Name=RH73606.3prime;Parent=101024219377304 4 sim4:na_dbEST.same.dmel match 12065 12680 . + . ID=101024219377304;Name=RH73606.3prime 4 sim4:na_dbEST.same.dmel match_part 12088 12645 . - . ID=10102428;Name=RH22614.5prime;Parent=101024279371908 4 sim4:na_dbEST.same.dmel match 12088 12645 . - . ID=101024279371908;Name=RH22614.5prime 4 sim4:na_dbEST.same.dmel match_part 12099 12645 . - . ID=10102430;Name=RH40331.5prime;Parent=101024299371892 4 sim4:na_dbEST.same.dmel match 12099 12645 . - . ID=101024299371892;Name=RH40331.5prime 4 sim4:na_transcript_dmel_r31 match 12291 13244 . + . ID=:5141327 4 sim4:na_dbEST.same.dmel match_part 12500 13159 . + . ID=10102424;Name=RE74714.3prime;Parent=101024239377301 4 sim4:na_dbEST.same.dmel match 12500 13159 . + . ID=101024239377301;Name=RE74714.3prime 4 sim4:na_dbEST.diff.dmel match_part 12654 13097 . - . ID=8868221;Name=SD03350.3prime;Parent=88682208868222 4 sim4:na_dbEST.diff.dmel match 12654 13097 . - . ID=88682208868222;Name=SD03350.3prime 4 sim4:na_transcript_dmel_r31 match 13288 13761 . - . ID=:5141586 4 . transcription_start_site 13733 13734 . + . ID=:5140357 4 . oligo 13735 13759 . + . ID=151319_at_40-hsp:196328;Name=151319_at_40 4 HDP match 13745 15728 . - . ID=:5141718 4 . repeat_region 13847 14009 . - . ID=:5142091 4 . transposable_element 13848 13898 . - . ID=TE62859;Name=R1{}4798;Dbxref=FlyBase:FBti0062859,Gadfly:TE62859;synonym=R1{}4798 4 . transposable_element 13913 16920 . - . ID=TE63397;Name=Rt1a{}5336;Dbxref=FlyBase:FBti0063397,Gadfly:TE63397;synonym=Rt1a{}5336 4 . repeat_region 14016 15300 . - . ID=:5142092 4 . repeat_region 15298 16140 . - . ID=:5142093 4 HDP match 16549 17324 . - . ID=:5141717 4 . transposable_element 17379 17472 . - . ID=TE62792;Name=Rt1b{}4731;Dbxref=FlyBase:FBti0062792,Gadfly:TE62792;synonym=Rt1b{}4731 4 . repeat_region 17379 17481 . - . ID=:5142094 4 sim4:na_transcript_dmel_r31 match 17702 18272 . - . ID=:5141585 4 . repeat_region 17702 18277 . - . ID=:5142095 4 . transposable_element 17702 24049 . - . ID=TE20401;Name=Rt1b{}1477;Dbxref=FlyBase:FBti0020401,Gadfly:TE20401;cyto_range=102A1-102A1;gbunit=AE003845;synonym=Rt1b{}1477,TE20401;synonym_2nd=Rt1b{}1477 4 HDP match 17946 19424 . - . ID=:5141716 4 . transposable_element 18281 23344 . + . ID=TE63368;Name=gypsy8{}5307;Dbxref=FlyBase:FBti0063368,Gadfly:TE63368;synonym=gypsy8{}5307 4 . repeat_region 18338 18730 . + . ID=:5142033 4 genscan match 18740 19127 . + . ID=:5141638 4 blastx:aa_SPTR.dmel match 18810 18941 . - . ID=:5142608 4 blastx:aa_SPTR.dmel match 19018 19188 . + . ID=:5142140 4 . repeat_region 19295 19668 . + . ID=:5142034 4 . transposable_element 19295 19668 . + . ID=TE62883;Name=Osvaldo-Dbuz-like{}4822;Dbxref=FlyBase:FBti0062883,Gadfly:TE62883;synonym=Osvaldo-Dbuz-like{}4822 4 . repeat_region 19753 20124 . + . ID=:5142035 4 . repeat_region 20125 20433 . + . ID=:5142036 4 HDP match 20207 21817 . + . ID=:5141703 4 sim4:na_dbEST.same.dmel match_part 21082 21535 . - . ID=10102434;Name=RH04454.3prime;Parent=1010243110102433 4 sim4:na_dbEST.same.dmel match 21082 21535 . - . ID=1010243110102433;Name=RH04454.3prime 4 . repeat_region 21236 21772 . + . ID=:5142037 4 sim4:na_dbEST.same.dmel match_part 21545 21617 . - . ID=10102432;Name=RH04454.3prime;Parent=1010243110102433 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152554 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152555 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152556 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152558 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152559 4 tblastx:na_dpse match 21774 21908 . + . ID=:5152573 4 tblastx:na_dpse match 21783 21908 . + . ID=:5152572 4 genscan match 21806 21906 . + . ID=:5141639 4 genie match 21901 23205 . - . ID=:5154252 4 . repeat_region 21911 21956 . + . ID=:5142038 4 . repeat_region 21959 22348 . + . ID=:5142039 4 . exon 22335 22528 . - . ID=CG32013:2;Parent=CG32013-RA 4 sim4:na_transcript_dmel_r31 match 22335 22528 . - . ID=:5141584 4 sim4:na_transcript_dmel_r32 match 22335 22528 . - . ID=:5141970 4 . gene 22335 23205 . - . ID=CG32013;Dbxref=FlyBase:FBan0032013,FlyBase:FBgn0052013;cyto_range=102A1-102A1;gbunit=AE003845;synonym=CG32013 4 . mRNA 22335 23205 . - . ID=CG32013-RA;Dbxref=FlyBase:FBtr0089183,FlyBase:FBgn0052013;Parent=CG32013;dbxref_2nd=Gadfly:CG32013-RA;synonym=CG32013-RA 4 . CDS 22338 23205 . - . ID=CG32013-PA;Dbxref=FlyBase:FBpp0088247,GB_protein:AAN06536.1,FlyBase:FBgn0052013;Parent=CG32013-RA;dbxref_2nd=Gadfly:CG32013-PA;synonym=CG32013-PA 4 . repeat_region 22360 22514 . + . ID=:5142040 4 . oligo 22451 22475 . + . ID=146624_at_344-hsp:196340;Name=146624_at_344 4 . exon 22617 23205 . - . ID=CG32013:1;Parent=CG32013-RA 4 sim4:na_transcript_dmel_r31 match 22617 23205 . - . ID=:5141583 4 sim4:na_transcript_dmel_r32 match 22617 23205 . - . ID=:5141969 4 genscan match 22634 22812 . + . ID=:5141640 4 blastx:aa_SPTR.dmel match 22792 23205 . - . ID=:5142565 4 genscan match 22822 23043 . + . ID=:5141641 4 . repeat_region 23071 23164 . + . ID=:5142041 4 . repeat_region 23345 24049 . - . ID=:5142096 4 . oligo 23689 23713 . - . ID=146635_at_262-hsp:196342;Name=146635_at_262 4 . oligo 23915 23939 . - . ID=146635_at_58-hsp:196341;Name=146635_at_58 4 tblastx:na_dpse match 24050 24187 . + . ID=:5152560 4 tblastx:na_dpse match 24050 24211 . + . ID=:5152557 4 tblastx:na_agambiae match 24050 24211 . + . ID=:5151345 -------------- next part -------------- 4 FlyBase start_codon 23203 23205 . - 0 gene_id 1;transcript_id 1;exon_id 1 4 FlyBase exon 22617 23205 . - . gene_id 1;transcript_id 1;exon_id 1 4 FlyBase CDS 22617 23205 . - 0 gene_id 1;transcript_id 1;exon_id 1 4 FlyBase exon 22335 22528 . - . gene_id 1;transcript_id 1;exon_id 2 4 FlyBase CDS 22338 23528 . - 0 gene_id 1;transcript_id 1;exon_id 2 4 FlyBase stop_codon 22335 22337 . - 0 gene_id 1;transcript_id 1;exon_id 2 From bli1 at bcm.tmc.edu Thu Nov 10 01:15:43 2005 From: bli1 at bcm.tmc.edu (Bingshan Li) Date: Thu Nov 10 01:31:02 2005 Subject: [Bioperl-l] PopGen modules In-Reply-To: <200511021018.jA2AIs8U023876@portal.open-bio.org> References: <200511021018.jA2AIs8U023876@portal.open-bio.org> Message-ID: <4372E58F.9020802@bcm.tmc.edu> Hi folks, I recently started to play with PopGen modules but am confused by the difference between "number of individuals" and "sample size". My understanding is that sample size is the number of haploids or chromosomes, and number of individuals is the number of diploids. For example, 100 humans are genotyped, then sample size should be 200 and number of individuals is 100. Am I right? I could be completely wrong but assume I am right for now. I constructed a population object (named $pop) using prettybase format. Then $stats = new Bio::PopGen::Statistics(); $number_individuals = $pop->get_number_individuals(); $seg_sites = $stats->segregating_sites_count($pop); $theta1 = $stats->theta($pop); $theta2 = $stats->theta($number_individuals, $seg_sites); $theta3 = $stats->theta($number_individuals*2, $seg_sites); In the above code, $theta1 == $theta2 != $theta3, and I think $theta3 should be the correct answer. I used "ms" program of Hudson to simulate 200 chromosomes and I used 200 as sample size which gives correct answers (double confirmed with other programs). Please let me know if I am too naive about this. From jason.stajich at duke.edu Thu Nov 10 09:51:44 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Nov 10 09:50:17 2005 Subject: [Bioperl-l] PopGen modules In-Reply-To: <4372E58F.9020802@bcm.tmc.edu> References: <200511021018.jA2AIs8U023876@portal.open-bio.org> <4372E58F.9020802@bcm.tmc.edu> Message-ID: <488C1D3F-3304-46FB-9090-CD5D438BF4C5@duke.edu> Whoops. Forgot to call the proper haploid_pop call on the population first. Apply this patch and it should work. Index: Bio/PopGen/Statistics.pm =================================================================== RCS file: /home/repository/bioperl/bioperl-live/Bio/PopGen/ Statistics.pm,v retrieving revision 1.28 diff -a -u -r1.28 Statistics.pm --- Bio/PopGen/Statistics.pm 23 Feb 2005 04:51:59 -0000 1.28 +++ Bio/PopGen/Statistics.pm 10 Nov 2005 14:51:08 -0000 @@ -750,7 +750,7 @@ # This will handle the case when we pass in a PopulationI object my $pop = $n; $totalsites = $seg_sites; # shift the arguments over by one - $n = $pop->get_number_individuals; + $n = $pop->haploid_population->get_number_individuals; $seg_sites = $self->segregating_sites_count($pop); } my $a1 = 0; On Nov 10, 2005, at 1:15 AM, Bingshan Li wrote: > Hi folks, > > I recently started to play with PopGen modules but am confused by > the difference between "number of individuals" and "sample size". > My understanding is that sample size is the number of haploids or > chromosomes, and number of individuals is the number of diploids. > For example, 100 humans are genotyped, then sample size should be > 200 and number of individuals is 100. Am I right? I could be > completely wrong but assume I am right for now. > > I constructed a population object (named $pop) using prettybase > format. Then > > $stats = new Bio::PopGen::Statistics(); > $number_individuals = $pop->get_number_individuals(); > $seg_sites = $stats->segregating_sites_count($pop); > $theta1 = $stats->theta($pop); > $theta2 = $stats->theta($number_individuals, $seg_sites); > $theta3 = $stats->theta($number_individuals*2, $seg_sites); > > In the above code, $theta1 == $theta2 != $theta3, and I think > $theta3 should be the correct answer. > > I used "ms" program of Hudson to simulate 200 chromosomes and I > used 200 as sample size which gives correct answers (double > confirmed with other programs). > > Please let me know if I am too naive about this. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From tembe at bioanalysis.org Thu Nov 10 11:12:49 2005 From: tembe at bioanalysis.org (Waibhav Tembe) Date: Thu Nov 10 11:26:46 2005 Subject: [Bioperl-l] Acknowledging BioPerl Message-ID: <43737181.5080408@bioanalysis.org> Hello List, Is there a standard way to acknowledge/cite in journal/conference papers the use of BioPerl modules? Will the following in acknowledgment suffice? "The authors would like to thank the BioPerl community (www.bioperl.org)" Thanks. From bmoore at genetics.utah.edu Thu Nov 10 11:57:07 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Thu Nov 10 11:52:52 2005 Subject: [Bioperl-l] Acknowledging BioPerl Message-ID: >From the FAQs: Q1.8: How should I cite Bioperl? A: Please cite it as: Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka ED, Wilkinson M, Birney E. The Bioperl Toolkit: Perl modules for the life sciences. Genome Research. 2002 Oct;12(10):1611-8. If you use the Bio::PopGen modules, please cite: Stajich JE and Hahn MW "Disentangling the Effects of Demography and Selection in Human History." (2005) Mol Biol Evol 22(1):63-73. -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Waibhav Tembe Sent: Thursday, November 10, 2005 9:13 AM To: Bioperl List Subject: [Bioperl-l] Acknowledging BioPerl Hello List, Is there a standard way to acknowledge/cite in journal/conference papers the use of BioPerl modules? Will the following in acknowledgment suffice? "The authors would like to thank the BioPerl community (www.bioperl.org)" Thanks. _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From tex at biocompute.net Thu Nov 10 11:56:33 2005 From: tex at biocompute.net (James Thompson) Date: Thu Nov 10 12:11:13 2005 Subject: [Bioperl-l] Acknowledging BioPerlx In-Reply-To: <43737181.5080408@bioanalysis.org> Message-ID: I'd cite the paper published in Genome Research: "The Bioperl Toolkit: Perl Modules for the Life Sciences." Vol. 12, Issue 10, 1611-1618, October 2002 Peace, James On Thu, 10 Nov 2005, Waibhav Tembe wrote: > Hello List, > > Is there a standard way to acknowledge/cite in journal/conference papers > the use of BioPerl modules? Will the following in acknowledgment suffice? > > "The authors would like to thank the BioPerl community (www.bioperl.org)" > > Thanks. > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > -- From kellert at ohsu.edu Thu Nov 10 17:32:35 2005 From: kellert at ohsu.edu (Thomas J Keller) Date: Thu Nov 10 17:33:02 2005 Subject: [Bioperl-l] installing bioperl-ext Message-ID: <7B5C9112-E08B-463C-BA5F-6DEE1CA8E026@ohsu.edu> Greetings, Trying to install the bioperl-ext-1.5.1 extensions I'm getting the following error: Writing Makefile for Bio::Ext::Align ERROR from evaluation of /usr/local/bioperl-ext-1.5.1/Bio/SeqIO/ staden/Makefile.PL: Invalid version '' for Bio::SeqIO::staden::read. Must be of the form '#.##'. (For instance '1.23') at ./Makefile.PL line 4 I installed the io_lib-1.8.11 in /usr/local/lib, /usr/local/include/ io_lib and /usr/local/bin (default locations) This isn't the "undefined symbol error" mentioned in the readme. I looked at the Makefile in Bio/SeqIO/staden but I don't see the problem: Any suggestions? running OS X 10.4.3 on an Apple G5. Thanks, From brian_osborne at cognia.com Thu Nov 10 19:07:33 2005 From: brian_osborne at cognia.com (Brian Osborne) Date: Thu Nov 10 19:06:00 2005 Subject: [Bioperl-l] RE:Problems to get secondary accessions from an object In-Reply-To: <43725342.3080908@ish.de> Message-ID: Stephan, You've lost me, I can't follow your code. Weren't you going to test your Bio::Index::Swissprot code under Bioperl 1.5.1? I think this is the best approach since there were significant changes in SeqFeature and Annotation between 1.4 and 1.5.1. Brian O. On 11/9/05 2:51 PM, "stephan" wrote: > Hi, > > I found a trace. > The problem is that after I add anotations to the object, the > rich-features are disappeared. > > snippet: > #prot is the seq object > > sub setProtAnnotations($$) { > my $prot = $_[0]; > my $col = new Bio::Annotation::Collection; > my $sv = new Bio::Annotation::SimpleValue(-value => > &getSimpleFam( $_[1] ) ); > $col->add_Annotation( 'family', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => &getWeight( $_[0] ) ); > $col->add_Annotation( 'weight', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => $link . > $prot->accession_number() ); > $col->add_Annotation( 'link', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => &getEval( $_[1] ) ); > $col->add_Annotation( 'e-val', $sv ); > $sv = new Bio::Annotation::SimpleValue( -value => $_[0]->seq() ); > $col->add_Annotation( 'sequence', $sv ); > $prot->annotation($col);} > > sub getProtAnnotation($$) { > my $ano = $_[0]->annotation(); > my @an = $ano->get_Annotations( $_[1] ); > my $erg = $an[0]->value();} > > sub setProtAnnotation($$$) { > my $prot = $_[0]; > my $ano = $prot->annotation(); > my @an = $ano->get_Annotations( $_[1] ); > my $erg = $an[0]->value( $_[2] );} > > sub getEval($) { > my $report = > $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); > my $hit = $report->next_hit(); > my $hsp = $hit->next_domain(); > my $eval = $hsp->evalue();} > > sub getSimpleFam($) { > my $report = > $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); > my $hit = $report->next_hit(); > my $fam = $hit->name();} > > > > > >> Hi, >>> >>> I have problems to get the secondary_accessions from an seq object. >>> >>> E.G >>> >>> $inx = Bio::Index::Swissprot->new($Index_File_Name); >>> $prot = $inx->fetch( $accarray[ $_[0] ] ); >>> #"$accarray[ $_[0]" is an array of accessions >>> >>> print "Description: " . $prot->description . "\n"; >>> print "Accessions: " .$sec . "\n"; >>> print "Species: " . $prot->species->binomial() . "\n"; >>> print "Length: " . $prot->length . "\n"; >>> #this looks good >>> >>> @a = $prot->get_secondary_accessions; >>> #@a is empty! >>> >>> Seems that $prot is not a reference to a rich:seq object or somthing >>> other is wrong. >>> >>> Hope that someone can help me. >>> >>> regards >>> stephan >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Thu Nov 10 20:46:32 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Thu Nov 10 20:44:57 2005 Subject: [Bioperl-l] installing bioperl-ext In-Reply-To: <7B5C9112-E08B-463C-BA5F-6DEE1CA8E026@ohsu.edu> References: <7B5C9112-E08B-463C-BA5F-6DEE1CA8E026@ohsu.edu> Message-ID: <04041328-5BBA-402C-8B4E-9650A249F2C3@duke.edu> I addressed this briefly here. http://portal.open-bio.org/pipermail/bioperl-l/2005-November/020087.html You just need to change the version to 1.51 or something. -jason On Nov 10, 2005, at 5:32 PM, Thomas J Keller wrote: > Greetings, > Trying to install the bioperl-ext-1.5.1 extensions > I'm getting the following error: > Writing Makefile for Bio::Ext::Align > ERROR from evaluation of /usr/local/bioperl-ext-1.5.1/Bio/SeqIO/ > staden/Makefile.PL: Invalid version '' for Bio::SeqIO::staden::read. > Must be of the form '#.##'. (For instance '1.23') > at ./Makefile.PL line 4 > > > I installed the io_lib-1.8.11 in /usr/local/lib, /usr/local/include/ > io_lib and /usr/local/bin (default locations) > This isn't the "undefined symbol error" mentioned in the readme. I > looked at the Makefile in Bio/SeqIO/staden but I don't see the > problem: > > > Any suggestions? > running OS X 10.4.3 on an Apple G5. > > Thanks, > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jay at jays.net Thu Nov 10 21:39:20 2005 From: jay at jays.net (Jay Hannah) Date: Thu Nov 10 22:56:46 2005 Subject: [Bioperl-l] Barry's challenge In-Reply-To: References: Message-ID: On Nov 7, 2005, at 8:53 AM, Barry Moore wrote: > Jason Stajich, who has been one of the lead developers in bioperl for > many years now, mentioned last week that: > > "Tools::StandAloneBlast could DEFINITELY be improved and needs people > to adopt it...." I'll try. :) > P.S. Write a script to use bioperl to blast search the following > sequence against a local copy of the nr database and decide what > protein > it is from and why this protein was your friend last Friday night. > MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA Thanks for the challenge!! Sweet! ... A little help? -grin- I installed bioperl, blast, and 2.6GB of nr* ~/src/blast-2.2.12/data $ du -k -c nr* 826904 nr.00.phr 22664 nr.00.pin 43776 nr.00.pnd 172 nr.00.pni 22664 nr.00.ppd 92 nr.00.ppi 593320 nr.00.psd 12920 nr.00.psi 976564 nr.00.psq 33252 nr.01.phr 964 nr.01.pin 1756 nr.01.pnd 8 nr.01.pni 964 nr.01.ppd 4 nr.01.ppi 21068 nr.01.psd 460 nr.01.psi 42436 nr.01.psq 4 nr.pal 2599992 total And then threw your challenge in a file $ cat barry.txt MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA But then my program (1) sees barry.txt, but isn't reading it...? $ cat j.pl use Bio::Tools::Run::StandAloneBlast; $ENV{BLASTDIR} = '/Users/jhannah/src/blast-2.2.12'; @params = ('database' => 'nr.00','outfile' => 'j.out'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'barry.txt' , -format => 'Fasta' ); $input = $str->next_seq(); $input2 = $str->next_seq(); $blast_report = $factory->blastall($input); $ perl j.pl -------------------- WARNING --------------------- MSG: Got a sequence with no letters in it cannot guess alphabet [] --------------------------------------------------- -------------------- WARNING --------------------- MSG: cannot find path to blastall --------------------------------------------------- So since I have no idea what I'm doing I'm hoping you can help. Thanks! I'm 2.6GB+ bio-smarter than I was last week. -laugh- j From amackey at pcbi.upenn.edu Fri Nov 11 08:01:10 2005 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Fri Nov 11 08:09:50 2005 Subject: [Bioperl-l] Barry's challenge In-Reply-To: References: Message-ID: <98540D1F-9692-4FC7-82A3-540712CA6F2A@pcbi.upenn.edu> barry.txt is not in FASTA format, it's in raw format On Nov 10, 2005, at 9:39 PM, Jay Hannah wrote: > $ cat barry.txt > MSTAGKVIKCKAAVLWELKKPFSIEEVEVAPPKAHEVRIKMVA > > But then my program (1) sees barry.txt, but isn't reading it...? -- Aaron J. Mackey, Ph.D. Project Manager, ApiDB Bioinformatics Resource Center Penn Genomics Institute, University of Pennsylvania email: amackey@pcbi.upenn.edu office: 215-898-1205 (Goddard) / 215-746-7018 (PCBI) fax: 215-746-6697 postal: Penn Genomics Institute Goddard Labs 212 415 S. University Avenue Philadelphia, PA 19104-6017 From chase.southard at uky.edu Fri Nov 11 10:07:48 2005 From: chase.southard at uky.edu (R. Chase Southard) Date: Fri Nov 11 10:07:07 2005 Subject: [Bioperl-l] your suggestions please Message-ID: I'm interested in finding a specific nuclear receptor response element (PPRE, ~13 bases, consensus TGACCTnTGACCT) in either genomic or selected gene promoter regions. After some searching, I'm unsure which method/tool I should use to match this cis-element sequence to unknowns. Would any of the following be more appropriate than another? 1. Simple Perl Regex 2. Hidden Markov Model 3. Bio::Tools::SeqPattern 4. Blast2seq - although, I thought that 13 bases may not be enough for blast 5. An application in EMBOSS or EMBASSY Thanks, Chase R. Chase Southard Research Analyst Molecular and Biomedical Pharmacology UK College of Medicine 800 Rose St MS305 UKMC Lexington, KY 40536 859-323-2604(p) 859-323-1981(f) Chase.Southard@uky.edu http://www.uky.edu/~rcsout0/ ===== STATEMENT OF CONFIDENTIALITY The contents of this e-mail message and any attachments are confidential and are intended solely for addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify the sender by reply e-mail or at (859) 323-2604 and delete this message and its attachments, if any. From jay at jays.net Fri Nov 11 13:10:32 2005 From: jay at jays.net (Jay Hannah) Date: Fri Nov 11 13:09:01 2005 Subject: [Bioperl-l] Barry's challenge In-Reply-To: <98540D1F-9692-4FC7-82A3-540712CA6F2A@pcbi.upenn.edu> References: <98540D1F-9692-4FC7-82A3-540712CA6F2A@pcbi.upenn.edu> Message-ID: On Nov 11, 2005, at 7:01 AM, Aaron J. Mackey wrote: > barry.txt is not in FASTA format, it's in raw format Thanks! On to the next challenge... My program is now: $ cat j.pl use Bio::Tools::Run::StandAloneBlast; $ENV{BLASTDIR} = '/Users/jhannah/src/blast-2.2.12/bin/'; @params = ('database' => 'nr.00','outfile' => 'j.out'); $factory = Bio::Tools::Run::StandAloneBlast->new(@params); $str = Bio::SeqIO->new(-file=>'barry.txt', -format => 'raw' ); $input = $str->next_seq(); $input2 = $str->next_seq(); $blast_report = $factory->blastall($input); When I run it it outputs: $ perl j.pl -------------------- WARNING --------------------- MSG: cannot find path to blastall --------------------------------------------------- But I think that's a red herring because when I run around in the debugger I see ================ [NULL_Caption] ERROR: Program Name was not given an argument ------------- EXCEPTION ------------- MSG: blastall call crashed: 256 /Users/jhannah/src/blast-2.2.12/bin/blastall -d "/nr.00" -i /tmp/KvbADjsmeq -o j.out STACK Bio::Tools::Run::StandAloneBlast::_runblast /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:759 STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:706 STACK Bio::Tools::Run::StandAloneBlast::blastall /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:557 STACK toplevel j.pl:8 -------------------------------------- Bio::Root::Root::throw('Bio::Tools::Run:: StandAloneBlast=HASH(0xb7cc34)','blastall call crashed: 256 /Users/jhannah/src/blast-2.2.12/bi...') called at /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 759 Bio::Tools::Run::StandAloneBlast::_runblast('Bio::Tools::Run:: StandAloneBlast=HASH(0xb7cc34)','blastall',' -d "/nr.00" -i /tmp/KvbADjsmeq -o j.out ') called at /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 706 Bio::Tools::Run::StandAloneBlast::_generic_local_blast('Bio::Tools:: Run::StandAloneBlast=HASH(0xb7cc34)','blastall','Bio:: Seq=HASH(0xb81924)','undef') called at /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 557 Bio::Tools::Run::StandAloneBlast::blastall('Bio::Tools::Run:: StandAloneBlast=HASH(0xb7cc34)','Bio::Seq=HASH(0xb81924)') called at j.pl line 8 scalar context return from CODE(0x96981c): '' ================ So I've hit my first bioperl bug, right? The output is the wrong error, yes? Should I submit a patch? To where? This mailing list? I see that Bio/Tools/Run/StandAloneBlast.pm is calling $self->throw("$executable call crashed: $? $commandstring\n") which lives down in Bio/Root/Root.pm. Is there a primer (from a user's perspective) on how I'm supposed to activate debugging/tracing? If not, should I try to figure it out and write one? Into Bio::Tools::Run::StandAloneBlast or somewhere more general purpose? Thanks all, j BioNewb From russman.dncl at gmail.com Fri Nov 11 06:12:45 2005 From: russman.dncl at gmail.com (Mikhail Pachkov) Date: Fri Nov 11 13:56:58 2005 Subject: [Bioperl-l] Drawing dna sequence Message-ID: Hello All, I have problem with drawing dna sequence using 'dna' glyph. I have a few tracks with some features and I want to draw a sequence for every track. Every track has its own sequence. I have tried to make a new feature for dna sequence and add it to the track, but it does not show anything. # $panel, $track and $sequence are defined before my $start = 0; my $end = length($sequence->seq()) - 1; my $feature = Bio::SeqFeature::Generic->new(-start=>$start, -end=>$end ); $feature->attach_seq($sequence); $track->add_feature($feature); Any suggestions appreciated. Thank you. Mikhail From Guido.Dieterich at gbf.de Thu Nov 10 03:04:44 2005 From: Guido.Dieterich at gbf.de (Guido Dieterich) Date: Fri Nov 11 14:39:39 2005 Subject: [Bioperl-l] modification in Bio::SeqIO::kegg.pm Message-ID: <1131609884.8302.270.camel@sb289.gbf-braunschweig.de> Hi Folks, I have found some errors in the kegg.pm module. I have also added some new code to read out more FIELDS in a KEGG entry ... Yours Guido #### MY CODE ##### # $Id: kegg.pm,v 1.10 2004/12/07 13:03:45 heikki Exp $ # # BioPerl module for Bio::SeqIO::kegg # # Cared for by Allen Day # # Copyright Allen Day # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::SeqIO::kegg - KEGG sequence input/output stream =head1 SYNOPSIS #It is probably best not to use this object directly, but #rather go through the SeqIO handler system. Go: $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG'); while ( my $seq = $stream->next_seq() ) { # do something with $seq } =head1 DESCRIPTION This class transforms KEGG gene records into Bio::Seq objects. =head2 Mapping of record properties to object properties This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It is far from complete and presently focuses only on those mappings which may be non-obvious. $seq in the text refers to the Bio::Seq::RichSeqI implementing object returned by the parser for each record. =over 4 =item 'ENTRY' $seq->primary_id =item 'NAME' $seq->display_id =item 'DEFINITION' $seq->annotation->get_Annotations('description'); =item 'ORTHOLOG' grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink') =item 'CLASS' grep {$_->database eq 'PATH'} $seq->annotation->get_Annotations('dblink') =item 'POSITION' FIXME, NOT IMPLEMENTED =item 'PATHWAY' for my $pathway ( $seq->annotation->get_Annotations('pathway') ) { } =item 'DBLINKS' $seq->annotation->get_Annotations('dblink') =item 'CODON_USAGE' FIXME, NOT IMPLEMENTED =item 'AASEQ' $seq->translate->seq =item 'NTSEQ' $seq-Eseq =back =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: http://bugzilla.bioperl.org/ =head1 AUTHOR - Allen Day Email allenday@ucla.edu =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqIO::kegg; use vars qw(@ISA); use strict; use Bio::SeqIO; use Bio::SeqFeature::Generic; use Bio::Species; use Bio::Seq::SeqFactory; use Bio::Annotation::Collection; use Bio::Annotation::Comment; use Bio::Annotation::DBLink; @ISA = qw(Bio::SeqIO); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); # hash for functions for decoding keys. $self->{'_func_ftunit_hash'} = {}; if( ! defined $self->sequence_factory ) { $self->sequence_factory(new Bio::Seq::SeqFactory (-verbose => $self->verbose(), -type => 'Bio::Seq::RichSeq')); } } =head2 next_seq Title : next_seq Usage : $seq = $stream->next_seq() Function: returns the next sequence in the stream Returns : Bio::Seq::RichSeq object Args : =cut sub next_seq { my ($self,@args) = @_; my $builder = $self->sequence_builder(); my $seq; my %params; my $buffer; my (@acc, @features); my ($display_id, $annotation); my $species; # initialize; we may come here because of starting over @features = (); $annotation = undef; @acc = (); $species = undef; %params = (-verbose => $self->verbose); # reset hash local($/) = "///\n"; $buffer = $self->_readline(); return undef if( !defined $buffer ); # end of file $buffer =~ /^ENTRY/ || $self->throw("KEGG stream with bad ENTRY line. Not KEGG in my book. Got '$buffer'"); my %FIELDS; my @chunks = split /\n(?=\S)/, $buffer; foreach my $chunk (@chunks){ my($key) = $chunk =~ /^(\S+)/; $FIELDS{$key} = $chunk; } # my($entry_id,$entry_seqtype,$entry_species) = $FIELDS{ENTRY} =~ /^ENTRY\s+(\d+)\s+(\S+)\s+(\S+)\s*$/; # changing to split method to get entry_ids that include sequence version like Whatever.1 my(undef,$entry_id,$entry_seqtype,$entry_species) = split(' ', $FIELDS{ENTRY}); my($name); if ($FIELDS{NAME}) { ($name) = $FIELDS{NAME} =~ /^NAME\s+(.+)$/; } my($definition) = $FIELDS{DEFINITION} =~ /^DEFINITION\s+(.+)$/s; $definition =~ s/\s+/ /gs; my($aa_length,$aa_seq) = $FIELDS{AASEQ} =~ /^AASEQ\s+(\d+)\n(.+)$/s; $aa_seq =~ s/\s+//g; my($nt_length,$nt_seq) = $FIELDS{NTSEQ} =~ /^NTSEQ\s+(\d+)\n(.+)$/s; $nt_seq =~ s/\s+//g; $annotation = Bio::Annotation::Collection->new(); $annotation->add_Annotation('description',Bio::Annotation::Comment->new(-text => $definition)); $annotation->add_Annotation('aa_seq', Bio::Annotation::Comment->new(-text => $aa_seq)); ################# NEW my($ortholog_db,$ortholog_id,$ortholog_desc); if ($FIELDS{ORTHOLOG}) { ($ortholog_db,$ortholog_id,$ortholog_desc) = $FIELDS{ORTHOLOG} =~ /^ORTHOLOG\s+(\S+):\s+(\S+)\s+(.*?)$/; $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $ortholog_db, -primary_id => $ortholog_id, -comment => $ortholog_desc) ); } ################ NEW if($FIELDS{MOTIF}){ $FIELDS{MOTIF} =~ s/^MOTIF\s+//; while($FIELDS{MOTIF} =~/\s*?(\S+):\s+(.+?)$/mg){ my $db = $1; my $ids = $2; foreach my $id (split(/\s+/, $ids)){ $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database =>$db, -primary_id => $id, -comment => "") ); } } } if($FIELDS{PATHWAY}){ $FIELDS{PATHWAY} =~ s/^PATHWAY\s+//; while($FIELDS{PATHWAY} =~ /\s*PATH:\s+(.+)$/mg){ $annotation->add_Annotation('pathway', Bio::Annotation::Comment->new(-text => "$1")); } } #################################### if ($FIELDS{CLASS}) { $FIELDS{CLASS} =~ s/^CLASS\s+//; $FIELDS{'CLASS'} =~ s/\n//g; while($FIELDS{CLASS} =~ /(.*?)\[(\S+):(\S+)\]/g){ my ($pathway,$db,$id) = ($1,$2,$3); $pathway =~ s/\s+/ /g; $pathway =~ s/\s$//g; $pathway =~ s/^\s+//; $annotation->add_Annotation('pathway', Bio::Annotation::Comment->new(-text => $pathway)); $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $db, -primary_id => $id)); } } if($FIELDS{DBLINKS}) { $FIELDS{DBLINKS} =~ s/^DBLINKS/ /; #print $FIELDS{DBLINKS}, "\n"; while($FIELDS{DBLINKS} =~ /\s+(\S+):\s+(\S+)\n?/gs){ ### modified #print "\$1 $1 \$2 $2\n"; $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => $1, -primary_id => $2)) if $1; } } $params{'-alphabet'} = 'dna'; $params{'-seq'} = $nt_seq; $params{'-display_id'} = $name; $params{'-accession_number'} = $entry_id; $params{'-species'} = Bio::Species->new(-common_name => $entry_species); $params{'-annotation'} = $annotation; $builder->add_slot_value(%params); $seq = $builder->make_object(); return $seq; } 1; From basu at pharm.sunysb.edu Fri Nov 11 13:50:37 2005 From: basu at pharm.sunysb.edu (Siddhartha Basu) Date: Fri Nov 11 14:51:12 2005 Subject: [Bioperl-l] Barry's challenge In-Reply-To: References: <98540D1F-9692-4FC7-82A3-540712CA6F2A@pcbi.upenn.edu> Message-ID: <4374E7FD.3010801@pharm.sunysb.edu> Hi, Jay Hannah wrote: > > On Nov 11, 2005, at 7:01 AM, Aaron J. Mackey wrote: > >> barry.txt is not in FASTA format, it's in raw format > > > Thanks! > > On to the next challenge... My program is now: > > $ cat j.pl > use Bio::Tools::Run::StandAloneBlast; > $ENV{BLASTDIR} = '/Users/jhannah/src/blast-2.2.12/bin/'; > @params = ('database' => 'nr.00','outfile' => 'j.out'); I think blastall is not getting the program name. Set the param with program name and rerun your script. @params = ('database' => 'nr.00','outfile' => 'j.out', 'program? => ?blastp'); -siddhartha > $factory = Bio::Tools::Run::StandAloneBlast->new(@params); > $str = Bio::SeqIO->new(-file=>'barry.txt', -format => 'raw' ); > $input = $str->next_seq(); > $input2 = $str->next_seq(); > $blast_report = $factory->blastall($input); > > > > When I run it it outputs: > > $ perl j.pl > > -------------------- WARNING --------------------- > MSG: cannot find path to blastall > --------------------------------------------------- > > > > But I think that's a red herring because when I run around in the > debugger I see > > ================ > [NULL_Caption] ERROR: Program Name was not given an argument > > ------------- EXCEPTION ------------- > MSG: blastall call crashed: 256 > /Users/jhannah/src/blast-2.2.12/bin/blastall -d "/nr.00" -i > /tmp/KvbADjsmeq -o j.out > > STACK Bio::Tools::Run::StandAloneBlast::_runblast > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:759 > STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:706 > STACK Bio::Tools::Run::StandAloneBlast::blastall > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:557 > STACK toplevel j.pl:8 > > -------------------------------------- > Bio::Root::Root::throw('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','blastall call crashed: 256 > /Users/jhannah/src/blast-2.2.12/bi...') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 759 > Bio::Tools::Run::StandAloneBlast::_runblast('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','blastall',' -d "/nr.00" -i > /tmp/KvbADjsmeq -o j.out ') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 706 > > Bio::Tools::Run::StandAloneBlast::_generic_local_blast('Bio::Tools:: > Run::StandAloneBlast=HASH(0xb7cc34)','blastall','Bio:: > Seq=HASH(0xb81924)','undef') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 557 > Bio::Tools::Run::StandAloneBlast::blastall('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','Bio::Seq=HASH(0xb81924)') called at > j.pl line 8 > scalar context return from CODE(0x96981c): '' > ================ > > > > So I've hit my first bioperl bug, right? The output is the wrong error, > yes? Should I submit a patch? To where? This mailing list? > > I see that Bio/Tools/Run/StandAloneBlast.pm is calling > > $self->throw("$executable call crashed: $? $commandstring\n") > > which lives down in Bio/Root/Root.pm. Is there a primer (from a user's > perspective) on how I'm supposed to activate debugging/tracing? If not, > should I try to figure it out and write one? Into > Bio::Tools::Run::StandAloneBlast or somewhere more general purpose? > > Thanks all, > > j > BioNewb > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Fri Nov 11 14:52:41 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Fri Nov 11 15:56:08 2005 Subject: [Bioperl-l] your suggestions please In-Reply-To: References: Message-ID: <2FAF25C2-E460-4E77-A479-3821248004FE@duke.edu> I'd just use fuzznuc from EMBOSS. depends on whether you only care about exact matches and whether or not you want gaps. On Nov 11, 2005, at 10:07 AM, R. Chase Southard wrote: > I'm interested in finding a specific nuclear receptor response > element (PPRE, ~13 bases, consensus TGACCTnTGACCT) in either > genomic or selected gene promoter regions. After some searching, > I'm unsure which method/tool I should use to match this cis-element > sequence to unknowns. > > Would any of the following be more appropriate than another? > > 1. Simple Perl Regex > 2. Hidden Markov Model > 3. Bio::Tools::SeqPattern > 4. Blast2seq - although, I thought that 13 bases may not be enough > for blast > 5. An application in EMBOSS or EMBASSY > > Thanks, > > Chase > > R. Chase Southard > Research Analyst > Molecular and Biomedical Pharmacology > UK College of Medicine > 800 Rose St MS305 UKMC > Lexington, KY 40536 > 859-323-2604(p) > 859-323-1981(f) > Chase.Southard@uky.edu > http://www.uky.edu/~rcsout0/ > > ===== > STATEMENT OF CONFIDENTIALITY > > The contents of this e-mail message and any attachments are > confidential and are intended solely for addressee. The information > may also be legally privileged. This transmission is sent in trust, > for the sole purpose of delivery to the intended recipient. If you > have received this transmission in error, any use, reproduction or > dissemination of this transmission is strictly prohibited. If you > are not the intended recipient, please immediately notify the > sender by reply e-mail or at (859) 323-2604 and delete this message > and its attachments, if any. > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From osborne1 at optonline.net Fri Nov 11 16:42:35 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Fri Nov 11 16:46:08 2005 Subject: [Bioperl-l] modification in Bio::SeqIO::kegg.pm In-Reply-To: <1131609884.8302.270.camel@sb289.gbf-braunschweig.de> Message-ID: Guido, Which new fields? Brian O. On 11/10/05 3:04 AM, "Guido Dieterich" wrote: > Hi Folks, > > I have found some errors in the kegg.pm module. > > I have also added some new code to read out more FIELDS in a KEGG > entry ... > > Yours > > Guido > > > #### MY CODE ##### > > > > # $Id: kegg.pm,v 1.10 2004/12/07 13:03:45 heikki Exp $ > # > # BioPerl module for Bio::SeqIO::kegg > # > # Cared for by Allen Day > # > # Copyright Allen Day > # > # You may distribute this module under the same terms as perl itself > > # POD documentation - main docs before the code > > =head1 NAME > > Bio::SeqIO::kegg - KEGG sequence input/output stream > > =head1 SYNOPSIS > > #It is probably best not to use this object directly, but > #rather go through the SeqIO handler system. Go: > > $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG'); > > while ( my $seq = $stream->next_seq() ) { > # do something with $seq > } > > =head1 DESCRIPTION > > This class transforms KEGG gene records into Bio::Seq objects. > > =head2 Mapping of record properties to object properties > > This section is supposed to document which sections and properties of > a KEGG databank record end up where in the Bioperl object model. It > is far from complete and presently focuses only on those mappings > which may be non-obvious. $seq in the text refers to the > Bio::Seq::RichSeqI implementing object returned by the parser for each > record. > > =over 4 > > =item 'ENTRY' > > $seq->primary_id > > =item 'NAME' > > $seq->display_id > > =item 'DEFINITION' > > $seq->annotation->get_Annotations('description'); > > =item 'ORTHOLOG' > > grep {$_->database eq 'KO'} $seq->annotation->get_Annotations('dblink') > > =item 'CLASS' > > grep {$_->database eq 'PATH'} > $seq->annotation->get_Annotations('dblink') > > =item 'POSITION' > > FIXME, NOT IMPLEMENTED > > =item 'PATHWAY' > > for my $pathway ( $seq->annotation->get_Annotations('pathway') ) { > > } > > =item 'DBLINKS' > > $seq->annotation->get_Annotations('dblink') > > =item 'CODON_USAGE' > > FIXME, NOT IMPLEMENTED > > =item 'AASEQ' > > $seq->translate->seq > > =item 'NTSEQ' > > $seq-Eseq > > =back > > =head1 FEEDBACK > > =head2 Mailing Lists > > User feedback is an integral part of the evolution of this > and other Bioperl modules. Send your comments and suggestions preferably > to one of the Bioperl mailing lists. > Your participation is much appreciated. > > bioperl-l@bioperl.org - General discussion > http://www.bioperl.org/MailList.shtml - About the mailing lists > > =head2 Reporting Bugs > > Report bugs to the Bioperl bug tracking system to help us keep track > the bugs and their resolution. > Bug reports can be submitted via email or the web: > > http://bugzilla.bioperl.org/ > > =head1 AUTHOR - Allen Day > > Email allenday@ucla.edu > > =head1 APPENDIX > > The rest of the documentation details each of the object > methods. Internal methods are usually preceded with a _ > > =cut > > # Let the code begin... > > package Bio::SeqIO::kegg; > use vars qw(@ISA); > use strict; > > use Bio::SeqIO; > use Bio::SeqFeature::Generic; > use Bio::Species; > use Bio::Seq::SeqFactory; > use Bio::Annotation::Collection; > use Bio::Annotation::Comment; > use Bio::Annotation::DBLink; > > @ISA = qw(Bio::SeqIO); > > sub _initialize { > my($self,@args) = @_; > > $self->SUPER::_initialize(@args); > # hash for functions for decoding keys. > $self->{'_func_ftunit_hash'} = {}; > if( ! defined $self->sequence_factory ) { > $self->sequence_factory(new Bio::Seq::SeqFactory > (-verbose => $self->verbose(), > -type => 'Bio::Seq::RichSeq')); > } > } > > =head2 next_seq > > Title : next_seq > Usage : $seq = $stream->next_seq() > Function: returns the next sequence in the stream > Returns : Bio::Seq::RichSeq object > Args : > > =cut > > sub next_seq { > my ($self,@args) = @_; > my $builder = $self->sequence_builder(); > my $seq; > my %params; > > my $buffer; > my (@acc, @features); > my ($display_id, $annotation); > my $species; > > # initialize; we may come here because of starting over > @features = (); > $annotation = undef; > @acc = (); > $species = undef; > %params = (-verbose => $self->verbose); # reset hash > local($/) = "///\n"; > > $buffer = $self->_readline(); > > return undef if( !defined $buffer ); # end of file > $buffer =~ /^ENTRY/ || > $self->throw("KEGG stream with bad ENTRY line. Not KEGG in my book. Got > '$buffer'"); > > my %FIELDS; > my @chunks = split /\n(?=\S)/, $buffer; > > foreach my $chunk (@chunks){ > my($key) = $chunk =~ /^(\S+)/; > $FIELDS{$key} = $chunk; > } > > # my($entry_id,$entry_seqtype,$entry_species) = $FIELDS{ENTRY} > =~ /^ENTRY\s+(\d+)\s+(\S+)\s+(\S+)\s*$/; > # changing to split method to get entry_ids that include sequence > version like Whatever.1 > my(undef,$entry_id,$entry_seqtype,$entry_species) = split(' ', > $FIELDS{ENTRY}); > > my($name); > if ($FIELDS{NAME}) { > ($name) = $FIELDS{NAME} =~ /^NAME\s+(.+)$/; > } > > my($definition) = $FIELDS{DEFINITION} =~ /^DEFINITION\s+(.+)$/s; > $definition =~ s/\s+/ /gs; > > my($aa_length,$aa_seq) = $FIELDS{AASEQ} =~ /^AASEQ\s+(\d+)\n(.+)$/s; > $aa_seq =~ s/\s+//g; > my($nt_length,$nt_seq) = $FIELDS{NTSEQ} =~ /^NTSEQ\s+(\d+)\n(.+)$/s; > $nt_seq =~ s/\s+//g; > > $annotation = Bio::Annotation::Collection->new(); > > $annotation->add_Annotation('description',Bio::Annotation::Comment->new(-text > => $definition)); > $annotation->add_Annotation('aa_seq', > Bio::Annotation::Comment->new(-text => $aa_seq)); ################# NEW > > my($ortholog_db,$ortholog_id,$ortholog_desc); > if ($FIELDS{ORTHOLOG}) { > ($ortholog_db,$ortholog_id,$ortholog_desc) = $FIELDS{ORTHOLOG} > =~ /^ORTHOLOG\s+(\S+):\s+(\S+)\s+(.*?)$/; > > $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => > $ortholog_db, > > -primary_id => $ortholog_id, > > -comment => $ortholog_desc) > ); > } > ################ NEW > if($FIELDS{MOTIF}){ > $FIELDS{MOTIF} =~ s/^MOTIF\s+//; > while($FIELDS{MOTIF} =~/\s*?(\S+):\s+(.+?)$/mg){ > my $db = $1; > my $ids = $2; > foreach my $id (split(/\s+/, $ids)){ > > $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database > =>$db, > > -primary_id => $id, > > -comment => "") > ); > } > } > } > > > if($FIELDS{PATHWAY}){ > $FIELDS{PATHWAY} =~ s/^PATHWAY\s+//; > while($FIELDS{PATHWAY} =~ /\s*PATH:\s+(.+)$/mg){ > $annotation->add_Annotation('pathway', > Bio::Annotation::Comment->new(-text => "$1")); > } > } > #################################### > > if ($FIELDS{CLASS}) { > $FIELDS{CLASS} =~ s/^CLASS\s+//; > $FIELDS{'CLASS'} =~ s/\n//g; > while($FIELDS{CLASS} =~ /(.*?)\[(\S+):(\S+)\]/g){ > my ($pathway,$db,$id) = ($1,$2,$3); > $pathway =~ s/\s+/ /g; > $pathway =~ s/\s$//g; > $pathway =~ s/^\s+//; > $annotation->add_Annotation('pathway', > Bio::Annotation::Comment->new(-text => $pathway)); > > $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => > $db, -primary_id => $id)); > } > } > > > if($FIELDS{DBLINKS}) { > $FIELDS{DBLINKS} =~ s/^DBLINKS/ /; > #print $FIELDS{DBLINKS}, "\n"; > while($FIELDS{DBLINKS} =~ /\s+(\S+):\s+(\S+)\n?/gs){ ### modified > #print "\$1 $1 \$2 $2\n"; > > $annotation->add_Annotation('dblink',Bio::Annotation::DBLink->new(-database => > $1, -primary_id => $2)) if $1; > } > } > > $params{'-alphabet'} = 'dna'; > $params{'-seq'} = $nt_seq; > $params{'-display_id'} = $name; > $params{'-accession_number'} = $entry_id; > $params{'-species'} = Bio::Species->new(-common_name => > $entry_species); > $params{'-annotation'} = $annotation; > > $builder->add_slot_value(%params); > $seq = $builder->make_object(); > > return $seq; > } > > 1; > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Fri Nov 11 18:41:17 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Fri Nov 11 18:37:09 2005 Subject: [Bioperl-l] Barry's challenge Message-ID: Jay- Blast is actually a collection of programs and blastall runs them all, so for each invocation of blastall you need to tell it which program you want to run. In this case you are "blasting" a protein sequence, so you want to run blastp therefore your parameters should include program => 'blastp' (of course you wouldn't know that since it wasn't in the documentation). BTW, I'm not sure what's going on with these environment variables, but in my hands setting BLASTDIR, and BLASTDATADIR don't seem to help. What works for me is 1) make sure the blast executables are in your path, 2) set BLASTDB to the location of your database, and BLASTMAT to the location of your matrix files which will be BLOSUM62. For my installation the last two are both /usr/local/share/blast-2.1.1/data. >From your script I'm guessing that yours is /Users/jhannah/src/blast-2.2.12/data/. Those are the two environment variables that the blast executable wants set, and I'm sure that they used to be documented in the blast docs as such, but now all I see in their docs is reference to a ncbi.rc file which for me and others I've talked to doesn't appear to do it's job. I'd love to hear what I'm missing here if someone else wants to chime in and set me straight on all of this, but that's what works for me right now. BTW, if you are going to get into Blast and sequence alignment, and you if you like O'Reilly books (and what perl hacker doesn't) you might want to have a look at the O'Reilly book on BLAST (http://www.oreilly.com/catalog/blast/index.html). It may be particularly helpful since it has a nice concise section on theory - both biological and computational behind blast sequence alignments. Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of Jay Hannah > Sent: Friday, November 11, 2005 11:11 AM > To: bioperl-l@bioperl.org > Subject: Re: [Bioperl-l] Barry's challenge > > > On Nov 11, 2005, at 7:01 AM, Aaron J. Mackey wrote: > > barry.txt is not in FASTA format, it's in raw format > > Thanks! > > On to the next challenge... My program is now: > > $ cat j.pl > use Bio::Tools::Run::StandAloneBlast; > $ENV{BLASTDIR} = ''; > @params = ('database' => 'nr.00','outfile' => 'j.out'); > $factory = Bio::Tools::Run::StandAloneBlast->new(@params); > $str = Bio::SeqIO->new(-file=>'barry.txt', -format => 'raw' ); > $input = $str->next_seq(); > $input2 = $str->next_seq(); > $blast_report = $factory->blastall($input); > > > > When I run it it outputs: > > $ perl j.pl > > -------------------- WARNING --------------------- > MSG: cannot find path to blastall > --------------------------------------------------- > > > > But I think that's a red herring because when I run around in the > debugger I see > > ================ > [NULL_Caption] ERROR: Program Name was not given an argument > > ------------- EXCEPTION ------------- > MSG: blastall call crashed: 256 > /Users/jhannah/src/blast-2.2.12/bin/blastall -d "/nr.00" -i > /tmp/KvbADjsmeq -o j.out > > STACK Bio::Tools::Run::StandAloneBlast::_runblast > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:759 > STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:706 > STACK Bio::Tools::Run::StandAloneBlast::blastall > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm:557 > STACK toplevel j.pl:8 > > -------------------------------------- > > Bio::Root::Root::throw('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','blastall call crashed: 256 > /Users/jhannah/src/blast-2.2.12/bi...') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 759 > > Bio::Tools::Run::StandAloneBlast::_runblast('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','blastall',' -d "/nr.00" -i > /tmp/KvbADjsmeq -o j.out ') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 706 > > Bio::Tools::Run::StandAloneBlast::_generic_local_blast('Bio::Tools:: > Run::StandAloneBlast=HASH(0xb7cc34)','blastall','Bio:: > Seq=HASH(0xb81924)','undef') called at > /Library/Perl/5.8.1/Bio/Tools/Run/StandAloneBlast.pm line 557 > > Bio::Tools::Run::StandAloneBlast::blastall('Bio::Tools::Run:: > StandAloneBlast=HASH(0xb7cc34)','Bio::Seq=HASH(0xb81924)') called at > j.pl line 8 > scalar context return from CODE(0x96981c): '' > ================ > > > > So I've hit my first bioperl bug, right? The output is the wrong error, > yes? Should I submit a patch? To where? This mailing list? > > I see that Bio/Tools/Run/StandAloneBlast.pm is calling > > $self->throw("$executable call crashed: $? $commandstring\n") > > which lives down in Bio/Root/Root.pm. Is there a primer (from a user's > perspective) on how I'm supposed to activate debugging/tracing? If not, > should I try to figure it out and write one? Into > Bio::Tools::Run::StandAloneBlast or somewhere more general purpose? > > Thanks all, > > j > BioNewb > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Sat Nov 12 17:46:31 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sat Nov 12 17:45:04 2005 Subject: [Bioperl-l] FAQ Message-ID: <2D1ACCCD-F380-4F65-BB37-D4F0F906EEFC@duke.edu> How do people feel about moving the FAQ to just the Wiki instead of a text file in the distribution? It seems to me it will be easier to keep updated if it is on the web as there is less activation energy in cutting+pasting from an email message to the website when a question is answered, while editing the XML and cvs committing is little more work. There may be some way to export the text from the Wiki into a suitable file for inclusion in the distribution. I think the ability to link to each q&a in the HTML, I'm sure there is a way to do it in the wiki, hopefully not too tedious. -jason -- Jason Stajich Duke University http://www.duke.edu/~jes12 From osborne1 at optonline.net Sat Nov 12 18:21:48 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Sat Nov 12 18:25:05 2005 Subject: [Bioperl-l] FAQ In-Reply-To: <2D1ACCCD-F380-4F65-BB37-D4F0F906EEFC@duke.edu> Message-ID: Jason, Good idea. Brian O. On 11/12/05 5:46 PM, "Jason Stajich" wrote: > How do people feel about moving the FAQ to just the Wiki instead of a > text file in the distribution? It seems to me it will be easier to > keep updated if it is on the web as there is less activation energy > in cutting+pasting from an email message to the website when a > question is answered, while editing the XML and cvs committing is > little more work. > > There may be some way to export the text from the Wiki into a > suitable file for inclusion in the distribution. I think the ability > to link to each q&a in the HTML, I'm sure there is a way to do it in > the wiki, hopefully not too tedious. > > -jason > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From stephan.rosecker at ish.de Sun Nov 13 14:12:26 2005 From: stephan.rosecker at ish.de (stephan) Date: Sun Nov 13 14:10:55 2005 Subject: [Bioperl-l] Problems to get secondary accessions Message-ID: <4377901A.6070802@ish.de> Hi, because I have still the same trouble, here is a example to retrace my problem. After a collection is added, the second call ($seq->get_secondary_accessions) gives nothing back. I get only: HAL007 C3PO01 Is it a bug, a feature, or normal behavior - ? I am a little bit confused - I am using bioper 1.4. regards stephan --------- the script ----------------------------- #!/xprog/perl/perl-5.9.1_inst/bin/perl use lib "perl5"; use strict; $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File"; $ENV{BIOPERL_INDEX} = "."; use Bio::Index::Swissprot; my $accs = qw(P09651); my $file_name = "swiss.dat"; my $inx = Bio::Index::Swissprot->new(-filename => $file_name . ".idx", -write_flag => 1); $inx->id_parser(\&get_id); $inx->make_index($file_name); my $seq = $inx->fetch($accs); my @sec1 = $seq->get_secondary_accessions; print "@sec1\n"; my $col = new Bio::Annotation::Collection; my $sv = new Bio::Annotation::SimpleValue(-value => 'foo' ); $col->add_Annotation( 'bar', $sv ); $seq->annotation($col); my @sec2 = $seq->get_secondary_accessions; print "@sec2\n"; sub get_id { my $line = shift; $line =~ /AC\s+([A-Z]\d+);/; $1; } ----------------And the flatfile (swiss.dat):----------------- ID 128U_DROME STANDARD; PRT; 368 AA. AC P09651; HAL007; C3PO01; DT 01-OCT-1993 (Rel. 27, Created) DT 01-OCT-1993 (Rel. 27, Last sequence update) DT 01-FEB-1996 (Rel. 33, Last annotation update) DE GTP-binding protein 128UP. GN 128UP OR GTP-BP. OS Drosophila melanogaster (Fruit fly). OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; OC Ephydroidea; Drosophilidae; Drosophila. OX NCBI_TaxID=7227; RN [1] RP SEQUENCE FROM N.A. RC STRAIN=Oregon-R; RX MEDLINE=94166747; PubMed=8121394; RA Sommer K.A., Petersen G., Bautz E.K.F.; RT "The gene upstream of DmRP128 codes for a novel GTP-binding protein RT of Drosophila melanogaster."; RL Mol. Gen. Genet. 242:391-398(1994). CC -!- SIMILARITY: Belongs to the GTP1 / OBG family. CC -------------------------------------------------------------------------- CC This SWISS-PROT entry is copyright. It is produced through a collaboration CC between the Swiss Institute of Bioinformatics and the EMBL outstation - CC the European Bioinformatics Institute. There are no restrictions on its CC use by non-profit institutions as long as its content is in no way CC modified and this statement is not removed. Usage by and for commercial CC entities requires a license agreement (See http://www.isb-sib.ch/announce/ CC or send an email to license@isb-sib.ch). CC -------------------------------------------------------------------------- DR EMBL; X71866; CAA50701.1; -. DR PIR; S42582; S42582. DR FlyBase; FBgn0010339; 128up. DR GO; GO:0005525; F:GTP binding; IDA. DR InterPro; IPR006074; GTP1/OBG_dom. DR InterPro; IPR006073; GTP1_OBG. DR InterPro; IPR006169; GTP1_OBG_sub. DR InterPro; IPR005225; Small_GTP. DR InterPro; IPR004095; TGS_dom. DR Pfam; PF01018; GTP1_OBG; 1. DR Pfam; PF02824; TGS; 1. DR PRINTS; PR00326; GTP1OBG. DR TIGRFAMs; TIGR00231; small_GTP; 1. DR PROSITE; PS00905; GTP1_OBG; 1. KW GTP-binding. FT NP_BIND 71 78 GTP (By similarity). FT NP_BIND 117 121 GTP (By similarity). FT NP_BIND 248 251 GTP (By similarity). SQ SEQUENCE 368 AA; 41129 MW; 07C592292BA12A6E CRC64; MITILEKISA IESEMARTQK NKATSAHLGL LKANVAKLRR ELISPKGGGG GTGEAGFEVA KTGDARVGFV GFPSVGKSTL LSNLAGVYSE VAAYEFTTLT TVPGCIKYKG AKIQLLDLPG IIEGAKDGKG RGRQVIAVAR TCNLIFMVLD CLKPLGHKKL LEHELEGFGI RLNKKPPNIY YKRKDKGGIN LNSMVPQSEL DTDLVKTILS EYKIHNADIT LRYDATSDDL IDVIEGNRIY IPCIYLLNKI DQISIEELDV IYKIPHCVPI SAHHHWNFDD LLELMWEYLR LQRIYTKPKG QLPDYNSPVV LHNERTSIED FCNKLHRSIA KEFKYALVWG SSVKHQPQKV GIEHVLNDED VVQIVKKV // From osborne1 at optonline.net Sun Nov 13 14:58:26 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Sun Nov 13 15:01:41 2005 Subject: [Bioperl-l] Problems to get secondary accessions In-Reply-To: <4377901A.6070802@ish.de> Message-ID: Stephan, Please test using Bioperl 1.5.1. Brian O. On 11/13/05 2:12 PM, "stephan" wrote: > Hi, > > because I have still the same trouble, > here is a example to retrace my problem. > > After a collection is added, the second call > ($seq->get_secondary_accessions) gives nothing back. > > I get only: HAL007 C3PO01 > > Is it a bug, a feature, or normal behavior - ? > I am a little bit confused - > I am using bioper 1.4. > > regards > stephan > > > > --------- the script ----------------------------- > > #!/xprog/perl/perl-5.9.1_inst/bin/perl > use lib "perl5"; > > use strict; > $ENV{BIOPERL_INDEX_TYPE} = "SDBM_File"; > $ENV{BIOPERL_INDEX} = "."; > > use Bio::Index::Swissprot; > > my $accs = qw(P09651); > my $file_name = "swiss.dat"; > my $inx = Bio::Index::Swissprot->new(-filename => $file_name . ".idx", > -write_flag => 1); > $inx->id_parser(\&get_id); > $inx->make_index($file_name); > > > my $seq = $inx->fetch($accs); > > my @sec1 = $seq->get_secondary_accessions; > print "@sec1\n"; > > my $col = new Bio::Annotation::Collection; > my $sv = new Bio::Annotation::SimpleValue(-value => 'foo' ); > $col->add_Annotation( 'bar', $sv ); > $seq->annotation($col); > > my @sec2 = $seq->get_secondary_accessions; > print "@sec2\n"; > > > sub get_id { > my $line = shift; > $line =~ /AC\s+([A-Z]\d+);/; > $1; > } > > > > ----------------And the flatfile (swiss.dat):----------------- > > ID 128U_DROME STANDARD; PRT; 368 AA. > AC P09651; HAL007; C3PO01; > DT 01-OCT-1993 (Rel. 27, Created) > DT 01-OCT-1993 (Rel. 27, Last sequence update) > DT 01-FEB-1996 (Rel. 33, Last annotation update) > DE GTP-binding protein 128UP. > GN 128UP OR GTP-BP. > OS Drosophila melanogaster (Fruit fly). > OC Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; > OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; > OC Ephydroidea; Drosophilidae; Drosophila. > OX NCBI_TaxID=7227; > RN [1] > RP SEQUENCE FROM N.A. > RC STRAIN=Oregon-R; > RX MEDLINE=94166747; PubMed=8121394; > RA Sommer K.A., Petersen G., Bautz E.K.F.; > RT "The gene upstream of DmRP128 codes for a novel GTP-binding protein > RT of Drosophila melanogaster."; > RL Mol. Gen. Genet. 242:391-398(1994). > CC -!- SIMILARITY: Belongs to the GTP1 / OBG family. > CC > -------------------------------------------------------------------------- > CC This SWISS-PROT entry is copyright. It is produced through a > collaboration > CC between the Swiss Institute of Bioinformatics and the EMBL > outstation - > CC the European Bioinformatics Institute. There are no restrictions > on its > CC use by non-profit institutions as long as its content is in > no way > CC modified and this statement is not removed. Usage by and for > commercial > CC entities requires a license agreement (See > http://www.isb-sib.ch/announce/ > CC or send an email to license@isb-sib.ch). > CC > -------------------------------------------------------------------------- > DR EMBL; X71866; CAA50701.1; -. > DR PIR; S42582; S42582. > DR FlyBase; FBgn0010339; 128up. > DR GO; GO:0005525; F:GTP binding; IDA. > DR InterPro; IPR006074; GTP1/OBG_dom. > DR InterPro; IPR006073; GTP1_OBG. > DR InterPro; IPR006169; GTP1_OBG_sub. > DR InterPro; IPR005225; Small_GTP. > DR InterPro; IPR004095; TGS_dom. > DR Pfam; PF01018; GTP1_OBG; 1. > DR Pfam; PF02824; TGS; 1. > DR PRINTS; PR00326; GTP1OBG. > DR TIGRFAMs; TIGR00231; small_GTP; 1. > DR PROSITE; PS00905; GTP1_OBG; 1. > KW GTP-binding. > FT NP_BIND 71 78 GTP (By similarity). > FT NP_BIND 117 121 GTP (By similarity). > FT NP_BIND 248 251 GTP (By similarity). > SQ SEQUENCE 368 AA; 41129 MW; 07C592292BA12A6E CRC64; > MITILEKISA IESEMARTQK NKATSAHLGL LKANVAKLRR ELISPKGGGG GTGEAGFEVA > KTGDARVGFV GFPSVGKSTL LSNLAGVYSE VAAYEFTTLT TVPGCIKYKG AKIQLLDLPG > IIEGAKDGKG RGRQVIAVAR TCNLIFMVLD CLKPLGHKKL LEHELEGFGI RLNKKPPNIY > YKRKDKGGIN LNSMVPQSEL DTDLVKTILS EYKIHNADIT LRYDATSDDL IDVIEGNRIY > IPCIYLLNKI DQISIEELDV IYKIPHCVPI SAHHHWNFDD LLELMWEYLR LQRIYTKPKG > QLPDYNSPVV LHNERTSIED FCNKLHRSIA KEFKYALVWG SSVKHQPQKV GIEHVLNDED > VVQIVKKV > // > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From avilella at ub.edu Mon Nov 14 05:16:30 2005 From: avilella at ub.edu (Albert Vilella) Date: Mon Nov 14 05:36:11 2005 Subject: [Bioperl-l] Bio::Tree newick and internal nodes Message-ID: <1131963390.8065.1.camel@localhost.localdomain> Hi all, I'm having a trouble with the newick module when trying to print out the tree coming from a mlc codeml result file. There is some combination of internal node arrangements that gives this tree: (Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5; Instead of what has to be... ((Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5); ...to play well with some programs (PAML's evolver in this case). Any hint if this is/should_be ok? Also, is there a way to print out a newick tree in which only the leaf nodes have the ids printed? E.g.: (Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239):0.000000); Thanks in advance, Bests, Albert. From jiesheng at bioteam.net Tue Nov 15 08:51:25 2005 From: jiesheng at bioteam.net (jiesheng zhang) Date: Tue Nov 15 08:38:13 2005 Subject: [Bioperl-l] is Bio::Tools:GuessSeqFormat in bioperl-1.4? Message-ID: <4379E7DD.1000800@bioteam.net> Hi, I just installed the bioperl-1.4 for a OSX box. From the bioperl complete modules documentation(http://doc.bioperl.org/releases/bioperl-1.4), the Bio::Tools::GuessSeqFormat should be in the bioperl-1.4 release. However, I could not find it anywhere in my system. After I installed the bioperl-1.5, the Bio::Tools::GuessSeqFormat was shown up in my system. Is the Bio::Tools::GuessSeqFormat is in bioperl-1.4 or it is new in bioperl-1.5? Thanks -jiesheng From Steve_Chervitz at affymetrix.com Tue Nov 15 13:47:54 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Tue Nov 15 13:57:24 2005 Subject: [Bioperl-l] FAQ In-Reply-To: <2D1ACCCD-F380-4F65-BB37-D4F0F906EEFC@duke.edu> Message-ID: Good plan. Easier to update, search, and reference. Steve > From: Jason Stajich > Date: Sat, 12 Nov 2005 17:46:31 -0500 > To: bioperl-ml List > Subject: [Bioperl-l] FAQ > > How do people feel about moving the FAQ to just the Wiki instead of a > text file in the distribution? It seems to me it will be easier to > keep updated if it is on the web as there is less activation energy > in cutting+pasting from an email message to the website when a > question is answered, while editing the XML and cvs committing is > little more work. > > There may be some way to export the text from the Wiki into a > suitable file for inclusion in the distribution. I think the ability > to link to each q&a in the HTML, I'm sure there is a way to do it in > the wiki, hopefully not too tedious. > > -jason > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From muratem at eng.uah.edu Tue Nov 15 14:57:29 2005 From: muratem at eng.uah.edu (Mike Muratet) Date: Tue Nov 15 15:10:44 2005 Subject: [Bioperl-l] biosql & bioperl-db on Solaris Message-ID: Greetings This is not strictly a bioperl or biosql issue, but is related. In the process of trying to install bioperl-db on a Solaris 9 system, I had to go back and install the latest bioperl, DBI, AND DBD modules. The DBD install via CPAN is failing for an ELF64 incompatibility when it tries to link to the mysql client libs because I also installed the latest 64bit mysql. According to the mysql docs, 64bit is 4% slower than the 32bit version, but you get more threads and memory (which would seem to be faster in the long run). Although I have installed gcc and gnu make, CPAN is picking up the native Sun compiler (and why do they spread things out over so many subdirectories?) and linker. Has anyone else come up against this before (I didn't find anything in the archives)? Is the best course to install a 32bit mysql? Should I forgo CPAN and try to do a manual install where I might have some control over Makefile.PL? Has anybody tried biosql on a 64bit system and does it make a difference? Thanks Mike From osborne1 at optonline.net Tue Nov 15 17:37:02 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Tue Nov 15 17:42:33 2005 Subject: [Bioperl-l] biosql & bioperl-db on Solaris In-Reply-To: Message-ID: Mike, If I'm understanding this correctly you'd like the build to use gcc. Did you try things like: setenv CC gcc ? The equivalent of the command above in the CPAN shell would be: cpan>o conf makepl_arg CC=gcc Brian O. > > This is not strictly a bioperl or biosql issue, but is related. In the > process of trying to install bioperl-db on a Solaris 9 system, I had to go > back and install the latest bioperl, DBI, AND DBD modules. The DBD install > via CPAN is failing for an ELF64 incompatibility when it tries to link to > the mysql client libs because I also installed the > latest 64bit mysql. According to the mysql docs, 64bit is 4% slower > than the 32bit version, but you get more threads and memory (which would > seem to be faster in the long run). > > Although I have installed gcc and gnu make, CPAN is picking up the native > Sun compiler (and why do they spread things out over so many > subdirectories?) and linker. > > Has anyone else come up against this before (I didn't find anything in the > archives)? Is the best course to install a 32bit mysql? Should I forgo > CPAN and try to do a manual install where I might have some control over > Makefile.PL? Has anybody tried biosql on a 64bit system and does it make a > difference? > > Thanks > > Mike > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From osborne1 at optonline.net Tue Nov 15 17:43:16 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Tue Nov 15 17:47:17 2005 Subject: [Bioperl-l] is Bio::Tools:GuessSeqFormat in bioperl-1.4? In-Reply-To: <4379E7DD.1000800@bioteam.net> Message-ID: Jiesheng, Yes, it's in 1.4: >tar tvf bioperl-1.4.tar | grep Guess -rw-r--r-- heikki/heikki 20927 2003-12-16 11:58:51 bioperl-1.4/Bio/Tools/GuessSeqFormat.pm Brian O. On 11/15/05 8:51 AM, "jiesheng zhang" wrote: > Hi, > I just installed the bioperl-1.4 for a OSX box. From the bioperl > complete modules > documentation(http://doc.bioperl.org/releases/bioperl-1.4), the > Bio::Tools::GuessSeqFormat should be in the bioperl-1.4 release. > However, I could not find it anywhere in my system. > After I installed the bioperl-1.5, the Bio::Tools::GuessSeqFormat was > shown up in my system. Is the Bio::Tools::GuessSeqFormat is in > bioperl-1.4 or it is new in bioperl-1.5? > > Thanks > > -jiesheng > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From slenk at emich.edu Tue Nov 15 18:59:40 2005 From: slenk at emich.edu (Stephen Gordon Lenk) Date: Tue Nov 15 19:57:58 2005 Subject: [Bioperl-l] Automatic design of gene fusion primers for pET-32 Message-ID: <4c76f034c726ae.4c726ae4c76f03@emich.edu> Hi, I've written a package to generate correct gene fusion primers for the pET-32a vector for a given gene sequence. It is flexible enough to use with other vectors (I believe), but I am working with the pET-32a vector (Novagen) now. I seek guidance on whether anyone is even interested in using this software, as the process of designing good gene fusion primers can be painful. In case this is unclear, the pET-32a vector allows for the directional cloning of a gene into a plasmid that can be inserted into a host, where the plasmid can be turned on to express the inserted gene. A matched pair of restriction enzymes is used to cut vector and gene, which are then ligated together. The PCR primers can be used to both amplify the gene and modify it so that the restriction enzymes will cut it correctly for proper insertion, where the ideal solution joins the gene to the plasmid in such a way that the ATG codon joins each at the front and the downstream join is past the end codon of the gene. THE WHOLE GENE AND NOTHING BUT THE GENE. Designing an optimal pair of primers takes time and insight. I have no desire to prevent such effort, but I have observed that it can be difficult and frustrating for non-experts. To assist such people, and for my own amusement, I have writen Perl software to automate this process. The software uses combinatorics, constraint satisfaction, and a small bit of expert system flavoring to produce as optimal a solution as it can. This solution is checked internally against Primer3 to see if the primers it has desugned are usable. The Primer3 check is automatic and those results are returned to the user, without striving to discourage later checks. The restriction enzyme pair used is also returned since this is useful information for those wishing to do a restriction digest. Is this of use to anyone? If it is of use, I'd like to appropriately package and distribute it under the same terms as Perl, that is without cost to a user, and without liability to myself. Please advise me as to potential inetrest. I do not plan to Bioperlify it, but it should be easy to call from a Bioperl environment. Steve Lenk slenk@emich.edu From hlapp at gnf.org Tue Nov 15 21:21:45 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Tue Nov 15 21:38:34 2005 Subject: [Bioperl-l] Re: [BioSQL-l] biosql & bioperl-db on Solaris In-Reply-To: <6D9E9B9DF347EF4385F6271C64FB8D5602656B0D@BIONIC.biopolis.one-north.com> References: <6D9E9B9DF347EF4385F6271C64FB8D5602656B0D@BIONIC.biopolis.one-north.com> Message-ID: <127e679dc3afe7d59f62ed4bd1719450@gnf.org> I believe the DBI docs make a pretty strong statement about perl, your database client library, and DBI/DBD having to be compiled by the same compiler using the same settings. This may be a bit too strong of a statement, but I'd definitely make sure that if you want 64bit in the DBD driver perl is also 64-bit compiled, and that they are all compiled by the same brand of compiler. I.e., you may have to compile perl and the mysql client lib yourself, using either the Sun native compiler, or gcc, for all of them consistently. Also, I'd definitely forgo CPAN for DBI and DBD::mysql; building and installing manually is fairly easy if you don't have dependencies (perl Makefile.PL; make; make test; make install), and the INSTALL or README document will tell you how to control the choice of compiler (often it's like 'make CC=gcc' or some such). -hilmar On Nov 15, 2005, at 5:47 PM, Richard HOLLAND wrote: > Hi, > > This may seem a bit basic but it's worth a go. > > CPAN looks for "cc" - which on a Sun machine is the Sun compiler. If > you > have "gcc" installed then you may need to create a soft-link to it > called "cc" and ensure that softlink appears earlier in your path than > the location of the Sun compiler. You must then export the path or add > it to your profile as CPAN starts new sub-shells internally). > > eg. if your gcc binary is /usr/bin/gcc, and assuming a bash-like shell: > > mkdir ~/bin > ln -s /usr/bin/gcc ~/bin/cc > PATH=~/bin:$PATH > export PATH > > Then run CPAN and see what happens. > > Hope it helps. > > cheers, > Richard > > Richard Holland > Bioinformatics Specialist > GIS extension 8199 > --------------------------------------------- > This email is confidential and may be privileged. If you are not the > intended recipient, please delete it and notify us immediately. Please > do not copy or use it for any purpose, or disclose its content to any > other person. Thank you. > --------------------------------------------- > > >> -----Original Message----- >> From: biosql-l-bounces@portal.open-bio.org >> [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of >> Mike Muratet >> Sent: Wednesday, November 16, 2005 3:57 AM >> To: biosql-l@open-bio.org >> Cc: bioperl-l@bioperl.org >> Subject: [BioSQL-l] biosql & bioperl-db on Solaris >> >> >> Greetings >> >> This is not strictly a bioperl or biosql issue, but is >> related. In the >> process of trying to install bioperl-db on a Solaris 9 >> system, I had to go >> back and install the latest bioperl, DBI, AND DBD modules. >> The DBD install >> via CPAN is failing for an ELF64 incompatibility when it >> tries to link to >> the mysql client libs because I also installed the >> latest 64bit mysql. According to the mysql docs, 64bit is 4% slower >> than the 32bit version, but you get more threads and memory >> (which would >> seem to be faster in the long run). >> >> Although I have installed gcc and gnu make, CPAN is picking >> up the native >> Sun compiler (and why do they spread things out over so many >> subdirectories?) and linker. >> >> Has anyone else come up against this before (I didn't find >> anything in the >> archives)? Is the best course to install a 32bit mysql? >> Should I forgo >> CPAN and try to do a manual install where I might have some >> control over >> Makefile.PL? Has anybody tried biosql on a 64bit system and >> does it make a >> difference? >> >> Thanks >> >> Mike >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l@open-bio.org >> http://open-bio.org/mailman/listinfo/biosql-l >> > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Wed Nov 16 05:41:42 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 16 05:46:41 2005 Subject: [Bioperl-l] load in biosql a genome genbank file In-Reply-To: <1131449201.8302.222.camel@sb289.gbf-braunschweig.de> References: <1131449201.8302.222.camel@sb289.gbf-braunschweig.de> Message-ID: The genome is in genbank format, right? Generally speaking there is little limit on what you can load into BioSQL; if you are referring to load_seqdatabase.pl, it can load any format that's understood by the Bio::SeqIO system in Bioperl. Let me know if you were thinking about something else. -hilmar On Nov 8, 2005, at 3:26 AM, Guido Dieterich wrote: > Hi > > is it possible to load into biosql a complete bacterial genome genbank > file > from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ > > Best regards > > Guido > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Wed Nov 16 05:47:03 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 16 05:52:03 2005 Subject: [Bioperl-l] RE:Problems to get secondary accessions from an object In-Reply-To: <43725342.3080908@ish.de> References: <43725342.3080908@ish.de> Message-ID: <0e2c030d54f9e3deb44ac49755616c5d@gmx.net> Stephan, is it necessary that you create your own annotation collection? If you replace the line my $col = new Bio::Annotation::Collection; with my $col = $prot->annotation; you wouldn't lose annotation that's already present in the sequence's existing annotation collection. (And you could then also remove the then superfluous setter call $prot->annotation($col);) -hilmar On Nov 9, 2005, at 11:51 AM, stephan wrote: > Hi, > > I found a trace. > The problem is that after I add anotations to the object, the > rich-features are disappeared. > > snippet: > #prot is the seq object > > sub setProtAnnotations($$) { > my $prot = $_[0]; > my $col = new Bio::Annotation::Collection; > my $sv = new Bio::Annotation::SimpleValue(-value => > &getSimpleFam( $_[1] ) ); > $col->add_Annotation( 'family', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => &getWeight( $_[0] > ) ); > $col->add_Annotation( 'weight', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => $link . > $prot->accession_number() ); > $col->add_Annotation( 'link', $sv ); > $sv = new Bio::Annotation::SimpleValue(-value => &getEval( $_[1] ) ); > $col->add_Annotation( 'e-val', $sv ); > $sv = new Bio::Annotation::SimpleValue( -value => $_[0]->seq() ); > $col->add_Annotation( 'sequence', $sv ); > $prot->annotation($col);} > > sub getProtAnnotation($$) { > my $ano = $_[0]->annotation(); > my @an = $ano->get_Annotations( $_[1] ); > my $erg = $an[0]->value();} > > sub setProtAnnotation($$$) { > my $prot = $_[0]; > my $ano = $prot->annotation(); > my @an = $ano->get_Annotations( $_[1] ); > my $erg = $an[0]->value( $_[2] );} > > sub getEval($) { > my $report = > $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); > my $hit = $report->next_hit(); > my $hsp = $hit->next_domain(); > my $eval = $hsp->evalue();} > > sub getSimpleFam($) { > my $report = > $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); > my $hit = $report->next_hit(); > my $fam = $hit->name();} > > > > > > >Hi, > >> > >> I have problems to get the secondary_accessions from an seq object. > >> > >> E.G > >> > >> $inx = Bio::Index::Swissprot->new($Index_File_Name); > >> $prot = $inx->fetch( $accarray[ $_[0] ] ); > >> #"$accarray[ $_[0]" is an array of accessions > >> > >> print "Description: " . $prot->description . "\n"; > >> print "Accessions: " .$sec . "\n"; > >> print "Species: " . $prot->species->binomial() . "\n"; > >> print "Length: " . $prot->length . "\n"; > >> #this looks good > >> > >> @a = $prot->get_secondary_accessions; > >> #@a is empty! > >> > >> Seems that $prot is not a reference to a rich:seq object or somthing > >> other is wrong. > >> > >> Hope that someone can help me. > >> > >> regards > >> stephan > >> > >> > >> _______________________________________________ > >> Bioperl-l mailing list > >> Bioperl-l@portal.open-bio.org > >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From avilella at ub.edu Wed Nov 16 05:56:31 2005 From: avilella at ub.edu (Albert Vilella) Date: Wed Nov 16 05:54:58 2005 Subject: [Bioperl-l] Bio::Tree newick and internal nodes In-Reply-To: <1131963390.8065.1.camel@localhost.localdomain> References: <1131963390.8065.1.camel@localhost.localdomain> Message-ID: <1132138591.13367.8.camel@localhost.localdomain> I respond to myself: There is a bit of commented code in newick.pm +237: if($data[-1] !~ /\)$/ ) { $data[0] = "(".$data[0]; $data[-1] .= ")"; } That if it is commented out, will add the latest pair of parenthesis. Does anybody know why this is commented? Any problem if I sync this in CVS? Albert. El dl 14 de 11 del 2005 a les 11:16 +0100, en/na Albert Vilella va escriure: > Hi all, > > I'm having a trouble with the newick module when trying to print out > the tree coming from a mlc codeml result file. There is some > combination of internal node arrangements that gives this tree: > > (Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5; > > Instead of what has to be... > > ((Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5); > > ...to play well with some programs (PAML's evolver in this case). > > Any hint if this is/should_be ok? > > Also, is there a way to print out a newick tree in which only the leaf > nodes have the ids printed? > > E.g.: > > (Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239):0.000000); > > Thanks in advance, > > Bests, > > Albert. > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Wed Nov 16 06:17:39 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 16 06:15:54 2005 Subject: [Bioperl-l] bioperl-db and MySQL In-Reply-To: <20051106012049.54727.qmail@web30801.mail.mud.yahoo.com> References: <20051106012049.54727.qmail@web30801.mail.mud.yahoo.com> Message-ID: Bioperl-db needs to be in your @INC (perl's path for loading perl modules) at runtime - so it doesn't matter where you put it so long as you have the location in the PERL5LIB environment variable before executing a script, or include the location at the top of the script via 'use lib c:\path\to\bioperl-db;'. Supposedly, simply installing bioperl-db should take care of the problem too. -hilmar On Nov 5, 2005, at 5:20 PM, chen li wrote: > Hello everyone, > > I want to install bioperl-db on my windows XP with > ActivePerl. I read the HOWTOs about installing( > http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/ > HOWTO-MySQL.html). > But I failed to do the nmake test. Then I read the > HOWTOs again, which points out that install will fail > if the DBD:: and DBI::Mysql modules cannot be found. > > On my PC MySQL, Perl, and Bioperl-db are kept in > different directory. I use PPM to install DBD::Mysql > and DBI::Mysql. I install MySQL using binary code. My > question: Where should I keep the Bioperl-db including > bioperl-schema so that installation will succeed? > > Thanks, > > Li > > > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From avilella at ub.edu Wed Nov 16 06:44:41 2005 From: avilella at ub.edu (Albert Vilella) Date: Wed Nov 16 06:43:24 2005 Subject: patch nointernalids for internal nodes Was: [Bioperl-l] Bio::Tree newick and internal nodes In-Reply-To: <1131963390.8065.1.camel@localhost.localdomain> References: <1131963390.8065.1.camel@localhost.localdomain> Message-ID: <1132141481.13367.20.camel@localhost.localdomain> I have added a (dummy) /nointernalids/ bootstrap_style flag in newick.pm that, if chosen, wont print the ids of internal nodes, having or not having branch_length defined: > ((Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239)6:0.000000)5); > > E.g.: > > (Tkodak:0.890176,Pfurio:0.256021,(Pabyss:0.203701,Phorik:0.327239):0.000000); ---- patch: --- newick.pm.~1.30.~ 2005-10-24 15:01:40.000000000 +0200 +++ newick.pm 2005-11-16 12:38:17.000000000 +0100 @@ -234,10 +234,10 @@ foreach my $tree( @trees ) { my @data = _write_tree_Helper($tree->get_root_node, $self->bootstrap_style); - #if($data[-1] !~ /\)$/ ) { - # $data[0] = "(".$data[0]; - # $data[-1] .= ")"; - #} + if($data[-1] !~ /\)$/ ) { + $data[0] = "(".$data[0]; + $data[-1] .= ")"; + } $self->_print(join(',', @data), ";\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; @@ -280,7 +280,10 @@ if( ! defined $bl || ! length($bl) || ($style && $style =~ /nobranchlength/i) ) { - if( defined $id || defined $bs ) { + if ($style && $style =~ /nointernalids/i) { + # do not print id even if no branchlength is + # defined + } elsif( defined $id || defined $bs ) { $data[-1] .= defined $bs ? $bs : $id; } } elsif( $style =~ /molphy/i ) { @@ -295,6 +298,15 @@ if( defined $bs ) { $data[-1] .= "[$bs]"; } + } elsif( $style =~ /nointernalids/i ) { + if( $bl =~ /\#/) { + $data[-1] .= $bl; + } else { + $data[-1] .= ":$bl"; + } + if( defined $bs ) { + $data[-1] .= "[$bs]"; + } } else { # traditional style of # ((A:1,B:2)81:3); where 3 is internal node branch length @@ -373,8 +385,8 @@ my $val = shift; if( defined $val ) { - if( $val !~ /^nobranchlength|molphy|traditional/i ) { - $self->warn("requested an unknown bootstrap style $val, expect one of nobranchlength,molphy,traditional, not updating value. Default is $DefaultBootstrapStyle\n"); + if( $val !~ /^nobranchlength|molphy|traditional|nointernalids/i ) { + $self->warn("requested an unknown bootstrap style $val, expect one of nobranchlength,molphy,traditional,nointernalids, not updating value. Default is $DefaultBootstrapStyle\n"); } else { $self->{'_bootstrap_style'} = $val; } From golharam at umdnj.edu Wed Nov 16 13:37:44 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed Nov 16 13:52:12 2005 Subject: [Bioperl-l] How to determine if GenBank record contains... Message-ID: <008601c5eadc$d53e1ed0$5022db82@GOLHARMOBILE1> How can I determine is a GenBank record containing a CDS entry has the join, or join-compliment keyword listed for CDS? For example, if you look up Accession AY628630 at NCBI, you'll see the CDS tag has "join(...)", but DQ202315 does not. Is there a way I can determine if a GenBank entry has this using BioPerl? Ryan From bmoore at genetics.utah.edu Wed Nov 16 14:33:33 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Wed Nov 16 14:41:07 2005 Subject: [Bioperl-l] How to determine if GenBank record contains... Message-ID: Ryan- See if the two method calls in the eval statement below don't get you what you want. my @CDS_feats = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures(); print ''; for my $feature (@CDS_feats) { my $location = $feature->location; eval { print "Single Sequence:\t", $location->is_single_sequence, "\n"; print "Split Type:\t", $location->splittype, "\n\n"; } } Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of Ryan Golhar > Sent: Wednesday, November 16, 2005 11:38 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] How to determine if GenBank record contains... > > How can I determine is a GenBank record containing a CDS entry has the > join, or join-compliment keyword listed for CDS? For example, if you > look up Accession AY628630 at NCBI, you'll see the CDS tag has > "join(...)", but DQ202315 does not. > > Is there a way I can determine if a GenBank entry has this using > BioPerl? > > Ryan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From golharam at umdnj.edu Wed Nov 16 14:52:32 2005 From: golharam at umdnj.edu (Ryan Golhar) Date: Wed Nov 16 14:50:04 2005 Subject: [Bioperl-l] How to determine if GenBank record contains... In-Reply-To: Message-ID: <009401c5eae7$48dcc4e0$5022db82@GOLHARMOBILE1> That works Barry. Thanks! Ryan -----Original Message----- From: Barry Moore [mailto:bmoore@genetics.utah.edu] Sent: Wednesday, November 16, 2005 2:34 PM To: golharam@umdnj.edu; bioperl-l@portal.open-bio.org Subject: RE: [Bioperl-l] How to determine if GenBank record contains... Ryan- See if the two method calls in the eval statement below don't get you what you want. my @CDS_feats = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures(); print ''; for my $feature (@CDS_feats) { my $location = $feature->location; eval { print "Single Sequence:\t", $location->is_single_sequence, "\n"; print "Split Type:\t", $location->splittype, "\n\n"; } } Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of Ryan Golhar > Sent: Wednesday, November 16, 2005 11:38 AM > To: bioperl-l@portal.open-bio.org > Subject: [Bioperl-l] How to determine if GenBank record contains... > > How can I determine is a GenBank record containing a CDS entry has the > join, or join-compliment keyword listed for CDS? For example, if you > look up Accession AY628630 at NCBI, you'll see the CDS tag has > "join(...)", but DQ202315 does not. > > Is there a way I can determine if a GenBank entry has this using > BioPerl? > > Ryan > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From pjm at sanger.ac.uk Wed Nov 16 16:03:16 2005 From: pjm at sanger.ac.uk (Paul Mooney) Date: Wed Nov 16 16:24:48 2005 Subject: [Bioperl-l] Bio::Annotation::SimpleValue Message-ID: <1132174996.4009.297.camel@localhost.localdomain> Hi, I have stumbled on a problem when writing out an EMBL file. If my input is; FT repeat_region 5..963 FT /colour="0" when I try to write it out I get FT repeat_region 5..963 FT /colour="" I think this is down to Bio::Annotation::SimpleVal doing a 'truth test' on the value of the qualifier (zero is false), hence I get an empty string. The code in SimpleValue.pm is; use overload '""' => sub { $_[0]->value || ''}; Thanks, Paul. PS, its the same on 1.5.1 and live. Heres a simple test; use strict; use Bio::Annotation::SimpleValue; my $simple = Bio::Annotation::SimpleValue->new( -tagname => 'colour', -value => '0', ); print "SimpleValue = $simple\n"; From osborne1 at optonline.net Wed Nov 16 16:39:34 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Wed Nov 16 16:37:46 2005 Subject: [Bioperl-l] Bio::Annotation::SimpleValue In-Reply-To: <1132174996.4009.297.camel@localhost.localdomain> Message-ID: Paul, Can you submit exactly what you've written below as a bug? The page is http://bugzilla.bioperl.org. If you submit it it's sure to be addressed, otherwise it may get lost in the email stream. Thank you, Brian O. On 11/16/05 4:03 PM, "Paul Mooney" wrote: > Hi, > > I have stumbled on a problem when writing out an EMBL file. If my input > is; > > FT repeat_region 5..963 > FT /colour="0" > > when I try to write it out I get > > FT repeat_region 5..963 > FT /colour="" > > I think this is down to Bio::Annotation::SimpleVal doing a 'truth test' > on the value of the qualifier (zero is false), hence I get an empty > string. The code in SimpleValue.pm is; > > use overload '""' => sub { $_[0]->value || ''}; > > Thanks, > Paul. > > PS, its the same on 1.5.1 and live. Heres a simple test; > > use strict; > use Bio::Annotation::SimpleValue; > > my $simple = Bio::Annotation::SimpleValue->new( > -tagname => 'colour', > -value => '0', > ); > print "SimpleValue = $simple\n"; > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From stephan.rosecker at ish.de Wed Nov 16 18:00:15 2005 From: stephan.rosecker at ish.de (stephan) Date: Wed Nov 16 18:58:28 2005 Subject: [Bioperl-l] RE:Problems to get secondary accessions from an object In-Reply-To: <0e2c030d54f9e3deb44ac49755616c5d@gmx.net> References: <43725342.3080908@ish.de> <0e2c030d54f9e3deb44ac49755616c5d@gmx.net> Message-ID: <437BB9FF.9080809@ish.de> Hilmar, you solved my problem. thanks a lot! stephan Hilmar Lapp schrieb: > Stephan, is it necessary that you create your own annotation collection? > If you replace the line > > my $col = new Bio::Annotation::Collection; > > with > > my $col = $prot->annotation; > > you wouldn't lose annotation that's already present in the sequence's > existing annotation collection. (And you could then also remove the then > superfluous setter call $prot->annotation($col);) > > -hilmar > > On Nov 9, 2005, at 11:51 AM, stephan wrote: > >> Hi, >> >> I found a trace. >> The problem is that after I add anotations to the object, the >> rich-features are disappeared. >> >> snippet: >> #prot is the seq object >> >> sub setProtAnnotations($$) { >> my $prot = $_[0]; >> my $col = new Bio::Annotation::Collection; >> my $sv = new Bio::Annotation::SimpleValue(-value => >> &getSimpleFam( $_[1] ) ); >> $col->add_Annotation( 'family', $sv ); >> $sv = new Bio::Annotation::SimpleValue(-value => >> &getWeight( $_[0] ) ); >> $col->add_Annotation( 'weight', $sv ); >> $sv = new Bio::Annotation::SimpleValue(-value => $link . >> $prot->accession_number() ); >> $col->add_Annotation( 'link', $sv ); >> $sv = new Bio::Annotation::SimpleValue(-value => &getEval( >> $_[1] ) ); >> $col->add_Annotation( 'e-val', $sv ); >> $sv = new Bio::Annotation::SimpleValue( -value => >> $_[0]->seq() ); >> $col->add_Annotation( 'sequence', $sv ); >> $prot->annotation($col);} >> >> sub getProtAnnotation($$) { >> my $ano = $_[0]->annotation(); >> my @an = $ano->get_Annotations( $_[1] ); >> my $erg = $an[0]->value();} >> >> sub setProtAnnotation($$$) { >> my $prot = $_[0]; >> my $ano = $prot->annotation(); >> my @an = $ano->get_Annotations( $_[1] ); >> my $erg = $an[0]->value( $_[2] );} >> >> sub getEval($) { >> my $report = >> $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); >> my $hit = $report->next_hit(); >> my $hsp = $hit->next_domain(); >> my $eval = $hsp->evalue();} >> >> sub getSimpleFam($) { >> my $report = >> $hmm_swiss_index->fetch_report( $accarray[ $_[0] ] ); >> my $hit = $report->next_hit(); >> my $fam = $hit->name();} >> >> >> >> >> >> >Hi, >> >> >> >> I have problems to get the secondary_accessions from an seq object. >> >> >> >> E.G >> >> >> >> $inx = Bio::Index::Swissprot->new($Index_File_Name); >> >> $prot = $inx->fetch( $accarray[ $_[0] ] ); >> >> #"$accarray[ $_[0]" is an array of accessions >> >> >> >> print "Description: " . $prot->description . "\n"; >> >> print "Accessions: " .$sec . "\n"; >> >> print "Species: " . $prot->species->binomial() . "\n"; >> >> print "Length: " . $prot->length . "\n"; >> >> #this looks good >> >> >> >> @a = $prot->get_secondary_accessions; >> >> #@a is empty! >> >> >> >> Seems that $prot is not a reference to a rich:seq object or somthing >> >> other is wrong. >> >> >> >> Hope that someone can help me. >> >> >> >> regards >> >> stephan >> >> >> >> >> >> _______________________________________________ >> >> Bioperl-l mailing list >> >> Bioperl-l@portal.open-bio.org >> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> From chen_li3 at yahoo.com Wed Nov 16 18:53:56 2005 From: chen_li3 at yahoo.com (chen li) Date: Wed Nov 16 18:58:48 2005 Subject: [Bioperl-l] bioperl-db and MySQL In-Reply-To: Message-ID: <20051116235356.68483.qmail@web30809.mail.mud.yahoo.com> I unzipped the download files and used "nmake install" to install bioperl-db on my computer. And it seems it works because I see many files/pm are copied to the defautl library(c:/Perl/site/lib/Bio/DB...." on my computer). Now my question: How do I know if it is installed correctly and will be working? Can I issue a command like "perldoc ???" to check if it is in the documantation? Thanks, Li --- Hilmar Lapp wrote: > Bioperl-db needs to be in your @INC (perl's path for > loading perl > modules) at runtime - so it doesn't matter where you > put it so long as > you have the location in the PERL5LIB environment > variable before > executing a script, or include the location at the > top of the script > via 'use lib c:\path\to\bioperl-db;'. Supposedly, > simply installing > bioperl-db should take care of the problem too. > > -hilmar > > On Nov 5, 2005, at 5:20 PM, chen li wrote: > > > Hello everyone, > > > > I want to install bioperl-db on my windows XP with > > ActivePerl. I read the HOWTOs about installing( > > > http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/ > > > HOWTO-MySQL.html). > > But I failed to do the nmake test. Then I read the > > HOWTOs again, which points out that install will > fail > > if the DBD:: and DBI::Mysql modules cannot be > found. > > > > On my PC MySQL, Perl, and Bioperl-db are kept in > > different directory. I use PPM to install > DBD::Mysql > > and DBI::Mysql. I install MySQL using binary code. > My > > question: Where should I keep the Bioperl-db > including > > bioperl-schema so that installation will succeed? > > > > Thanks, > > > > Li > > > > > > > > > > > > > > __________________________________ > > Yahoo! Mail - PC Magazine Editors' Choice 2005 > > http://mail.yahoo.com > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp > at gnf.org > GNF, San Diego, Ca. 92121 phone: > +1-858-812-1757 > ------------------------------------------------------------- > > > __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From jay at jays.net Wed Nov 16 22:53:57 2005 From: jay at jays.net (Jay Hannah) Date: Thu Nov 17 00:33:52 2005 Subject: [Bioperl-l] Bio::Annotation::SimpleValue In-Reply-To: References: Message-ID: On Nov 16, 2005, at 3:39 PM, Brian Osborne wrote: > Can you submit exactly what you've written below as a bug? The page is > http://bugzilla.bioperl.org. If you submit it it's sure to be > addressed, > otherwise it may get lost in the email stream. Hi Brian -- Nov 11 12:13pm subject "Barry's challenge" I asked what I should do with a bug I think I found. Should I submit it into bugzilla and/or prep a CVS patch? Post the patch into bugzilla, or the list? Thanks, j From hlapp at gmx.net Thu Nov 17 03:19:18 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Nov 17 03:17:40 2005 Subject: [Bioperl-l] load in biosql a genome genbank file In-Reply-To: <1140.84.134.47.39.1132168090.squirrel@webmail.gbf.de> References: <1131449201.8302.222.camel@sb289.gbf-braunschweig.de> <1140.84.134.47.39.1132168090.squirrel@webmail.gbf.de> Message-ID: <4224c3e797438e83f7431486a323d394@gmx.net> Which file exactly do you mean? The .gbk I find at NCBI looks like a perfectly normal genbank formatted file, and so shouldn't pose a problem for bioperl. Also, you need to post the full error message or otherwise explain what you think isn't going the way you thought it should if you want help because otherwise I don't know what exactly you mean by 'works not'. -hilmar On Nov 16, 2005, at 11:08 AM, gdi@gbf.de wrote: > Hi Hilmar, > > the ncbi genome files are different from "normal" genbank files eg. for > one gene. I tried it with the load_seqdatabase.pl, with a) swissprot > genome file. (eg. LISMO.dat), b) genbank lmo genome file > a) works > b) not > > Or i am wrong? > > Guido > > >> The genome is in genbank format, right? Generally speaking there is >> little limit on what you can load into BioSQL; if you are referring to >> load_seqdatabase.pl, it can load any format that's understood by the >> Bio::SeqIO system in Bioperl. >> >> Let me know if you were thinking about something else. >> >> -hilmar >> >> On Nov 8, 2005, at 3:26 AM, Guido Dieterich wrote: >> >>> Hi >>> >>> is it possible to load into biosql a complete bacterial genome >>> genbank >>> file >>> from ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ >>> >>> Best regards >>> >>> Guido >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> -- >> ------------------------------------------------------------- >> Hilmar Lapp email: lapp at gnf.org >> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 >> ------------------------------------------------------------- >> >> > > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Thu Nov 17 03:30:25 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu Nov 17 03:28:42 2005 Subject: [Bioperl-l] bioperl-db and MySQL In-Reply-To: <20051116235356.68483.qmail@web30809.mail.mud.yahoo.com> References: <20051116235356.68483.qmail@web30809.mail.mud.yahoo.com> Message-ID: You run 'make test' to see if it works. Installation itself can't really get much wrong. You need to follow the instructions for t/DBHarness.conf.example before you can successfully run 'make test'. -hilmar On Nov 16, 2005, at 3:53 PM, chen li wrote: > I unzipped the download files and used "nmake install" > to install bioperl-db on my computer. And it seems it > works because I see many files/pm are copied to the > defautl library(c:/Perl/site/lib/Bio/DB...." on my > computer). Now my question: How do I know if it is > installed correctly and will be working? Can I issue a > command like "perldoc ???" to check if it is in the > documantation? > > Thanks, > > Li > > --- Hilmar Lapp wrote: > >> Bioperl-db needs to be in your @INC (perl's path for >> loading perl >> modules) at runtime - so it doesn't matter where you >> put it so long as >> you have the location in the PERL5LIB environment >> variable before >> executing a script, or include the location at the >> top of the script >> via 'use lib c:\path\to\bioperl-db;'. Supposedly, >> simply installing >> bioperl-db should take care of the problem too. >> >> -hilmar >> >> On Nov 5, 2005, at 5:20 PM, chen li wrote: >> >>> Hello everyone, >>> >>> I want to install bioperl-db on my windows XP with >>> ActivePerl. I read the HOWTOs about installing( >>> >> > http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/ >> >>> HOWTO-MySQL.html). >>> But I failed to do the nmake test. Then I read the >>> HOWTOs again, which points out that install will >> fail >>> if the DBD:: and DBI::Mysql modules cannot be >> found. >>> >>> On my PC MySQL, Perl, and Bioperl-db are kept in >>> different directory. I use PPM to install >> DBD::Mysql >>> and DBI::Mysql. I install MySQL using binary code. >> My >>> question: Where should I keep the Bioperl-db >> including >>> bioperl-schema so that installation will succeed? >>> >>> Thanks, >>> >>> Li >>> >>> >>> >>> >>> >>> >>> __________________________________ >>> Yahoo! Mail - PC Magazine Editors' Choice 2005 >>> http://mail.yahoo.com >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> >>> >> -- >> > ------------------------------------------------------------- >> Hilmar Lapp email: lapp >> at gnf.org >> GNF, San Diego, Ca. 92121 phone: >> +1-858-812-1757 >> > ------------------------------------------------------------- >> >> >> > > > > > __________________________________ > Yahoo! FareChase: Search multiple travel sites in one click. > http://farechase.yahoo.com > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From ste.ghi at libero.it Thu Nov 17 09:10:30 2005 From: ste.ghi at libero.it (Stefano Ghignone) Date: Thu Nov 17 09:17:10 2005 Subject: [Bioperl-l] annot8r_blast2GO Message-ID: Hi all. I'm an enthusiast user of annot8r_blast2GO, a sequence annotation script by Ralf Schmid & Mark Blaxter (http://www.nematodes.org/PartiGene/index.html). The script (that uses the StandAloneBlast) was working fine until I had to upgrade bioperl to 1.5.1 release, to have other scripts working with NCBI. At the moment I get the following error message for each sequence that I try to parse: [blastall] WARNING: [000.000] seqID: SetUpBlastSearch failed. [blastall] ERROR: [000.000] seqID: BLASTSetUpSearch: Unable to calculate Karlin-Altschul params, check query sequence. Regarding this error message, NBCI BLAST Faq says that "This will happen if your entire query sequence has been masked by low complexity filtering", but this is not my case... Local BLAST installation is working fine; scripts that use StandAloneBlast module are working fine, too (using the same sequence batch I'm trying to annotate). Is someone experiencing the same problem and/or has a resolution? Thanks a lot. stefano From niraj at ku.edu.np Thu Nov 17 14:04:54 2005 From: niraj at ku.edu.np (kumail) Date: Thu Nov 17 11:58:17 2005 Subject: [Bioperl-l] need info Message-ID: <006401c5eba9$cbd37340$ec02a8c0@niraj> dear sir i am niraj shrestha from Nepal. currently i am teaching at Kathmandu University. i am graduated from the university in 2001 in computer science & engineering. my research interest is in bioinformatics, parallel and distributed network, semantic web. so if i can help or can do some work for bio-pearl then i am ready for that. looking forward to your kind suggestions. with regards, _____________________________________ Niraj Shrestha Department of Computer Science & Engineering Kathmandu University, Dhulikhel, Nepal P.O.Box: 6250, Kathmandu, Nepal email: niraj@ku.edu.np, niraj_sh@hotmail.com, niraj_sh@yahoo.com website: http://ku.edu.np/~niraj From hollandr at gis.a-star.edu.sg Tue Nov 15 20:47:07 2005 From: hollandr at gis.a-star.edu.sg (Richard HOLLAND) Date: Thu Nov 17 11:58:25 2005 Subject: [Bioperl-l] RE: [BioSQL-l] biosql & bioperl-db on Solaris Message-ID: <6D9E9B9DF347EF4385F6271C64FB8D5602656B0D@BIONIC.biopolis.one-north.com> Hi, This may seem a bit basic but it's worth a go. CPAN looks for "cc" - which on a Sun machine is the Sun compiler. If you have "gcc" installed then you may need to create a soft-link to it called "cc" and ensure that softlink appears earlier in your path than the location of the Sun compiler. You must then export the path or add it to your profile as CPAN starts new sub-shells internally). eg. if your gcc binary is /usr/bin/gcc, and assuming a bash-like shell: mkdir ~/bin ln -s /usr/bin/gcc ~/bin/cc PATH=~/bin:$PATH export PATH Then run CPAN and see what happens. Hope it helps. cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: biosql-l-bounces@portal.open-bio.org > [mailto:biosql-l-bounces@portal.open-bio.org] On Behalf Of > Mike Muratet > Sent: Wednesday, November 16, 2005 3:57 AM > To: biosql-l@open-bio.org > Cc: bioperl-l@bioperl.org > Subject: [BioSQL-l] biosql & bioperl-db on Solaris > > > Greetings > > This is not strictly a bioperl or biosql issue, but is > related. In the > process of trying to install bioperl-db on a Solaris 9 > system, I had to go > back and install the latest bioperl, DBI, AND DBD modules. > The DBD install > via CPAN is failing for an ELF64 incompatibility when it > tries to link to > the mysql client libs because I also installed the > latest 64bit mysql. According to the mysql docs, 64bit is 4% slower > than the 32bit version, but you get more threads and memory > (which would > seem to be faster in the long run). > > Although I have installed gcc and gnu make, CPAN is picking > up the native > Sun compiler (and why do they spread things out over so many > subdirectories?) and linker. > > Has anyone else come up against this before (I didn't find > anything in the > archives)? Is the best course to install a 32bit mysql? > Should I forgo > CPAN and try to do a manual install where I might have some > control over > Makefile.PL? Has anybody tried biosql on a 64bit system and > does it make a > difference? > > Thanks > > Mike > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > From heikki at sanbi.ac.za Thu Nov 17 07:29:33 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Thu Nov 17 11:58:26 2005 Subject: [Bioperl-l] Bio::Annotation::SimpleValue In-Reply-To: References: Message-ID: <200511171429.34153.heikki@sanbi.ac.za> I fixed that on both head and branch. The method worked but overload messed things up. -Heikki On Wednesday 16 November 2005 23:39, Brian Osborne wrote: > Paul, > > Can you submit exactly what you've written below as a bug? The page is > http://bugzilla.bioperl.org. If you submit it it's sure to be addressed, > otherwise it may get lost in the email stream. > > Thank you, > > Brian O. > > On 11/16/05 4:03 PM, "Paul Mooney" wrote: > > Hi, > > > > I have stumbled on a problem when writing out an EMBL file. If my input > > is; > > > > FT repeat_region 5..963 > > FT /colour="0" > > > > when I try to write it out I get > > > > FT repeat_region 5..963 > > FT /colour="" > > > > I think this is down to Bio::Annotation::SimpleVal doing a 'truth test' > > on the value of the qualifier (zero is false), hence I get an empty > > string. The code in SimpleValue.pm is; > > > > use overload '""' => sub { $_[0]->value || ''}; > > > > Thanks, > > Paul. > > > > PS, its the same on 1.5.1 and live. Heres a simple test; > > > > use strict; > > use Bio::Annotation::SimpleValue; > > > > my $simple = Bio::Annotation::SimpleValue->new( > > -tagname => 'colour', > > -value => '0', > > ); > > print "SimpleValue = $simple\n"; > > > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From osborne1 at optonline.net Thu Nov 17 12:20:31 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Thu Nov 17 12:24:12 2005 Subject: [Bioperl-l] Bio::Annotation::SimpleValue In-Reply-To: Message-ID: j, No need for a double post, just doing Bugzilla is perfect. Many subscribers to bioperl-l also read bioperl-guts, which is all the notifications from Bugzilla. Please submit the patch as an attachment, not a copy-paste, to Bugzilla (the word wrapping on the Web page always messes up the patch if it's a copy-paste). Thank _you_. Brian O. On 11/16/05 10:53 PM, "Jay Hannah" wrote: > > On Nov 16, 2005, at 3:39 PM, Brian Osborne wrote: >> Can you submit exactly what you've written below as a bug? The page is >> http://bugzilla.bioperl.org. If you submit it it's sure to be >> addressed, >> otherwise it may get lost in the email stream. > > Hi Brian -- > > Nov 11 12:13pm subject "Barry's challenge" I asked what I should do > with a bug I think I found. Should I submit it into bugzilla and/or > prep a CVS patch? Post the patch into bugzilla, or the list? > > Thanks, > > j > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Thu Nov 17 12:50:55 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Thu Nov 17 12:46:31 2005 Subject: [Bioperl-l] need info Message-ID: Niraj, This is the place to hang out if you are interested in helping with the bioperl project. My suggestion would be to get bioperl and some of it's accessory programs installed on you computer. Start running some of scripts that are installed with it, follow this list and maybe even look over the list archives for the last couple months. It shouldn't take long to see areas where help is needed. If you are already familiar with bioperl, you could jump in right away by looking through the bug list at http://bugzilla.bioperl.org/. Thanks for your interest. Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of kumail > Sent: Thursday, November 17, 2005 12:05 PM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] need info > > dear sir > i am niraj shrestha from Nepal. currently i am teaching at Kathmandu > University. i am graduated from the university in 2001 in computer science > & engineering. my research interest is in bioinformatics, parallel and > distributed network, semantic web. > so if i can help or can do some work for bio-pearl then i am ready for > that. > looking forward to your kind suggestions. > > with regards, > _____________________________________ > > Niraj Shrestha > Department of Computer Science & Engineering > Kathmandu University, > Dhulikhel, Nepal > P.O.Box: 6250, Kathmandu, Nepal > email: niraj@ku.edu.np, niraj_sh@hotmail.com, niraj_sh@yahoo.com > website: http://ku.edu.np/~niraj > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From chen_li3 at yahoo.com Thu Nov 17 16:24:40 2005 From: chen_li3 at yahoo.com (chen li) Date: Thu Nov 17 16:29:34 2005 Subject: [Bioperl-l] bioperl-db and MySQL In-Reply-To: Message-ID: <20051117212440.30324.qmail@web30810.mail.mud.yahoo.com> Hi Hilmar, I ran "make test" but it still failed. But I were able to create a biosql instance within MySQL (same as those described in mysql HOWTO) after I loaded the schema of seqdatabase.spl. So I think I might succeed in installing Bioperl-db. Now I want to go to the next step: loading a test EST database file(fasta format)into the database. I already download the mouse EEST, unzip the file, and put it as c:/perl/EST/est_mouse( and C:/bioperl-db-0.1/scripts/load_seqdatabase.pl). By following HOWTO I am supposed to the use syntax below to load the file into databse. ./load_seqdatabase.pl /path/to/data/file(s) My questions: in which windows should I type this line of command, mysql,Perl,or the directory containing load_seqdatabase.pl? And how do I issue the command in this specific case? Thanks, Li --- Hilmar Lapp wrote: > You run 'make test' to see if it works. Installation > itself can't > really get much wrong. > > You need to follow the instructions for > t/DBHarness.conf.example before > you can successfully run 'make test'. > > -hilmar > > On Nov 16, 2005, at 3:53 PM, chen li wrote: > > > I unzipped the download files and used "nmake > install" > > to install bioperl-db on my computer. And it seems > it > > works because I see many files/pm are copied to > the > > defautl library(c:/Perl/site/lib/Bio/DB...." on my > > computer). Now my question: How do I know if it is > > installed correctly and will be working? Can I > issue a > > command like "perldoc ???" to check if it is in > the > > documantation? > > > > Thanks, > > > > Li > > > > --- Hilmar Lapp wrote: > > > >> Bioperl-db needs to be in your @INC (perl's path > for > >> loading perl > >> modules) at runtime - so it doesn't matter where > you > >> put it so long as > >> you have the location in the PERL5LIB environment > >> variable before > >> executing a script, or include the location at > the > >> top of the script > >> via 'use lib c:\path\to\bioperl-db;'. Supposedly, > >> simply installing > >> bioperl-db should take care of the problem too. > >> > >> -hilmar > >> > >> On Nov 5, 2005, at 5:20 PM, chen li wrote: > >> > >>> Hello everyone, > >>> > >>> I want to install bioperl-db on my windows XP > with > >>> ActivePerl. I read the HOWTOs about installing( > >>> > >> > > > http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/ > >> > >>> HOWTO-MySQL.html). > >>> But I failed to do the nmake test. Then I read > the > >>> HOWTOs again, which points out that install will > >> fail > >>> if the DBD:: and DBI::Mysql modules cannot be > >> found. > >>> > >>> On my PC MySQL, Perl, and Bioperl-db are kept in > >>> different directory. I use PPM to install > >> DBD::Mysql > >>> and DBI::Mysql. I install MySQL using binary > code. > >> My > >>> question: Where should I keep the Bioperl-db > >> including > >>> bioperl-schema so that installation will > succeed? > >>> > >>> Thanks, > >>> > >>> Li > >>> > >>> > >>> > >>> > >>> > >>> > >>> __________________________________ > >>> Yahoo! Mail - PC Magazine Editors' Choice 2005 > >>> http://mail.yahoo.com > >>> _______________________________________________ > >>> Bioperl-l mailing list > >>> Bioperl-l@portal.open-bio.org > >>> > >> > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > >>> > >>> > >> -- > >> > > > ------------------------------------------------------------- > >> Hilmar Lapp email: > lapp > >> at gnf.org > >> GNF, San Diego, Ca. 92121 phone: > >> +1-858-812-1757 > >> > > > ------------------------------------------------------------- > >> > >> > >> > > > > > > > > > > __________________________________ > > Yahoo! FareChase: Search multiple travel sites in > one click. > > http://farechase.yahoo.com > > > > > -- > ------------------------------------------------------------- > Hilmar Lapp email: lapp > at gnf.org > GNF, San Diego, Ca. 92121 phone: > +1-858-812-1757 > ------------------------------------------------------------- > > > __________________________________ Yahoo! FareChase: Search multiple travel sites in one click. http://farechase.yahoo.com From jarthur at med.usyd.edu.au Thu Nov 17 23:20:51 2005 From: jarthur at med.usyd.edu.au (Jonathan Arthur) Date: Thu Nov 17 23:40:44 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" Message-ID: <437D56A3.8070902@med.usyd.edu.au> Hello all, I am having difficulty installing BioPerl. I am running Windows XP Professional with cygwin. I am using the CPAN installer to attempt to install the Bundle::BioPerl modules. The installation appears to go relatively smoothly and end normally. It does note at the end that there were installation problems with File::Spec, GD::SVG, and Data::Stag. Nonetheless, when I try to "use Bio::Perl" Perl cannot find the module and exploring /usr/lib confirms the modules are not present. I then tried installing the problem modules above on the assumption that the final installation of Bio::Perl was dependent on these modules being successfully installed. The creation of the makefile for GD::SVG dies with: C:\cygwin\bin\perl.exe (800): *** unable to remap c:\cygwin\bin\cygfreetype-6.dll to same address as parent(0xE100000) != 0xEA0000 Data::Stag installation experiences a similar error (with different .dll) when trying to install the Tk dependency. File::Spec installation appears to install fine (bar some failed tests because it can't load File::Spec::VMS) and it is present in /usr/lib/perl5 so it is not clear what the cpan installation is complaining about in regard to this module. Could anyone assist with these installation problems? Regards, Jonathan -- Dr Jonathan Arthur Sesqui Lecturer in Bioinformatics Central Clinical School, Faculty of Medicine and SUBIT Medical Foundation Building, K25 University of Sydney Ph: +61 2 9036 3132 Email: jarthur@med.usyd.edu.au From heikki at sanbi.ac.za Fri Nov 18 01:53:58 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Fri Nov 18 01:52:32 2005 Subject: [Bioperl-l] need info In-Reply-To: <006401c5eba9$cbd37340$ec02a8c0@niraj> References: <006401c5eba9$cbd37340$ec02a8c0@niraj> Message-ID: <200511180853.59494.heikki@sanbi.ac.za> Kumailj, Like Barry said, familiarizing yourself with bioperl is the first thing to do. Most of people have per project s that they pursue. I am sure you will come up with one in due time. Here is one area that needs a lot of help. Although, we have a huge collection of tests, there are still modules with no tests at all. We'd like to test at least all public methods. Look for examples in the t directory of bioperl. A more computer science related problem is to identify classes that do not have tests. There are quite a few tightly linked clusters of classes that that do not make sense to tests individually, like SearchIO modules related to BLAST/FASTA parsing. The problem is to identify those modules. At some point I tried to scan through all test files and compare that to the list of classes produced by the maintenance/modules.pl script to identify the ones in need of testing but got so many false positives, that I moved on to other things. If you, or anyone, could create a script, e.g. maintenance/needtesting.pl, that would do that task, it would be a big step ahead. A way to do it would be take the code in maintenance/modules.pl that creates a hash of modules and their immediate parents, scan the t/*.t files to see which modules are being tested, follow the inheritance of path of every module and check which modules within Bio namespace they 'use', and mark all those a tested, and finally print out a list of untested modules. Yous, -Heikki On Thursday 17 November 2005 21:04, kumail wrote: > dear sir > i am niraj shrestha from Nepal. currently i am teaching at Kathmandu > University. i am graduated from the university in 2001 in computer science > & engineering. my research interest is in bioinformatics, parallel and > distributed network, semantic web. so if i can help or can do some work for > bio-pearl then i am ready for that. looking forward to your kind > suggestions. > > with regards, > _____________________________________ > > Niraj Shrestha > Department of Computer Science & Engineering > Kathmandu University, > Dhulikhel, Nepal > P.O.Box: 6250, Kathmandu, Nepal > email: niraj@ku.edu.np, niraj_sh@hotmail.com, niraj_sh@yahoo.com > website: http://ku.edu.np/~niraj > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From hlapp at gmx.net Fri Nov 18 03:50:19 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Fri Nov 18 03:48:38 2005 Subject: [Bioperl-l] bioperl-db and MySQL In-Reply-To: <20051117212440.30324.qmail@web30810.mail.mud.yahoo.com> References: <20051117212440.30324.qmail@web30810.mail.mud.yahoo.com> Message-ID: <76ff505d37cb20e0fed92d8a4e4cf3e8@gmx.net> On Nov 17, 2005, at 1:24 PM, chen li wrote: > Hi Hilmar, > > I ran "make test" but it still failed. Please post the error message; generally it should not fail. > But I were able > to create a biosql instance within MySQL (same as > those described in mysql HOWTO) after I loaded the > schema of seqdatabase.spl. So I think I might succeed > in installing Bioperl-db. Now I want to go to the > next step: loading a test EST database file(fasta > format)into the database. I already download the mouse > EEST, unzip the file, and put it as > c:/perl/EST/est_mouse( and > C:/bioperl-db-0.1/scripts/load_seqdatabase.pl). This looks like you are using the old 0.1 release. You will need a post-Capetown/pre-Singapore BioSQL schema in order for this to work - the current download from CVS will *not* work with this release. I recommend you use a CVS download for both the BioSQL schema and Bioperl-db, using the main trunk in both cases. > By > following HOWTO I am supposed to the use syntax below > to load the file into databse. > > ./load_seqdatabase.pl > /path/to/data/file(s) > > My questions: in which windows should I type this line > of command, mysql,Perl,or the directory containing > load_seqdatabase.pl? Given that you are calling the script as sitting in the current directory, that's where you should be ... Generally speaking you can call it from anywhere though, just give the full location. -hilmar > And how do I issue the command > in this specific case? > > Thanks, > > Li > > > > > > --- Hilmar Lapp wrote: > >> You run 'make test' to see if it works. Installation >> itself can't >> really get much wrong. >> >> You need to follow the instructions for >> t/DBHarness.conf.example before >> you can successfully run 'make test'. >> >> -hilmar >> >> On Nov 16, 2005, at 3:53 PM, chen li wrote: >> >>> I unzipped the download files and used "nmake >> install" >>> to install bioperl-db on my computer. And it seems >> it >>> works because I see many files/pm are copied to >> the >>> defautl library(c:/Perl/site/lib/Bio/DB...." on my >>> computer). Now my question: How do I know if it is >>> installed correctly and will be working? Can I >> issue a >>> command like "perldoc ???" to check if it is in >> the >>> documantation? >>> >>> Thanks, >>> >>> Li >>> >>> --- Hilmar Lapp wrote: >>> >>>> Bioperl-db needs to be in your @INC (perl's path >> for >>>> loading perl >>>> modules) at runtime - so it doesn't matter where >> you >>>> put it so long as >>>> you have the location in the PERL5LIB environment >>>> variable before >>>> executing a script, or include the location at >> the >>>> top of the script >>>> via 'use lib c:\path\to\bioperl-db;'. Supposedly, >>>> simply installing >>>> bioperl-db should take care of the problem too. >>>> >>>> -hilmar >>>> >>>> On Nov 5, 2005, at 5:20 PM, chen li wrote: >>>> >>>>> Hello everyone, >>>>> >>>>> I want to install bioperl-db on my windows XP >> with >>>>> ActivePerl. I read the HOWTOs about installing( >>>>> >>>> >>> >> > http://cvs.biomoby.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/docs/ >>>> >>>>> HOWTO-MySQL.html). >>>>> But I failed to do the nmake test. Then I read >> the >>>>> HOWTOs again, which points out that install will >>>> fail >>>>> if the DBD:: and DBI::Mysql modules cannot be >>>> found. >>>>> >>>>> On my PC MySQL, Perl, and Bioperl-db are kept in >>>>> different directory. I use PPM to install >>>> DBD::Mysql >>>>> and DBI::Mysql. I install MySQL using binary >> code. >>>> My >>>>> question: Where should I keep the Bioperl-db >>>> including >>>>> bioperl-schema so that installation will >> succeed? >>>>> >>>>> Thanks, >>>>> >>>>> Li >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> __________________________________ >>>>> Yahoo! Mail - PC Magazine Editors' Choice 2005 >>>>> http://mail.yahoo.com >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l@portal.open-bio.org >>>>> >>>> >>> >> > http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>>>> >>>> -- >>>> >>> >> > ------------------------------------------------------------- >>>> Hilmar Lapp email: >> lapp >>>> at gnf.org >>>> GNF, San Diego, Ca. 92121 phone: >>>> +1-858-812-1757 >>>> >>> >> > ------------------------------------------------------------- >>>> >>>> >>>> >>> >>> >>> >>> >>> __________________________________ >>> Yahoo! FareChase: Search multiple travel sites in >> one click. >>> http://farechase.yahoo.com >>> >>> >> -- >> > ------------------------------------------------------------- >> Hilmar Lapp email: lapp >> at gnf.org >> GNF, San Diego, Ca. 92121 phone: >> +1-858-812-1757 >> > ------------------------------------------------------------- >> >> >> > > > > > __________________________________ > Yahoo! FareChase: Search multiple travel sites in one click. > http://farechase.yahoo.com > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From osborne1 at optonline.net Fri Nov 18 10:24:14 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Fri Nov 18 10:23:36 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" In-Reply-To: <437D56A3.8070902@med.usyd.edu.au> Message-ID: Jonathan, This is a Cygwin thing. Try: >rebaseall Then shut down and restart Cygwin. If rebaseall is not installed then go back to cygwin.com and install the rebase package. Brian O. On 11/17/05 11:20 PM, "Jonathan Arthur" wrote: > Hello all, > > I am having difficulty installing BioPerl. I am running Windows XP > Professional with cygwin. I am using the CPAN installer to attempt to > install the Bundle::BioPerl modules. > > The installation appears to go relatively smoothly and end normally. It > does note at the end that there were installation problems with > File::Spec, GD::SVG, and Data::Stag. Nonetheless, when I try to "use > Bio::Perl" Perl cannot find the module and exploring /usr/lib confirms > the modules are not present. > > I then tried installing the problem modules above on the assumption that > the final installation of Bio::Perl was dependent on these modules being > successfully installed. The creation of the makefile for GD::SVG dies with: > > C:\cygwin\bin\perl.exe (800): *** unable to remap > c:\cygwin\bin\cygfreetype-6.dll to same address as parent(0xE100000) != > 0xEA0000 > > Data::Stag installation experiences a similar error (with different > .dll) when trying to install the Tk dependency. > > File::Spec installation appears to install fine (bar some failed tests > because it can't load File::Spec::VMS) and it is present in > /usr/lib/perl5 so it is not clear what the cpan installation is > complaining about in regard to this module. > > Could anyone assist with these installation problems? > > Regards, > > Jonathan From lupey+ at pitt.edu Fri Nov 18 09:05:32 2005 From: lupey+ at pitt.edu (Paul G Cantalupo) Date: Fri Nov 18 15:49:41 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" In-Reply-To: <437D56A3.8070902@med.usyd.edu.au> References: <437D56A3.8070902@med.usyd.edu.au> Message-ID: Jonathan, The problem is cygwin Perl. See the following: 1) http://sources.redhat.com/ml/cygwin-announce/2005-07/msg00031.html 2) The 'rebase' README file in /usr/share/doc/Cygwin/ Paul Paul Cantalupo Research Specialist/Systems Programmer 559 Crawford Hall Department of Biological Sciences University of Pittsburgh Pittsburgh, PA 15260 Work: 412-624-4687 Fax: 412-624-4759 Ask me about Toastmasters: www.toastmasters.org Midday Club Treasurer On Fri, 18 Nov 2005, Jonathan Arthur wrote: > Hello all, > > I am having difficulty installing BioPerl. I am running Windows XP > Professional with cygwin. I am using the CPAN installer to attempt to install > the Bundle::BioPerl modules. > > The installation appears to go relatively smoothly and end normally. It does > note at the end that there were installation problems with File::Spec, > GD::SVG, and Data::Stag. Nonetheless, when I try to "use Bio::Perl" Perl > cannot find the module and exploring /usr/lib confirms the modules are not > present. > > I then tried installing the problem modules above on the assumption that the > final installation of Bio::Perl was dependent on these modules being > successfully installed. The creation of the makefile for GD::SVG dies with: > > C:\cygwin\bin\perl.exe (800): *** unable to remap > c:\cygwin\bin\cygfreetype-6.dll to same address as parent(0xE100000) != > 0xEA0000 > > Data::Stag installation experiences a similar error (with different .dll) > when trying to install the Tk dependency. > > File::Spec installation appears to install fine (bar some failed tests > because it can't load File::Spec::VMS) and it is present in /usr/lib/perl5 so > it is not clear what the cpan installation is complaining about in regard to > this module. > > Could anyone assist with these installation problems? > > Regards, > > Jonathan > > -- > Dr Jonathan Arthur > Sesqui Lecturer in Bioinformatics > Central Clinical School, Faculty of Medicine and SUBIT > Medical Foundation Building, K25 > University of Sydney > Ph: +61 2 9036 3132 > Email: jarthur@med.usyd.edu.au > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From barry.m.dancis at gsk.com Fri Nov 18 12:47:36 2005 From: barry.m.dancis at gsk.com (barry.m.dancis@gsk.com) Date: Sun Nov 20 12:31:55 2005 Subject: [Bioperl-l] Tree Path In-Reply-To: <76ff505d37cb20e0fed92d8a4e4cf3e8@gmx.net> Message-ID: Hi-- I would like to have a string to represent the node path of a leaf on a phylogeny tree such that when the paths are sorted, they are arranged in the same order as displayed by Forrester or tree view. The code below produces this output: leaf creation path iiiiii, 14, 11: gggggg, 11, 121: hhhhhh, 12, 122: aaaaaa, 0, 21111: bbbbbb, 1, 21112: cccccc, 3, 2112: dddddd, 5, 212: eeeeee, 7, 221: ffffff, 8, 222: for the tree: (((((aaaaaa:0.03000,bbbbbb:0.06091):0.04740,cccccc:0.12143):0.23166,dddddd:0.36034):0.00914,(eeeeee:0.30561,ffffff:0.36105):0.01494):0.01961,((gggggg:0.30365,hhhhhh:0.33271):0.02358,iiiiii:0.32490):0.02788); Notice that the order of the output is the same as the order in the dnd file except that the last major branch of 3 nodes in shown first. if I create the paths using the order sorted by creation id @nodes = sort { $a->_creation_id <=> $b->_creation_id; } $tree->each_Descendent; I get: leaf creation path aaaaaa, 0, 11111: bbbbbb, 1, 11112: cccccc, 3, 1112: dddddd, 5, 112: eeeeee, 7, 121: ffffff, 8, 122: gggggg, 11, 211: hhhhhh, 12, 212: iiiiii, 14, 22: which is now the same as the order in the dnd file. Unfortunately, Forrester gives the order as: bbbbbb, 1, 11112: aaaaaa, 0, 11111: cccccc, 3, 1112: dddddd, 5, 112: ffffff, 8, 122: eeeeee, 7, 121: hhhhhh, 12, 212: gggggg, 11, 211: iiiiii, 14, 22: and tree view gives the order as: dddddd, 5, 112: cccccc, 3, 1112: aaaaaa, 0, 11111: bbbbbb, 1, 11112: eeeeee, 7, 121: ffffff, 8, 122: iiiiii, 14, 22: gggggg, 11, 211: hhhhhh, 12, 212: As expected, the differences in the orders only represent differences caused by flipping the order of branches and not due to some fundamental differences in the trees For some other trees, treeview will give the same order as the path. When there are differences between the path and the location in the displays, it is difficult to find a leaf on a large tree diagram from the node path. The following almost reproduces the Forrester order(igh branch appears at the top instead of the bottom): @nodes = $tree->each_Descendent; #unsorted if ($nodes[0]->is_Leaf) { @nodes = reverse @nodes; } My questions are: How do I need to change my sorting so that the order of the path is the same as the order on the display in Forrestor and/or Tree View. Has anyone else done similar things? Are there bioperl routines to do this? Thanks, Barry ========================================================================================================== sub get_phylo_paths { my ($treefile) = @_; my $treeio = new Bio::TreeIO( -format => 'newick', -file => $treefile); $tree = $treeio->next_tree; # get the tree my $path = []; get_phylo_path ($tree->get_root_node,$path); } # end get_phylo_paths sub get_phylo_path { my ($tree, $ancestor_path) = @_; my @nodes; if ($tree->is_Leaf) { #Include ':' at end so that path is treated as a string not a number by Excel, Spotfire, etc print $tree->id . ', ' . $tree->_creation_id . ', ' . join ($NODE_SEPARATOR,@$ancestor_path) . ":\n"; } else { @nodes = $tree->each_Descendent; #unsorted my $i = 1; foreach my $node (@nodes) { my @path = @$ancestor_path; push @path, $i++;#adds a number to the path node - either 1 or 2 except for the root node where there will be a 3 as well get_phylo_path ($node, \@path); } } } From slimick at warren.upb.pitt.edu Thu Nov 17 15:43:09 2005 From: slimick at warren.upb.pitt.edu (John Slimick) Date: Sun Nov 20 12:34:23 2005 Subject: [Bioperl-l] Problem with bioperl installation Message-ID: Help! I have tried to install Bioperl for use in one of my classes, but I have found a roadblock. I have installed current Bioperl by using the CPAN route and also using the "make" approach. This is on a RH 9.0 system. I get the same error on either installation. Here is the file I wished to test (from the Bioperl document): ======================================================= #!/usr/bin/perl -w use strict; use Bio::Perl; $seq_object = get_sequence('swiss',"ROA_HUMAN"); write_sequence(">roa1.fasta",'fasta',$seq_object); ========================================================== I get the following message: Can't locate Bio/Perl.pm in @INC( @INC contains ,,long file list) When I do: $ find / -name Perl.pm -print as _root_ all I get is a single hit of .../READLINE/Perl.pm Any thoughts? Thanks in advance. john slimick slimick@pitt.edu From bmoore at genetics.utah.edu Sun Nov 20 13:35:27 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Sun Nov 20 13:32:55 2005 Subject: [Bioperl-l] Problem with bioperl installation Message-ID: John, I doesn't sound like your installation succeeded. Did you get errors with make install? Do you know where locate perl modules are installed on yours system (/usr/lib/perl5/site_perl/5.8.5/ on my system)? If so is there a Bio directory there? Can you give us more details on your install process? Barry -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of John Slimick Sent: Thursday, November 17, 2005 1:43 PM To: bioperl-l@bioperl.org Subject: [Bioperl-l] Problem with bioperl installation Help! I have tried to install Bioperl for use in one of my classes, but I have found a roadblock. I have installed current Bioperl by using the CPAN route and also using the "make" approach. This is on a RH 9.0 system. I get the same error on either installation. Here is the file I wished to test (from the Bioperl document): ======================================================= #!/usr/bin/perl -w use strict; use Bio::Perl; $seq_object = get_sequence('swiss',"ROA_HUMAN"); write_sequence(">roa1.fasta",'fasta',$seq_object); ========================================================== I get the following message: Can't locate Bio/Perl.pm in @INC( @INC contains ,,long file list) When I do: $ find / -name Perl.pm -print as _root_ all I get is a single hit of .../READLINE/Perl.pm Any thoughts? Thanks in advance. john slimick slimick@pitt.edu _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From jason.stajich at duke.edu Sun Nov 20 14:04:04 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sun Nov 20 14:02:02 2005 Subject: [Bioperl-l] Tree Path In-Reply-To: References: Message-ID: <132FCEA5-3A68-44ED-BF07-3EB47D6E9CC3@duke.edu> I just added the ability to request the order sorted alphabetically (available from CVS). So each_Descendent('alpha') or each_Descendent ('revalpha'). You can now also supply -order_by in Bio::TreeIO so that the order can be specified when writing out. I'm not sure we can guarantee the order is the same at the read order right now with the way the parser is coded. Creation id is somewhat arbitrary as it has to do with the parse order not necessarily left-to-right reading of nodes. So what I don't understand is what Forrester sort order is based on? If you can describe that you can write a sort function to achieve it, each_Descendent already accepts a code reference so you can pass in an arbitrary subroutine to do the sort. You can always as TreeView to re-do the layout for you tree so that it is alphabetical or ladderized. Is this what you mean? -jason On Nov 18, 2005, at 12:47 PM, barry.m.dancis@gsk.com wrote: > Hi-- > > I would like to have a string to represent the node path of > a leaf > on a phylogeny tree such that when the paths are sorted, they are > arranged > in the same order as displayed by Forrester or tree view. The code > below > produces this output: > > leaf creation path > iiiiii, 14, 11: > gggggg, 11, 121: > hhhhhh, 12, 122: > aaaaaa, 0, 21111: > bbbbbb, 1, 21112: > cccccc, 3, 2112: > dddddd, 5, 212: > eeeeee, 7, 221: > ffffff, 8, 222: > > for the tree: > > (((((aaaaaa:0.03000,bbbbbb:0.06091):0.04740,cccccc:0.12143): > 0.23166,dddddd:0.36034):0.00914,(eeeeee:0.30561,ffffff:0.36105): > 0.01494):0.01961,((gggggg:0.30365,hhhhhh:0.33271):0.02358,iiiiii: > 0.32490):0.02788); > > Notice that the order of the output is the same as the order in the > dnd > file except that the last major branch of 3 nodes in shown first. > > if I create the paths using the order sorted by creation id > > @nodes = sort { $a->_creation_id <=> $b->_creation_id; } > $tree->each_Descendent; > > I get: > > leaf creation path > aaaaaa, 0, 11111: > bbbbbb, 1, 11112: > cccccc, 3, 1112: > dddddd, 5, 112: > eeeeee, 7, 121: > ffffff, 8, 122: > gggggg, 11, 211: > hhhhhh, 12, 212: > iiiiii, 14, 22: > > which is now the same as the order in the dnd file. > > Unfortunately, Forrester gives the order as: > > bbbbbb, 1, 11112: > aaaaaa, 0, 11111: > cccccc, 3, 1112: > dddddd, 5, 112: > ffffff, 8, 122: > eeeeee, 7, 121: > hhhhhh, 12, 212: > gggggg, 11, 211: > iiiiii, 14, 22: > > and tree view gives the order as: > > dddddd, 5, 112: > cccccc, 3, 1112: > aaaaaa, 0, 11111: > bbbbbb, 1, 11112: > eeeeee, 7, 121: > ffffff, 8, 122: > iiiiii, 14, 22: > gggggg, 11, 211: > hhhhhh, 12, 212: > > > As expected, the differences in the orders only represent differences > caused by flipping the order of branches and not due to some > fundamental > differences in the trees > For some other trees, treeview will give the same order as the > path. When > there are differences between the path and the location in the > displays, > it is difficult to find a leaf on a large tree diagram from the > node path. > > The following almost reproduces the Forrester order(igh branch > appears at > the top instead of the bottom): > > @nodes = $tree->each_Descendent; #unsorted > if ($nodes[0]->is_Leaf) { > @nodes = reverse @nodes; > } > > My questions are: > How do I need to change my sorting so that the order of the path is > the > same as the order on the display in Forrestor and/or Tree View. > Has anyone else done similar things? Are there bioperl routines to do > this? > > Thanks, > > Barry > > ====================================================================== > ==================================== > sub get_phylo_paths { > > my ($treefile) = @_; > > my $treeio = new Bio::TreeIO( -format => 'newick', -file => > $treefile); > $tree = $treeio->next_tree; # get the tree > my $path = []; > get_phylo_path ($tree->get_root_node,$path); > } # end get_phylo_paths > > > sub get_phylo_path { > my ($tree, $ancestor_path) = @_; > my @nodes; > if ($tree->is_Leaf) { > #Include ':' at end so that path is treated as a string not a > number by Excel, Spotfire, etc > print $tree->id . ', ' . $tree->_creation_id . ', ' . join > ($NODE_SEPARATOR,@$ancestor_path) . ":\n"; > } > else { > @nodes = $tree->each_Descendent; #unsorted > my $i = 1; > foreach my $node (@nodes) { > my @path = @$ancestor_path; > push @path, $i++;#adds a number to the path node - either 1 > or 2 > except for the root node where there will be a 3 as well > get_phylo_path ($node, \@path); > } > } > } > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jason.stajich at duke.edu Sun Nov 20 13:40:47 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sun Nov 20 14:42:41 2005 Subject: [Bioperl-l] Problem with bioperl installation In-Reply-To: References: Message-ID: <4A1E1ECD-CB01-4AB5-904A-4E53E4C097C8@duke.edu> Doesn't sound like anything was installed. What are the errors during installation? Did you try the RPM approach? http://apt.bea.ki.se/ -jason On Nov 17, 2005, at 3:43 PM, John Slimick wrote: > > Help! > > I have tried to install Bioperl for use in > one of my classes, but I have found a roadblock. > I have installed current Bioperl by using > the CPAN route and also using the "make" > approach. This is on a RH 9.0 system. > I get the same error on either installation. > > Here is the file I wished to test (from the Bioperl > document): > > ======================================================= > #!/usr/bin/perl -w > use strict; > > use Bio::Perl; > > $seq_object = get_sequence('swiss',"ROA_HUMAN"); > > write_sequence(">roa1.fasta",'fasta',$seq_object); > ========================================================== > > I get the following message: > > Can't locate Bio/Perl.pm in @INC( @INC contains ,,long file list) > > When I do: > > $ find / -name Perl.pm -print > > as _root_ all I get is a single hit > of > > .../READLINE/Perl.pm > > Any thoughts? > > Thanks in advance. > > john slimick > slimick@pitt.edu > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jarthur at med.usyd.edu.au Sun Nov 20 17:38:48 2005 From: jarthur at med.usyd.edu.au (Jonathan Arthur) Date: Sun Nov 20 17:34:44 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" In-Reply-To: References: <437D56A3.8070902@med.usyd.edu.au> Message-ID: <4380FAF8.2000308@med.usyd.edu.au> Hello all, Thanks Paul and Brian for your help.This has helped me make some progress, but I am still having installation problems. Now, using cpan, when I type: install Bundle::BioPerl all I get is a long list of models marked as "up to date" e.g. CPAN: Storable loaded ok Going to read /home/jonathan/.cpan/Metadata Database was generated on Thu, 10 Nov 2005 07:02:24 GMT MIME::Base64 is up to date. Digest::Md5 is up to date. URI is up to date. ... Graph::Directed is up to date. and that's it. No error messages, no failed tests, nothing. However: perl -e "use Bio::Perl" gives "Can't locate Bio/Perl.pm in @INC (.......)" Any ideas? Thanks again for your help. Jonathan Paul G Cantalupo wrote: > Jonathan, > > The problem is cygwin Perl. See the following: > > 1) http://sources.redhat.com/ml/cygwin-announce/2005-07/msg00031.html > 2) The 'rebase' README file in /usr/share/doc/Cygwin/ > > Paul > > Paul Cantalupo > Research Specialist/Systems Programmer > 559 Crawford Hall > Department of Biological Sciences > University of Pittsburgh > Pittsburgh, PA 15260 > Work: 412-624-4687 > Fax: 412-624-4759 > > Ask me about Toastmasters: www.toastmasters.org > Midday Club Treasurer > > On Fri, 18 Nov 2005, Jonathan Arthur wrote: > >> Hello all, >> >> I am having difficulty installing BioPerl. I am running Windows XP >> Professional with cygwin. I am using the CPAN installer to attempt to >> install the Bundle::BioPerl modules. >> >> The installation appears to go relatively smoothly and end normally. >> It does note at the end that there were installation problems with >> File::Spec, GD::SVG, and Data::Stag. Nonetheless, when I try to "use >> Bio::Perl" Perl cannot find the module and exploring /usr/lib >> confirms the modules are not present. >> >> I then tried installing the problem modules above on the assumption >> that the final installation of Bio::Perl was dependent on these >> modules being successfully installed. The creation of the makefile >> for GD::SVG dies with: >> >> C:\cygwin\bin\perl.exe (800): *** unable to remap >> c:\cygwin\bin\cygfreetype-6.dll to same address as parent(0xE100000) >> != 0xEA0000 >> >> Data::Stag installation experiences a similar error (with different >> .dll) when trying to install the Tk dependency. >> >> File::Spec installation appears to install fine (bar some failed >> tests because it can't load File::Spec::VMS) and it is present in >> /usr/lib/perl5 so it is not clear what the cpan installation is >> complaining about in regard to this module. >> >> Could anyone assist with these installation problems? >> >> Regards, >> >> Jonathan >> >> -- >> Dr Jonathan Arthur >> Sesqui Lecturer in Bioinformatics >> Central Clinical School, Faculty of Medicine and SUBIT >> Medical Foundation Building, K25 >> University of Sydney >> Ph: +61 2 9036 3132 >> Email: jarthur@med.usyd.edu.au >> >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> -- Dr Jonathan Arthur Sesqui Lecturer in Bioinformatics Central Clinical School, Faculty of Medicine and SUBIT Medical Foundation Building, K25 University of Sydney Ph: +61 2 9036 3132 Email: jarthur@med.usyd.edu.au From jason.stajich at duke.edu Sun Nov 20 21:37:12 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Sun Nov 20 22:18:14 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" In-Reply-To: <4380FAF8.2000308@med.usyd.edu.au> References: <437D56A3.8070902@med.usyd.edu.au> <4380FAF8.2000308@med.usyd.edu.au> Message-ID: <061F94D0-8C65-4A62-9968-6D662E970973@duke.edu> Did you actually install Bioperl? It isn't part of Bundle::BioPerl. -jason On Nov 20, 2005, at 5:38 PM, Jonathan Arthur wrote: > Hello all, > > Thanks Paul and Brian for your help.This has helped me make some > progress, but I am still having installation problems. Now, using > cpan, when I type: install Bundle::BioPerl all I get is a long list > of models marked as "up to date" e.g. > > CPAN: Storable loaded ok > Going to read /home/jonathan/.cpan/Metadata > Database was generated on Thu, 10 Nov 2005 07:02:24 GMT > MIME::Base64 is up to date. > Digest::Md5 is up to date. > URI is up to date. > ... > Graph::Directed is up to date. > > and that's it. No error messages, no failed tests, nothing. However: > > perl -e "use Bio::Perl" gives > > "Can't locate Bio/Perl.pm in @INC (.......)" > > Any ideas? > > Thanks again for your help. > > Jonathan > > Paul G Cantalupo wrote: > >> Jonathan, >> >> The problem is cygwin Perl. See the following: >> >> 1) http://sources.redhat.com/ml/cygwin-announce/2005-07/msg00031.html >> 2) The 'rebase' README file in /usr/share/doc/Cygwin/ >> >> Paul >> >> Paul Cantalupo >> Research Specialist/Systems Programmer >> 559 Crawford Hall >> Department of Biological Sciences >> University of Pittsburgh >> Pittsburgh, PA 15260 >> Work: 412-624-4687 >> Fax: 412-624-4759 >> >> Ask me about Toastmasters: www.toastmasters.org >> Midday Club Treasurer >> >> On Fri, 18 Nov 2005, Jonathan Arthur wrote: >> >>> Hello all, >>> >>> I am having difficulty installing BioPerl. I am running Windows >>> XP Professional with cygwin. I am using the CPAN installer to >>> attempt to install the Bundle::BioPerl modules. >>> >>> The installation appears to go relatively smoothly and end >>> normally. It does note at the end that there were installation >>> problems with File::Spec, GD::SVG, and Data::Stag. Nonetheless, >>> when I try to "use Bio::Perl" Perl cannot find the module and >>> exploring /usr/lib confirms the modules are not present. >>> >>> I then tried installing the problem modules above on the >>> assumption that the final installation of Bio::Perl was dependent >>> on these modules being successfully installed. The creation of >>> the makefile for GD::SVG dies with: >>> >>> C:\cygwin\bin\perl.exe (800): *** unable to remap c:\cygwin\bin >>> \cygfreetype-6.dll to same address as parent(0xE100000) != 0xEA0000 >>> >>> Data::Stag installation experiences a similar error (with >>> different .dll) when trying to install the Tk dependency. >>> >>> File::Spec installation appears to install fine (bar some failed >>> tests because it can't load File::Spec::VMS) and it is present >>> in /usr/lib/perl5 so it is not clear what the cpan installation >>> is complaining about in regard to this module. >>> >>> Could anyone assist with these installation problems? >>> >>> Regards, >>> >>> Jonathan >>> >>> -- >>> Dr Jonathan Arthur >>> Sesqui Lecturer in Bioinformatics >>> Central Clinical School, Faculty of Medicine and SUBIT >>> Medical Foundation Building, K25 >>> University of Sydney >>> Ph: +61 2 9036 3132 >>> Email: jarthur@med.usyd.edu.au >>> >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>> > > > -- > Dr Jonathan Arthur > Sesqui Lecturer in Bioinformatics > Central Clinical School, Faculty of Medicine and SUBIT > Medical Foundation Building, K25 > University of Sydney > Ph: +61 2 9036 3132 > Email: jarthur@med.usyd.edu.au > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jdw at ou.edu Mon Nov 21 08:38:40 2005 From: jdw at ou.edu (James D. White) Date: Mon Nov 21 10:47:17 2005 Subject: [Bioperl-l] Installation problems: "unable to remap" Message-ID: <4381CDE0.70305@ou.edu> > > >Message: 13 >Date: Mon, 21 Nov 2005 09:38:48 +1100 >From: Jonathan Arthur >Subject: Re: [Bioperl-l] Installation problems: "unable to remap" >To: bioperl-l@bioperl.org >Message-ID: <4380FAF8.2000308@med.usyd.edu.au> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Hello all, > >Thanks Paul and Brian for your help.This has helped me make some >progress, but I am still having installation problems. Now, using cpan, >when I type: install Bundle::BioPerl all I get is a long list of models >marked as "up to date" e.g. > > Bundle::BioPerl does not install Bioperl itself, only the prerequisites for Bioperl. You are now ready to install Bioperl. >CPAN: Storable loaded ok >Going to read /home/jonathan/.cpan/Metadata > Database was generated on Thu, 10 Nov 2005 07:02:24 GMT >MIME::Base64 is up to date. >Digest::Md5 is up to date. >URI is up to date. >... >Graph::Directed is up to date. > >and that's it. No error messages, no failed tests, nothing. However: > >perl -e "use Bio::Perl" gives > >"Can't locate Bio/Perl.pm in @INC (.......)" > >Any ideas? > >Thanks again for your help. > >Jonathan > >Paul G Cantalupo wrote: > > > >>> Jonathan, >>> >>> The problem is cygwin Perl. See the following: >>> >>> 1) http://sources.redhat.com/ml/cygwin-announce/2005-07/msg00031.html >>> 2) The 'rebase' README file in /usr/share/doc/Cygwin/ >>> >>> Paul >>> >>> Paul Cantalupo >>> Research Specialist/Systems Programmer >>> 559 Crawford Hall >>> Department of Biological Sciences >>> University of Pittsburgh >>> Pittsburgh, PA 15260 >>> Work: 412-624-4687 >>> Fax: 412-624-4759 >>> >>> Ask me about Toastmasters: www.toastmasters.org >>> Midday Club Treasurer >>> >>> On Fri, 18 Nov 2005, Jonathan Arthur wrote: >>> >> >> >>>>> Hello all, >>>>> >>>>> I am having difficulty installing BioPerl. I am running Windows XP >>>>> Professional with cygwin. I am using the CPAN installer to attempt to >>>>> install the Bundle::BioPerl modules. >>>>> >>>>> The installation appears to go relatively smoothly and end normally. >>>>> It does note at the end that there were installation problems with >>>>> File::Spec, GD::SVG, and Data::Stag. Nonetheless, when I try to "use >>>>> Bio::Perl" Perl cannot find the module and exploring /usr/lib >>>>> confirms the modules are not present. >>>>> >>>>> I then tried installing the problem modules above on the assumption >>>>> that the final installation of Bio::Perl was dependent on these >>>>> modules being successfully installed. The creation of the makefile >>>>> for GD::SVG dies with: >>>>> >>>>> C:\cygwin\bin\perl.exe (800): *** unable to remap >>>>> c:\cygwin\bin\cygfreetype-6.dll to same address as parent(0xE100000) >>>>> != 0xEA0000 >>>>> >>>>> Data::Stag installation experiences a similar error (with different >>>>> .dll) when trying to install the Tk dependency. >>>>> >>>>> File::Spec installation appears to install fine (bar some failed >>>>> tests because it can't load File::Spec::VMS) and it is present in >>>>> /usr/lib/perl5 so it is not clear what the cpan installation is >>>>> complaining about in regard to this module. >>>>> >>>>> Could anyone assist with these installation problems? >>>>> >>>>> Regards, >>>>> >>>>> Jonathan >>>>> >>>>> -- >>>>> Dr Jonathan Arthur >>>>> Sesqui Lecturer in Bioinformatics >>>>> Central Clinical School, Faculty of Medicine and SUBIT >>>>> Medical Foundation Building, K25 >>>>> University of Sydney >>>>> Ph: +61 2 9036 3132 >>>>> Email: jarthur@med.usyd.edu.au >>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioperl-l mailing list >>>>> Bioperl-l@portal.open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >>>>> >>> >>> > > > -- Dr Jonathan Arthur Sesqui Lecturer in Bioinformatics Central > Clinical School, Faculty of Medicine and SUBIT Medical Foundation > Building, K25 University of Sydney Ph: +61 2 9036 3132 > > Email: jarthur@med.usyd.edu.au ------------------------------ > From timreid at gmail.com Mon Nov 21 13:49:19 2005 From: timreid at gmail.com (Tim Reid) Date: Mon Nov 21 15:51:32 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? Message-ID: i am trying to reproduce the NCBI's html organism report of BLAST results, but i can't figure out how they obtain taxonomy information for each hit. as far as i can tell this information is not contained within a hit object, although it is sometimes embedded in the description string. i have looked at the Bio::Taxonomy::FactoryI interface, which would appear to offer some sort of solution by way of passing the entire description string to the fuzzy_search method, but i cannot seem to find an implementation for this interface. also, Bio::DB::Taxonomy::entrez seemed promising except that it does not appear to return any results when passed a description string. i would appreciate some help. how does the NCBI's organism report generator work? From jason.stajich at duke.edu Mon Nov 21 16:00:32 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Nov 21 16:30:28 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? In-Reply-To: References: Message-ID: <87DA4900-7409-417C-BD2A-9DB38D286C7D@duke.edu> You need to look up the taxonomid ID from the gi number for a record. So you do: gi -> taxid taxid -> species string You can download the two column datafile from NCBI for all the GIs (separated by protein and nt) from ftp://ftp.ncbi.nih.gov/pub/taxonomy -jason On Nov 21, 2005, at 1:49 PM, Tim Reid wrote: > i am trying to reproduce the NCBI's html organism report of BLAST > results, > but i can't figure out how they obtain taxonomy information for > each hit. > > as far as i can tell this information is not contained within a hit > object, > although it is sometimes embedded in the description string. > > i have looked at the Bio::Taxonomy::FactoryI interface, which would > appear > to offer some sort of solution by way of passing the entire > description > string to the fuzzy_search method, but i cannot seem to find an > implementation for this interface. > > also, Bio::DB::Taxonomy::entrez seemed promising except that it > does not > appear to return any results when passed a description string. > > i would appreciate some help. how does the NCBI's organism report > generator > work? > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jason.stajich at duke.edu Mon Nov 21 16:26:23 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Nov 21 19:01:51 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? In-Reply-To: References: <87DA4900-7409-417C-BD2A-9DB38D286C7D@duke.edu> Message-ID: <49A1DC8A-84B3-489B-83DA-9B70210A6AEC@duke.edu> Well isn't encoded in the hit name? my ($gi) = ($hit->name =~ /gi\|(\d+)/ ); If you run WU-BLAST you need to provide the -gi option on the command line. If you run NCBI-BLAST you need to provide the -I option From the blastall help: -I Show GI's in deflines [T/F] default = F -jason On Nov 21, 2005, at 4:22 PM, Tim Reid wrote: > > You need to look up the taxonomid ID from the gi number for a record. > > thanks for your reply, but i am unable to find the gi number of a > blast hit. > > i have looked at the each_accession_number method in > Bio::Search::HitI, but it does not appear to yield a gi number. > > your help is appreciated. -- Jason Stajich Duke University http://www.duke.edu/~jes12 From jason.stajich at duke.edu Tue Nov 22 09:25:46 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 22 09:23:46 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? In-Reply-To: References: <87DA4900-7409-417C-BD2A-9DB38D286C7D@duke.edu> <49A1DC8A-84B3-489B-83DA-9B70210A6AEC@duke.edu> Message-ID: Tim - Will have to consult other members of the list for StandAloneBlast and RemoteBlast help, sorry. -jason On Nov 21, 2005, at 5:04 PM, Tim Reid wrote: > i am using NCBI-BLAST by way of Bio::Tools::Run::RemoteBlast. > > i tried adding "-I" =>'T' to the @params used to instantiate my > RemoteBlast object, but this did not work. > > further help appreciated. can you tell me if StandAloneBlast > supports the use of NCBI's netblast? i couldn't tell, but if it > does that could be another option. > > thanks. > > -- Jason Stajich Duke University http://www.duke.edu/~jes12 From unforgetable_manish at yahoo.com Tue Nov 22 06:48:24 2005 From: unforgetable_manish at yahoo.com (Manish Kumar) Date: Tue Nov 22 09:31:24 2005 Subject: [Bioperl-l] Program Message-ID: <20051122114824.64151.qmail@web34507.mail.mud.yahoo.com> Hello, I am Manish Kumar n I m M.Sc (Bioinfomatics) student n i need the perl program for BLAST. I mean what is the program for BLAST that it gives this type of results. For example:- Score = 40.1 bits (20), Expect = 0.16 Identities = 23/24 (95%), Gaps = 0/24 (0%) Strand=Plus/Minus Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 ||||||||||| |||||||||||| Sbjct 8466 ATGTGTACGTGTGTGGTTACGTGC 8443 The above is an example of the BLAST output. Now i need the program for this output. thanking you Best Regards Manish __________________________________ Start your day with Yahoo! - Make it your home page! http://www.yahoo.com/r/hs From jason at portal.open-bio.org Tue Nov 22 09:31:58 2005 From: jason at portal.open-bio.org (Jason Stajich) Date: Tue Nov 22 11:17:10 2005 Subject: [Bioperl-l] Fwd: Program References: <20051122120754.49882.qmail@web34515.mail.mud.yahoo.com> Message-ID: <7629DD58-DFF3-4977-8AA0-C9E2CEC4EAFC@bioperl.org> Manish - Please address your query to the Bioperl mailing list. -jason Begin forwarded message: > From: Manish Kumar > Date: November 22, 2005 7:07:54 AM EST > To: jason@bioperl.org > Subject: Program > > Hello, > I am Manish Kumar n I m M.Sc > (Bioinfomatics) student n i need the perl program for > BLAST. I mean what is the program for BLAST that it > gives this type of results. > > > For example:- > Score = 40.1 bits (20), Expect = 0.16 > Identities = 23/24 (95%), Gaps = 0/24 (0%) > Strand=Plus/Minus > > Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 > ||||||||||| |||||||||||| > Sbjct 8466 ATGTGTACGTGTGTGGTTACGTGC 8443 > > The above is an example of the BLAST output. Now i > need the program for this output. > thanking you > Best Regards > Manish > > > > > > > __________________________________ > Start your day with Yahoo! - Make it your home page! > http://www.yahoo.com/r/hs -- Jason Stajich jason@bioperl.org http://jason.open-bio.org/ From bmoore at genetics.utah.edu Tue Nov 22 11:27:15 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Tue Nov 22 11:24:44 2005 Subject: FW: [Bioperl-l] Program Message-ID: Manish, That comes from NCBI which is separate from the Bioperl project. http://www.ncbi.nlm.nih.gov/BLAST/download.shtml Barry > > -----Original Message----- > > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > > bounces@portal.open-bio.org] On Behalf Of Manish Kumar > > Sent: Tuesday, November 22, 2005 4:48 AM > > To: bioperl-l@bioperl.org > > Subject: [Bioperl-l] Program > > > > Hello, > > I am Manish Kumar n I m M.Sc > > (Bioinfomatics) student n i need the perl program for > > BLAST. I mean what is the program for BLAST that it > > gives this type of results. > > > > > > For example:- > > Score = 40.1 bits (20), Expect = 0.16 > > Identities = 23/24 (95%), Gaps = 0/24 (0%) > > Strand=Plus/Minus > > > > Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 > > ||||||||||| |||||||||||| > > Sbjct 8466 ATGTGTACGTGTGTGGTTACGTGC 8443 > > > > The above is an example of the BLAST output. Now i > > need the program for this output. > > thanking you > > Best Regards > > Manish > > > > > > > > __________________________________ > > Start your day with Yahoo! - Make it your home page! > > http://www.yahoo.com/r/hs > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Tue Nov 22 13:11:47 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Tue Nov 22 13:09:15 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? Message-ID: Tim- The blastall command line options are sent in the http header when using RemoteBlast, and you add them like this (some can also be passed as a hash to new): $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'yes'; The above example should be equivalent to the blastall -I T option. Bioperl's RemoteBlast uses the urlapi for blast from NCBI which is documented here: http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html. You can see all of the parameters there. I tried the above example, and I don't get the gi numbers in the report. I suspected that they weren't making it through the parser, so I stepped through the bioperl blast submission and retrieval process, and there are no gi numbers in the report even before the bioperl parser gets a hold of them. However, I can see the gi numbers come and go in the web based output by modifying this url: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?NCBI_GI=yes&DATABASE=swisspr ot&QUERY=%3E+%0Anmpkvileshskptdsvflqpwikaliednsehdqyhpsghvipsltkqdlalphm sptiltn&COMPOSITION_BASED_STATISTICS=off&EXPECT=1&SERVICE=plain&FORMAT_O BJECT=Alignment&CMD=Put&FILTER=L&PROGRAM=blastp This is the same URL used by bioperl to submit this query (in fact I copied it from the debugger as I was stepping through the bioperl code). Below is the script I used for testing. If anyone wants to look at the POST and the results, fire up this script in the debugger and run the following commands from the debugger prompt. Keep repeating c 561 until the NCBI server returns a report. You should see both the URL used, and the output of the report. c Bio::Tools::Run::RemoteBlast::retrieve_blast n $self->verbose(1); c 561 Anyone else got any ideas why we're not getting gi numbers, or if we are getting them, how you access them? Barry use strict; use Bio::PrimarySeq; use Bio::Tools::Run::RemoteBlast; use Bio::SearchIO; use Bio::SearchIO::Writer::TextResultWriter; my @sequences; for my $seq ("nmpkvileshskptdsvflqpwikaliednsehdqyhpsghvipsltkqdlalphmsptiltn", "edwckgmdmdprkallivgipmecseveiqdtvkaglqplcayrvlgrmfrrednakavf") { push @sequences, Bio::PrimarySeq->new(-seq => $seq, -alphabet => 'protein'); } #Remote-BLAST factory object creation and blast-parameter initialization my $BLAST_factory = Bio::Tools::Run::RemoteBlast->new('-prog' => 'blastp', '-data' => 'swissprot', '-expect' => '1', '-readmethod' => 'SearchIO' ); $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'yes'; #Loop to BLAST each seq against the database, and check for a hit. for my $seq (@sequences) { print "Blasting Sequence: " . $seq->seq. "\n"; #Blast the sequence against a database: my $job = $BLAST_factory->submit_blast($seq); #Load the RID returned for the BLAST job submitted my @rids = $BLAST_factory->each_rid; my $rid = shift @rids; my $blast_results; until ($blast_results) { print "Checking RID: $rid\n"; $blast_results = $BLAST_factory->retrieve_blast($rid); sleep 5; } #Was a result returned? if( !ref($blast_results) ) { #If so and it returned an error remove that RID from the stack if ($blast_results < 0) { $BLAST_factory->remove_rid($rid); } } #If a result was returned and it isn't an error, then pass it to a #variable... else { my $result = $blast_results->next_result(); my $writer = new Bio::SearchIO::Writer::TextResultWriter(); my $out = new Bio::SearchIO(-writer => $writer); $out->write_result($result); $BLAST_factory->remove_rid($rid); #...and remove it's RID } } } From timreid at gmail.com Tue Nov 22 15:38:14 2005 From: timreid at gmail.com (Tim Reid) Date: Tue Nov 22 16:03:03 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? In-Reply-To: References: Message-ID: On 11/22/05, Barry Moore wrote: > > $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'yes'; > > The above example should be equivalent to the blastall -I T option. > by looking thru the source (which appears to be rather out of sync with the documentation) i discovered that this line has to be: $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'NCBI_GI'} = 'yes'; because NCBI_GI is a paramater of the GET cmd. this is an odd arrangement (shouldn't these paramaters be set via the RemoteBlast constructor?) but it works. i have not yet been able to obtain the taxonomy relating to a gi number, but i am still working at it. From Marc.Logghe at DEVGEN.com Tue Nov 22 16:34:16 2005 From: Marc.Logghe at DEVGEN.com (Marc Logghe) Date: Tue Nov 22 16:48:45 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? Message-ID: <0C528E3670D8CE4B8E013F6749231AA607D937@ANTARESIA.be.devgen.com> Hi Tim, I am getting confused. Are you looking for a way to get your hands on the taxblast report as a result of performing a remote blast @ NCBI. Or rather, trying to implement locally a blast facility producing a taxblast report similar to the NCBI web site ? Regards, Marc -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org on behalf of Tim Reid Sent: Tue 11/22/2005 9:38 PM Cc: bioperl-l@bioperl.org Subject: Re: [Bioperl-l] producing an organism report from BLAST results? On 11/22/05, Barry Moore wrote: > > $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'yes'; > > The above example should be equivalent to the blastall -I T option. > by looking thru the source (which appears to be rather out of sync with the documentation) i discovered that this line has to be: $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'NCBI_GI'} = 'yes'; because NCBI_GI is a paramater of the GET cmd. this is an odd arrangement (shouldn't these paramaters be set via the RemoteBlast constructor?) but it works. i have not yet been able to obtain the taxonomy relating to a gi number, but i am still working at it. _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From bmoore at genetics.utah.edu Tue Nov 22 23:14:17 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Tue Nov 22 23:11:51 2005 Subject: [Bioperl-l] producing an organism report from BLAST results? Message-ID: > > $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'NCBI_GI'} = 'yes'; > > because NCBI_GI is a paramater of the GET cmd. > Ahh, that's what I was missing. Thanks Tim for sharing the solution. Barry From heikki at sanbi.ac.za Wed Nov 23 01:53:49 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed Nov 23 01:52:44 2005 Subject: [Bioperl-l] Fwd: Program In-Reply-To: <7629DD58-DFF3-4977-8AA0-C9E2CEC4EAFC@bioperl.org> References: <20051122120754.49882.qmail@web34515.mail.mud.yahoo.com> <7629DD58-DFF3-4977-8AA0-C9E2CEC4EAFC@bioperl.org> Message-ID: <200511230853.49576.heikki@sanbi.ac.za> Manish, BioPerl has modules for parsing BLAST output. Install BioPerl and read the SearchIO HOWTO to get started (http://bioperl.org/HOWTOs/html/SearchIO.html). -Heikki On Tuesday 22 November 2005 16:31, Jason Stajich wrote: > Manish - > > Please address your query to the Bioperl mailing list. > > -jason > > Begin forwarded message: > > From: Manish Kumar > > Date: November 22, 2005 7:07:54 AM EST > > To: jason@bioperl.org > > Subject: Program > > > > Hello, > > I am Manish Kumar n I m M.Sc > > (Bioinfomatics) student n i need the perl program for > > BLAST. I mean what is the program for BLAST that it > > gives this type of results. > > > > > > For example:- > > Score = 40.1 bits (20), Expect = 0.16 > > Identities = 23/24 (95%), Gaps = 0/24 (0%) > > Strand=Plus/Minus > > > > Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 > > > > Sbjct 8466 ATGTGTACGTGTGTGGTTACGTGC 8443 > > > > The above is an example of the BLAST output. Now i > > need the program for this output. > > thanking you > > Best Regards > > Manish > > > > > > > > > > > > > > __________________________________ > > Start your day with Yahoo! - Make it your home page! > > http://www.yahoo.com/r/hs > > -- > Jason Stajich > jason@bioperl.org > http://jason.open-bio.org/ > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From olenka.m at gmail.com Tue Nov 22 19:43:16 2005 From: olenka.m at gmail.com (Olena Morozova) Date: Wed Nov 23 02:07:02 2005 Subject: [Bioperl-l] clustalw.pm not installed Message-ID: <259a224c0511221643u2e26fde7vddcee979a6d10710@mail.gmail.com> Hello, I am trying to do a multiple sequence alignment using clustalw.pm, but I noticed that I do not have Alignment::clustalw in my site::lib::Bio::Tools::Run directory or elsewhere on my computer. Is it possible that it did not get installed correctly during my installation of Bioperl (I am using complete bioperl 1.4 installation on Windows platform)? If so, where can I get the clustalw.pm module without having to install the whole bioperl again? Thank you very much for your help! Olena From arareko at campus.iztacala.unam.mx Wed Nov 23 02:00:59 2005 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed Nov 23 02:08:39 2005 Subject: [Bioperl-l] Cleaning up dependencies Message-ID: <438413AB.8020109@campus.iztacala.unam.mx> Does any of the modules in the 1.5.1 release still require XML::Node, Parse::RecDescent and Test::Simple ? Regards, Mauricio. -- MAURICIO HERRERA CUADRA arareko@campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From heikki at sanbi.ac.za Wed Nov 23 02:59:37 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed Nov 23 02:57:27 2005 Subject: [Bioperl-l] Cleaning up dependencies In-Reply-To: <438413AB.8020109@campus.iztacala.unam.mx> References: <438413AB.8020109@campus.iztacala.unam.mx> Message-ID: <200511230959.37944.heikki@sanbi.ac.za> A quick find/grep proved that none of these modules are used in bioperl 1.5.1 nor in CVS head. -Heikki On Wednesday 23 November 2005 09:00, Mauricio Herrera Cuadra wrote: > Does any of the modules in the 1.5.1 release still require XML::Node, > Parse::RecDescent and Test::Simple ? > > Regards, > Mauricio. -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From heikki at sanbi.ac.za Wed Nov 23 03:16:28 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Wed Nov 23 03:14:27 2005 Subject: [Bioperl-l] clustalw.pm not installed In-Reply-To: <259a224c0511221643u2e26fde7vddcee979a6d10710@mail.gmail.com> References: <259a224c0511221643u2e26fde7vddcee979a6d10710@mail.gmail.com> Message-ID: <200511231016.28921.heikki@sanbi.ac.za> Olena, Your Run directory is empty, right? You have not installed the bioperl run package. Go back to where you got the bioperl core package and install it, too. -Heikki On Wednesday 23 November 2005 02:43, Olena Morozova wrote: > Hello, > > I am trying to do a multiple sequence alignment using clustalw.pm, but > I noticed that I do not have Alignment::clustalw in my > site::lib::Bio::Tools::Run directory or elsewhere on my computer. Is > it possible that it did not get installed correctly during my > installation of Bioperl (I am using complete bioperl 1.4 installation > on Windows platform)? If so, where can I get the clustalw.pm module > without having to install the whole bioperl again? > Thank you very much for your help! > > Olena > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From arareko at campus.iztacala.unam.mx Wed Nov 23 09:51:47 2005 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Wed Nov 23 09:54:14 2005 Subject: [Bioperl-l] Cleaning up dependencies In-Reply-To: <200511230959.37944.heikki@sanbi.ac.za> References: <438413AB.8020109@campus.iztacala.unam.mx> <200511230959.37944.heikki@sanbi.ac.za> Message-ID: <43848203.9070902@campus.iztacala.unam.mx> I was figuring out how those came up as dependencies into the FreeBSD port. Still a mystery... Thanks Heikki. Heikki Lehvaslaiho wrote: > A quick find/grep proved that none of these modules are used in bioperl 1.5.1 > nor in CVS head. > > -Heikki > > > On Wednesday 23 November 2005 09:00, Mauricio Herrera Cuadra wrote: > >>Does any of the modules in the 1.5.1 release still require XML::Node, >>Parse::RecDescent and Test::Simple ? >> >>Regards, >>Mauricio. > > -- MAURICIO HERRERA CUADRA arareko@campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From slimick at warren.upb.pitt.edu Wed Nov 23 12:49:50 2005 From: slimick at warren.upb.pitt.edu (John Slimick) Date: Wed Nov 23 12:47:55 2005 Subject: [Bioperl-l] Problem with bioperl installation In-Reply-To: References: Message-ID: Hello All: I tried working with the Swedish site, but I got confused by all the files there that I returned to the CPAN installation. The final lines of a failed install: txml-mode ok All tests successful, 1 test and 1 subtest dropped Files = /usr/bin/make -- OK Running make install mkdir /usr/bin/perl: File exists at /usr/local/lib/perl5/5.8.7/ExtUtils/Install.pm line 112 make *** [pure_site_install] Error 17 /usr/bin/make isntall -- Not OK and back to the prompt. Earlier in the tests, one was failed with the message Can't locate HTTP/Headers.pm in @INC(.....) Thanks in advance. john slimick slimick@pitt.edu ============================================================== On Sun, 20 Nov 2005, Barry Moore wrote: > John, > > I doesn't sound like your installation succeeded. Did you get errors > with make install? Do you know where locate perl modules are installed > on yours system (/usr/lib/perl5/site_perl/5.8.5/ on my system)? If so > is there a Bio directory there? Can you give us more details on your > install process? > > Barry > > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org > [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of John Slimick > Sent: Thursday, November 17, 2005 1:43 PM > To: bioperl-l@bioperl.org > Subject: [Bioperl-l] Problem with bioperl installation > > > Help! > > I have tried to install Bioperl for use in > one of my classes, but I have found a roadblock. > I have installed current Bioperl by using > the CPAN route and also using the "make" > approach. This is on a RH 9.0 system. > I get the same error on either installation. > > Here is the file I wished to test (from the Bioperl > document): > > ======================================================= > #!/usr/bin/perl -w > use strict; > > use Bio::Perl; > > $seq_object = get_sequence('swiss',"ROA_HUMAN"); > > write_sequence(">roa1.fasta",'fasta',$seq_object); > ========================================================== > > I get the following message: > > Can't locate Bio/Perl.pm in @INC( @INC contains ,,long file list) > > When I do: > > $ find / -name Perl.pm -print > > as _root_ all I get is a single hit > of > > .../READLINE/Perl.pm > > Any thoughts? > > Thanks in advance. > > john slimick > slimick@pitt.edu > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From mbasu at mail.nih.gov Wed Nov 23 15:21:44 2005 From: mbasu at mail.nih.gov (Malay) Date: Wed Nov 23 15:31:48 2005 Subject: [Bioperl-l] Ontology ".obo" parser Message-ID: <4384CF58.6020503@mail.nih.gov> Hi: Am I missing something or there is there no parser for the new ".obo" files of Gene Ontology in BioPerl. -Malay From olenka.m at gmail.com Wed Nov 23 15:22:59 2005 From: olenka.m at gmail.com (Olena Morozova) Date: Wed Nov 23 15:48:38 2005 Subject: [Bioperl-l] Re: clustalw.pm not installed In-Reply-To: <200511231016.28921.heikki@sanbi.ac.za> References: <259a224c0511221643u2e26fde7vddcee979a6d10710@mail.gmail.com> <200511231016.28921.heikki@sanbi.ac.za> Message-ID: <259a224c0511231222k58673f3bma023126f2fa9feeb@mail.gmail.com> Thanks a lot for your help! Olena On 11/23/05, Heikki Lehvaslaiho wrote: > Olena, > > Your Run directory is empty, right? You have not installed the bioperl run > package. Go back to where you got the bioperl core package and install it, > too. > > -Heikki > > On Wednesday 23 November 2005 02:43, Olena Morozova wrote: > > Hello, > > > > I am trying to do a multiple sequence alignment using clustalw.pm, but > > I noticed that I do not have Alignment::clustalw in my > > site::lib::Bio::Tools::Run directory or elsewhere on my computer. Is > > it possible that it did not get installed correctly during my > > installation of Bioperl (I am using complete bioperl 1.4 installation > > on Windows platform)? If so, where can I get the clustalw.pm module > > without having to install the whole bioperl again? > > Thank you very much for your help! > > > > Olena > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- > ______ _/ _/_____________________________________________________ > _/ _/ > _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za > _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho > _/ _/ _/ SANBI, South African National Bioinformatics Institute > _/ _/ _/ University of the Western Cape, South Africa > _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 > ___ _/_/_/_/_/________________________________________________________ > From zhangchn2004 at gmail.com Tue Nov 22 11:37:35 2005 From: zhangchn2004 at gmail.com (Zhang Chen) Date: Wed Nov 23 21:13:57 2005 Subject: FW: [Bioperl-l] Program In-Reply-To: References: Message-ID: <24301eb00511220837l5b4014b9m@mail.gmail.com> Seems that NCBI Blast is not an oss project, anyway, but I still wonder if there're some hints of its source code. 2005/11/23, Barry Moore : > Manish, > > That comes from NCBI which is separate from the Bioperl project. > > http://www.ncbi.nlm.nih.gov/BLAST/download.shtml > > Barry > > > > -----Original Message----- > > > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > > > bounces@portal.open-bio.org] On Behalf Of Manish Kumar > > > Sent: Tuesday, November 22, 2005 4:48 AM > > > To: bioperl-l@bioperl.org > > > Subject: [Bioperl-l] Program > > > > > > Hello, > > > I am Manish Kumar n I m M.Sc > > > (Bioinfomatics) student n i need the perl program for > > > BLAST. I mean what is the program for BLAST that it > > > gives this type of results. > > > > > > > > > For example:- > > > Score = 40.1 bits (20), Expect = 0.16 > > > Identities = 23/24 (95%), Gaps = 0/24 (0%) > > > Strand=Plus/Minus > > > > > > Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 > > > ||||||||||| |||||||||||| > > > Sbjct 8466 ATGTGTACGTGTGTGGTTACGTGC 8443 > > > > > > The above is an example of the BLAST output. Now i > > > need the program for this output. > > > thanking you > > > Best Regards > > > Manish > > > > > > > > > > > > __________________________________ > > > Start your day with Yahoo! - Make it your home page! > > > http://www.yahoo.com/r/hs > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From heikki at sanbi.ac.za Thu Nov 24 01:26:37 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Thu Nov 24 01:24:38 2005 Subject: [Bioperl-l] Ontology ".obo" parser In-Reply-To: <4384CF58.6020503@mail.nih.gov> References: <4384CF58.6020503@mail.nih.gov> Message-ID: <200511240826.37680.heikki@sanbi.ac.za> Chris Mungall said that he'll try to find time to port the go-perl library code: http://bioperl.org/pipermail/bioperl-l/2004-August/016692.html but as far as I can see, it has not happend. Use go-perl. -Heikki On Wednesday 23 November 2005 22:21, Malay wrote: > Hi: > > Am I missing something or there is there no parser for the new ".obo" > files of Gene Ontology in BioPerl. > > -Malay > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From pwilkinson_m at xbioinformatics.org Thu Nov 24 16:23:59 2005 From: pwilkinson_m at xbioinformatics.org (Peter Wilkinson) Date: Thu Nov 24 16:28:53 2005 Subject: FW: [Bioperl-l] Program In-Reply-To: <24301eb00511220837l5b4014b9m@mail.gmail.com> Message-ID: <200511242128.jAOLSd8U010153@portal.open-bio.org> Blast is open source, and I think you will find the source code in the NCBI toolkit under tools under NCBI ftp site. Otherwise it should be there under the ftp somewhere else under tools; all ncbi resources are public, except for the blast load balancing software that they use behind the web site. You can download the local blast binaries from their ftp site as well. Peter W. -----Original Message----- From: Zhang Chen [mailto:zhangchn2004@gmail.com] Sent: November 22, 2005 11:38 AM To: Barry Moore Cc: bioperl-l@bioperl.org Subject: Re: FW: [Bioperl-l] Program Seems that NCBI Blast is not an oss project, anyway, but I still wonder if there're some hints of its source code. 2005/11/23, Barry Moore : > Manish, > > That comes from NCBI which is separate from the Bioperl project. > > http://www.ncbi.nlm.nih.gov/BLAST/download.shtml > > Barry > > > > -----Original Message----- > > > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > > > bounces@portal.open-bio.org] On Behalf Of Manish Kumar > > > Sent: Tuesday, November 22, 2005 4:48 AM > > > To: bioperl-l@bioperl.org > > > Subject: [Bioperl-l] Program > > > > > > Hello, > > > I am Manish Kumar n I m M.Sc > > > (Bioinfomatics) student n i need the perl program for BLAST. I > > > mean what is the program for BLAST that it gives this type of > > > results. > > > > > > > > > For example:- > > > Score = 40.1 bits (20), Expect = 0.16 Identities = 23/24 (95%), > > > Gaps = 0/24 (0%) Strand=Plus/Minus > > > > > > Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 > > > ||||||||||| |||||||||||| Sbjct 8466 > > > ATGTGTACGTGTGTGGTTACGTGC 8443 > > > > > > The above is an example of the BLAST output. Now i need the > > > program for this output. > > > thanking you > > > Best Regards > > > Manish > > > > > > > > > > > > __________________________________ > > > Start your day with Yahoo! - Make it your home page! > > > http://www.yahoo.com/r/hs > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From osborne1 at optonline.net Thu Nov 24 18:26:40 2005 From: osborne1 at optonline.net (Brian Osborne) Date: Thu Nov 24 18:32:22 2005 Subject: [Bioperl-l] Program In-Reply-To: <200511242128.jAOLSd8U010153@portal.open-bio.org> Message-ID: Zhang, All of NCBI's applications are available as source, just as all the data at NCBI is freely available to all and easily accessed. See, for example: http://www.ncbi.nlm.nih.gov/IEB/ToolBox/index.cgi Brian O. > Seems that NCBI Blast is not an oss project, anyway, but I still wonder if > there're some hints of its source code. > > 2005/11/23, Barry Moore : >> Manish, >> >> That comes from NCBI which is separate from the Bioperl project. >> >> http://www.ncbi.nlm.nih.gov/BLAST/download.shtml >> >> Barry >> >>>> -----Original Message----- >>>> From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >>>> bounces@portal.open-bio.org] On Behalf Of Manish Kumar >>>> Sent: Tuesday, November 22, 2005 4:48 AM >>>> To: bioperl-l@bioperl.org >>>> Subject: [Bioperl-l] Program >>>> >>>> Hello, >>>> I am Manish Kumar n I m M.Sc >>>> (Bioinfomatics) student n i need the perl program for BLAST. I >>>> mean what is the program for BLAST that it gives this type of >>>> results. >>>> >>>> >>>> For example:- >>>> Score = 40.1 bits (20), Expect = 0.16 Identities = 23/24 (95%), >>>> Gaps = 0/24 (0%) Strand=Plus/Minus >>>> >>>> Query 1 ATGTGTACGTGCGTGGTTACGTGC 24 >>>> ||||||||||| |||||||||||| Sbjct 8466 >>>> ATGTGTACGTGTGTGGTTACGTGC 8443 >>>> >>>> The above is an example of the BLAST output. Now i need the >>>> program for this output. >>>> thanking you >>>> Best Regards >>>> Manish >>>> >>>> >>>> >>>> __________________________________ >>>> Start your day with Yahoo! - Make it your home page! >>>> http://www.yahoo.com/r/hs >>>> _______________________________________________ >>>> Bioperl-l mailing list >>>> Bioperl-l@portal.open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From torsten.seemann at infotech.monash.edu.au Thu Nov 24 22:22:23 2005 From: torsten.seemann at infotech.monash.edu.au (Torsten Seemann) Date: Fri Nov 25 00:06:37 2005 Subject: [Bioperl-l] StandAloneBlast.pm - rpsblast support? Message-ID: <1132888943.20249.57.camel@chauvel.csse.monash.edu.au> Hello Peter & BioPerl team, Are there any plans to add NCBI 'rpsblast' support to StandAloneBlast.pm ? The binary is called 'rpsblast'. The command line options are a similar to 'blastall' and 'blastpgp'. The databases are often stored in $BLASTDB/CDD/ but don't have to be. I've looked at StandAloneBlast.pm and I think I could maybe patch in support but thought I should check with the experts who might have advice on any refactoring or re-use of existing code. Thanks for any help, -- Torsten Seemann Victorian Bioinformatics Consortium From alaguraj_v at yahoo.com Fri Nov 25 01:20:05 2005 From: alaguraj_v at yahoo.com (Alaguraj Veluchamy) Date: Fri Nov 25 14:31:38 2005 Subject: [Bioperl-l] volunteering Message-ID: <20051125062005.22526.qmail@web60723.mail.yahoo.com> hello sir/madam, I like to contribute to the documentation/testing /coding. i just need a "from where to start". i am a PhD student in Bioinfo from india. Thanking you ALAGURAJ VELUCHAMY c/o Dr.S.KRISHNASWAMY, BIOINFORMATICS CENTRE, MADURAI KAMARAJ UNIVERSITY, MADURAI, TN. Ph:09865444819 __________________________________ Yahoo! Music Unlimited Access over 1 million songs. Try it free. http://music.yahoo.com/unlimited/ From heikki at sanbi.ac.za Mon Nov 28 08:05:10 2005 From: heikki at sanbi.ac.za (Heikki Lehvaslaiho) Date: Mon Nov 28 08:02:22 2005 Subject: [Bioperl-l] volunteering In-Reply-To: <20051125062005.22526.qmail@web60723.mail.yahoo.com> References: <20051125062005.22526.qmail@web60723.mail.yahoo.com> Message-ID: <200511281505.11023.heikki@sanbi.ac.za> Start writing tests to bioperl modules. See: http://bioperl.org/pipermail/bioperl-l/2005-November/020173.html -Heikki On Friday 25 November 2005 08:20, Alaguraj Veluchamy wrote: > hello sir/madam, > I like to contribute to the documentation/testing > /coding. > i just need a "from where to start". > i am a PhD student in Bioinfo from india. > Thanking you > > > > ALAGURAJ VELUCHAMY > c/o Dr.S.KRISHNASWAMY, > BIOINFORMATICS CENTRE, > MADURAI KAMARAJ UNIVERSITY, > MADURAI, TN. > Ph:09865444819 > > > > __________________________________ > Yahoo! Music Unlimited > Access over 1 million songs. Try it free. > http://music.yahoo.com/unlimited/ > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ _/ _/ _/ Heikki Lehvaslaiho heikki at_sanbi _ac _za _/_/_/_/_/ Associate Professor skype: heikki_lehvaslaiho _/ _/ _/ SANBI, South African National Bioinformatics Institute _/ _/ _/ University of the Western Cape, South Africa _/ Phone: +27 21 959 2096 FAX: +27 21 959 2512 ___ _/_/_/_/_/________________________________________________________ From neetisomaiya at gmail.com Mon Nov 28 08:06:03 2005 From: neetisomaiya at gmail.com (neeti somaiya) Date: Mon Nov 28 10:37:31 2005 Subject: [Bioperl-l] need BLAT parse code Message-ID: <764978cf0511280506x7c5e731ep6f71602347b66421@mail.gmail.com> Hi, I am using BLAT in a project.I am having simple .psl output files after running BLAT of a gene sequences against full chromosomal sequences.Doesanyone have a simple BLAT parse code. I am only interested in obtaining the alignment start and end positions on the target. -- -Neeti Even my blood says, B positive From jason.stajich at duke.edu Mon Nov 28 10:51:32 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Mon Nov 28 11:21:01 2005 Subject: [Bioperl-l] need BLAT parse code In-Reply-To: <764978cf0511280506x7c5e731ep6f71602347b66421@mail.gmail.com> References: <764978cf0511280506x7c5e731ep6f71602347b66421@mail.gmail.com> Message-ID: <80D0757F-0282-4679-84E9-6DA013C2E067@duke.edu> Bio::SearchIO::psl can parse psl output. or more simply: while(<>) { if( /^psLayout/ ) { # if there is a header for( 1..4 ) { <> } # take next 4 lines to skip the header } my @line = split; my ( $matches,$mismatches,$rep_matches,$n_count, $q_num_insert,$q_base_insert, $t_num_insert, $t_base_insert, $strand, $q_name, $q_length, $q_start, $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, $block_sizes, $q_starts, $t_starts ) = split; # query aln vals are $q_start, and $q_end values # hit aln vals are $t_start, $t_end } On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: > Hi, > > I am using BLAT in a project.I am having simple .psl output files > after > running BLAT of a gene sequences against full chromosomal > sequences.Doesanyone have a simple BLAT parse code. I am only > interested in obtaining the > alignment start and end positions on the target. > -- > -Neeti > Even my blood says, B positive > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From rwang at bccrc.ca Mon Nov 28 14:20:00 2005 From: rwang at bccrc.ca (Renxue Wang) Date: Mon Nov 28 16:17:29 2005 Subject: [Bioperl-l] bioperl-ext installation Message-ID: <0BE438149FF2254DB4199E2682C8DFEB7028F5@crcmail1.BCCRC.CA> Hi, There, I am trying to install bioperl-ext package, but the hit a lot of problems. We follow the instructions of README and some points in some web postings, but it did not go through properly. I thought someone might have some better ideas on what is going on there and what to do next. Would you let me know if you do? I attach the error messages below. Thanks a lot, Renxue _______________________________________________________________ Here is what I got, > perl Makefile.PL Writing Makefile for Bio::Ext::Align Found Staden io_lib "libread" in /usr/local/lib ... Automatically using the Read.h found in /usr/local/include/io_lib ... Writing Makefile for Bio::SeqIO::staden::read Writing Makefile for Bio One or more DATA sections were not processed by Inline. [root@VLING010 bioperl-ext]# also, in "make", I got this in the end, read.xs:145: request for member `info' in something not a structure or union make[2]: *** [read.o] Error 1 make[2]: Leaving directory `/home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/r ead' A problem was encountered while attempting to compile and install your Inline C code. The command that failed was: make The build directory was: /home/hok/bioperl-ext/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden/re ad To debug the problem, cd to the build directory, and inspect the output files. at -e line 0 INIT failed--call queue aborted. make[1]: *** [read.inl] Error 2 make[1]: Leaving directory `/home/hok/bioperl-ext/Bio/SeqIO/staden' make: *** [subdirs] Error 2 in "make test", this came up, [root@VLING010 Align]# make test PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl 1..9 # Running under perl version 5.008 for linux # Current time local: Thu Nov 17 13:21:45 2005 # Current time GMT: Thu Nov 17 21:21:45 2005 # Using Test.pm version 1.23 Can't locate Bio/Ext/Align.pm in @INC (@INC contains: blib/lib blib/arch /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at test.pl line 14. BEGIN failed--compilation aborted at test.pl line 14. make: *** [test_dynamic] Error 2 [root@VLING010 Align]# I ignored these and went ahead with make install. The program did not work with my alignment script using Bio::Tools::pSW. Seems some components (here "blosum62.bla") was not installed properly. [root@VLING010 melan_simu4th]# ./align.pl test.ORTH test Warning Error Could not open blosum62.bla as a filename for read Blast matrix ------------- EXCEPTION ------------- MSG: blosum62.bla cannot be read as a BLAST comparison matrix file STACK Bio::Tools::pSW::matrix /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:360 STACK Bio::Tools::pSW::new /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/pSW.pm:155 STACK toplevel ./align.pl:11 -------------------------------------- [root@VLING010 melan_simu4th]# From neetisomaiya at gmail.com Tue Nov 29 05:35:19 2005 From: neetisomaiya at gmail.com (neeti somaiya) Date: Tue Nov 29 05:39:25 2005 Subject: [Bioperl-l] query in BLAT usage Message-ID: <764978cf0511290235g698ddb80ofb3e0bfc5639dfa@mail.gmail.com> Hi, I am using BLAT in a project. I have read that each blat run is typically done against a single chromosome, but with a large number of query sequences. I have to BLAT gene sequences against a chromosomes sequence. Can I have sequences of all the genes in FASTA format, one following the other, in a single .fa file as the query file and BLAT it against a .fa file as the database, which has the sequence of the chromosome in FASTA format? Also, running a BLAT of a 27025 bases gene, against a chromosome of size 57701691 bases took 70 mins to run (on a Linux machine). Is there any means of increasing the speed of the BLAT run? Thanks and Regards, Neeti. From sdavis2 at mail.nih.gov Tue Nov 29 06:35:14 2005 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue Nov 29 06:42:28 2005 Subject: [Bioperl-l] query in BLAT usage In-Reply-To: <764978cf0511290235g698ddb80ofb3e0bfc5639dfa@mail.gmail.com> Message-ID: On 11/29/05 5:35 AM, "neeti somaiya" wrote: > Hi, > > I am using BLAT in a project. I have read that each blat run is typically > done against a single chromosome, but with a large number of query > sequences. > I have to BLAT gene sequences against a chromosomes sequence. > Can I have sequences of all the genes in FASTA format, one following the > other, in a single .fa file as the query file and BLAT it against a .fa file > as the database, which has the sequence of the chromosome in FASTA format? Yes. Unlike BLAST, there is a very significant startup time for blat, so you are MUCH better off running blat with your chromosome as the database and put all your queries in one fasta file. > Also, running a BLAT of a 27025 bases gene, against a chromosome of size > 57701691 bases took 70 mins to run (on a Linux machine). Is there any means > of increasing the speed of the BLAT run? I'm not sure, but I think something is wrong. I can typically blat about 50,000 different sequences against all the human chromosomes in about an hour on my Mac G5. I don't think your linux machine is that much slower than my machine. When you blat your gene using the UCSC website, how long does it take? The server version that they run on the website is actually slightly slower than the standalone blat (but runs all chromosomes simultaneously and doesn't have startup time), but you should get an idea of how fast things should be. Sean From jason.stajich at duke.edu Tue Nov 29 09:43:40 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 29 10:29:34 2005 Subject: Fwd: [Bioperl-l] need BLAT parse code References: <764978cf0511282227q693277f2ud5aea6feb7bd6dc5@mail.gmail.com> Message-ID: Begin forwarded message: > From: neeti somaiya > Date: November 29, 2005 1:27:27 AM EST > To: Jason Stajich > Subject: Re: [Bioperl-l] need BLAT parse code > > I use the following code : > > open(FH,"output.psl"); > while() > { > if( /^psLayout/ ) > { > for( 1..4 ) { <> } > } > my @line = split; > my ( $matches,$mismatches,$rep_matches,$n_count, > $q_num_insert,$q_base_insert, > $t_num_insert, $t_base_insert, > $strand, $q_name, $q_length, $q_start, > $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, > $block_sizes, $q_starts, $t_starts > ) = split; > > > print $t_start; > print "\n"; > print $t_end; > > } > > for output.psl file : > > match mis- rep. N's Q gap Q gap T gap T gap > strand Q Q Q Q T > T T T block blockSizes qStarts tStarts > match match count bases count > bases name size start end > name size start end count > ---------------------------------------------------------------------- > ---------------------------------------------------------------------- > ------------------- > 27025 0 0 0 0 0 0 0 > + query_sequence3 27025 0 27025 > database_sequence3 57701691 132995 160020 1 > 27025, 0, 132995, > ~ > > > It gave me output : > > Q > Q > > 132995 > 160020 > > What is the Q? Cant I obtain the coordinates (132995, 160020) alone? > > Please let me know. > Thanks. > > On 11/28/05, Jason Stajich wrote: > Bio::SearchIO::psl can parse psl output. > > or more simply: > > while(<>) { > if( /^psLayout/ ) { # if there is a header > for( 1..4 ) { <> } # take next 4 lines to skip the header > } > my @line = split; > my ( $matches,$mismatches,$rep_matches,$n_count, > $q_num_insert,$q_base_insert, > $t_num_insert, $t_base_insert, > $strand, $q_name, $q_length, $q_start, > $q_end, $t_name, $t_length,$t_start, $t_end, > $block_count, > $block_sizes, $q_starts, $t_starts > ) = split; > > # query aln vals are $q_start, and $q_end values > # hit aln vals are $t_start, $t_end > } > > On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: > > > Hi, > > > > I am using BLAT in a project.I am having simple .psl output files > > after > > running BLAT of a gene sequences against full chromosomal > > sequences.Doesanyone have a simple BLAT parse code. I am only > > interested in obtaining the > > alignment start and end positions on the target. > > -- > > -Neeti > > Even my blood says, B positive > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > > > > -- > -Neeti > Even my blood says, B positive -- Jason Stajich Duke University http://www.duke.edu/~jes12 From sdavis2 at mail.nih.gov Tue Nov 29 12:18:30 2005 From: sdavis2 at mail.nih.gov (Sean Davis) Date: Tue Nov 29 12:29:22 2005 Subject: [Bioperl-l] need BLAT parse code In-Reply-To: Message-ID: Neeti, You could simply put the file in a text editor and take out the header. Alternatively, type: blat without any arguments. You will notice that there are many options to blat, one of which is -noHead, which suppresses the header. Or, look at only lines that begin with a number using a regular expression. Ultimately, I think that it will serve you well to read a perl book, though, as parsing a text file is an important and basic topic to grasp if you want to use perl for data analysis. Sean On 11/29/05 9:43 AM, "Jason Stajich" wrote: > > > Begin forwarded message: > >> From: neeti somaiya >> Date: November 29, 2005 1:27:27 AM EST >> To: Jason Stajich >> Subject: Re: [Bioperl-l] need BLAT parse code >> >> I use the following code : >> >> open(FH,"output.psl"); >> while() >> { >> if( /^psLayout/ ) >> { >> for( 1..4 ) { <> } >> } >> my @line = split; >> my ( $matches,$mismatches,$rep_matches,$n_count, >> $q_num_insert,$q_base_insert, >> $t_num_insert, $t_base_insert, >> $strand, $q_name, $q_length, $q_start, >> $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, >> $block_sizes, $q_starts, $t_starts >> ) = split; >> >> >> print $t_start; >> print "\n"; >> print $t_end; >> >> } >> >> for output.psl file : >> >> match mis- rep. N's Q gap Q gap T gap T gap >> strand Q Q Q Q T >> T T T block blockSizes qStarts tStarts >> match match count bases count >> bases name size start end >> name size start end count >> ---------------------------------------------------------------------- >> ---------------------------------------------------------------------- >> ------------------- >> 27025 0 0 0 0 0 0 0 >> + query_sequence3 27025 0 27025 >> database_sequence3 57701691 132995 160020 1 >> 27025, 0, 132995, >> ~ >> >> >> It gave me output : >> >> Q >> Q >> >> 132995 >> 160020 >> >> What is the Q? Cant I obtain the coordinates (132995, 160020) alone? >> >> Please let me know. >> Thanks. >> >> On 11/28/05, Jason Stajich wrote: >> Bio::SearchIO::psl can parse psl output. >> >> or more simply: >> >> while(<>) { >> if( /^psLayout/ ) { # if there is a header >> for( 1..4 ) { <> } # take next 4 lines to skip the header >> } >> my @line = split; >> my ( $matches,$mismatches,$rep_matches,$n_count, >> $q_num_insert,$q_base_insert, >> $t_num_insert, $t_base_insert, >> $strand, $q_name, $q_length, $q_start, >> $q_end, $t_name, $t_length,$t_start, $t_end, >> $block_count, >> $block_sizes, $q_starts, $t_starts >> ) = split; >> >> # query aln vals are $q_start, and $q_end values >> # hit aln vals are $t_start, $t_end >> } >> >> On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: >> >>> Hi, >>> >>> I am using BLAT in a project.I am having simple .psl output files >>> after >>> running BLAT of a gene sequences against full chromosomal >>> sequences.Doesanyone have a simple BLAT parse code. I am only >>> interested in obtaining the >>> alignment start and end positions on the target. >>> -- >>> -Neeti >>> Even my blood says, B positive >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> Jason Stajich >> Duke University >> http://www.duke.edu/~jes12 >> >> >> >> >> >> -- >> -Neeti >> Even my blood says, B positive > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jason.stajich at duke.edu Tue Nov 29 11:41:16 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Tue Nov 29 13:00:32 2005 Subject: [Bioperl-l] need BLAT parse code In-Reply-To: <764978cf0511282227q693277f2ud5aea6feb7bd6dc5@mail.gmail.com> References: <764978cf0511280506x7c5e731ep6f71602347b66421@mail.gmail.com> <80D0757F-0282-4679-84E9-6DA013C2E067@duke.edu> <764978cf0511282227q693277f2ud5aea6feb7bd6dc5@mail.gmail.com> Message-ID: You probably need to change this line, > for( 1..4 ) { <> } to > for( 1..4 ) { } If your BLAT result file doesn't start with psLayout then you need to make move that if statement BEFORE the while() loop starts, it is stripping off the header lines (and hence where the mysterious 'Q' is coming from in you output!). You can also run blat to just return output without the header and you don't need those skipping steps at all. From the blat options: -noHead suppress .psl header (so it's just a tab-separated file) If parsing tab delimited files seems difficult go buy a book on programming perl or read some of the myriad of freely available online documentation and read about the split function. -jason On Nov 29, 2005, at 1:27 AM, neeti somaiya wrote: > I use the following code : > > open(FH,"output.psl"); > while() > { > if( /^psLayout/ ) > { > for( 1..4 ) { } > } > my @line = split; > my ( $matches,$mismatches,$rep_matches,$n_count, > $q_num_insert,$q_base_insert, > $t_num_insert, $t_base_insert, > $strand, $q_name, $q_length, $q_start, > $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, > $block_sizes, $q_starts, $t_starts > ) = split; > > > print $t_start; > print "\n"; > print $t_end; > > } > > for output.psl file : > > match mis- rep. N's Q gap Q gap T gap T gap > strand Q Q Q Q T > T T T block blockSizes qStarts tStarts > match match count bases count > bases name size start end > name size start end count > ---------------------------------------------------------------------- > ---------------------------------------------------------------------- > ------------------- > 27025 0 0 0 0 0 0 0 > + query_sequence3 27025 0 27025 > database_sequence3 57701691 132995 160020 1 > 27025, 0, 132995, > ~ > > > It gave me output : > > Q > Q > > 132995 > 160020 > > What is the Q? Cant I obtain the coordinates (132995, 160020) alone? > > Please let me know. > Thanks. > > On 11/28/05, Jason Stajich wrote: > Bio::SearchIO::psl can parse psl output. > > or more simply: > > while(<>) { > if( /^psLayout/ ) { # if there is a header > for( 1..4 ) { <> } # take next 4 lines to skip the header > } > my @line = split; > my ( $matches,$mismatches,$rep_matches,$n_count, > $q_num_insert,$q_base_insert, > $t_num_insert, $t_base_insert, > $strand, $q_name, $q_length, $q_start, > $q_end, $t_name, $t_length,$t_start, $t_end, > $block_count, > $block_sizes, $q_starts, $t_starts > ) = split; > > # query aln vals are $q_start, and $q_end values > # hit aln vals are $t_start, $t_end > } > > On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: > > > Hi, > > > > I am using BLAT in a project.I am having simple .psl output files > > after > > running BLAT of a gene sequences against full chromosomal > > sequences.Doesanyone have a simple BLAT parse code. I am only > > interested in obtaining the > > alignment start and end positions on the target. > > -- > > -Neeti > > Even my blood says, B positive > > > > _______________________________________________ > > Bioperl-l mailing list > > Bioperl-l@portal.open-bio.org > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > > > > -- > -Neeti > Even my blood says, B positive -- Jason Stajich Duke University http://www.duke.edu/~jes12 From hotafin at gmail.com Tue Nov 29 11:28:51 2005 From: hotafin at gmail.com (Tamas Horvath) Date: Tue Nov 29 13:03:31 2005 Subject: [Bioperl-l] need BLAT parse code In-Reply-To: References: <764978cf0511282227q693277f2ud5aea6feb7bd6dc5@mail.gmail.com> Message-ID: what kind of blast output format do u use? On 11/29/05, Jason Stajich wrote:>>>> Begin forwarded message:>> > From: neeti somaiya > > Date: November 29, 2005 1:27:27 AM EST> > To: Jason Stajich > > Subject: Re: [Bioperl-l] need BLAT parse code> >> > I use the following code :> >> > open(FH,"output.psl");> > while()> > {> > if( /^psLayout/ )> > {> > for( 1..4 ) { <> }> > }> > my @line = split;> > my ( $matches,$mismatches,$rep_matches,$n_count,> > $q_num_insert,$q_base_insert,> > $t_num_insert, $t_base_insert,> > $strand, $q_name, $q_length, $q_start,> > $q_end, $t_name, $t_length,$t_start, $t_end, $block_count,> > $block_sizes, $q_starts, $t_starts> > ) = split;> >> >> > print $t_start;> > print "\n";> > print $t_end;> >> > }> >> > for output.psl file :> >> > match mis- rep. N's Q gap Q gap T gap T gap> > strand Q Q Q Q T> > T T T block blockSizes qStarts tStarts> > match match count bases count> > bases name size start end> > name size start end count> > ----------------------------------------------------------------------> > ----------------------------------------------------------------------> > -------------------> > 27025 0 0 0 0 0 0 0> > + query_sequence3 27025 0 27025> > database_sequence3 57701691 132995 160020 1> > 27025, 0, 132995,> > ~> >> >> > It gave me output :> >> > Q> > Q> >> > 132995> > 160020> >> > What is the Q? Cant I obtain the coordinates (132995, 160020) alone?> >> > Please let me know.> > Thanks.> >> > On 11/28/05, Jason Stajich wrote:> > Bio::SearchIO::psl can parse psl output.> >> > or more simply:> >> > while(<>) {> > if( /^psLayout/ ) { # if there is a header> > for( 1..4 ) { <> } # take next 4 lines to skip the header> > }> > my @line = split;> > my ( $matches,$mismatches,$rep_matches,$n_count,> > $q_num_insert,$q_base_insert,> > $t_num_insert, $t_base_insert,> > $strand, $q_name, $q_length, $q_start,> > $q_end, $t_name, $t_length,$t_start, $t_end,> > $block_count,> > $block_sizes, $q_starts, $t_starts> > ) = split;> >> > # query aln vals are $q_start, and $q_end values> > # hit aln vals are $t_start, $t_end> > }> >> > On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote:> >> > > Hi,> > >> > > I am using BLAT in a project.I am having simple .psl output files> > > after> > > running BLAT of a gene sequences against full chromosomal> > > sequences.Doesanyone have a simple BLAT parse code. I am only> > > interested in obtaining the> > > alignment start and end positions on the target.> > > --> > > -Neeti> > > Even my blood says, B positive> > >> > > _______________________________________________> > > Bioperl-l mailing list> > > Bioperl-l@portal.open-bio.org> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l> >> > --> > Jason Stajich> > Duke University> > http://www.duke.edu/~jes12> >> >> >> >> >> > --> > -Neeti> > Even my blood says, B positive>> --> Jason Stajich> Duke University> http://www.duke.edu/~jes12>>> _______________________________________________> Bioperl-l mailing list> Bioperl-l@portal.open-bio.org> http://portal.open-bio.org/mailman/listinfo/bioperl-l> From h.w.p.vandentoorn at bio.uu.nl Tue Nov 29 13:08:24 2005 From: h.w.p.vandentoorn at bio.uu.nl (Henk van den Toorn) Date: Tue Nov 29 13:18:18 2005 Subject: [Bioperl-l] need BLAT parse code In-Reply-To: Message-ID: <001601c5f50f$e4437d70$0f33d383@HENKMACHINE> Hello Neeti, Using the Bio::SearchIO module for this kind of output is just what Bioperl is for! Try the following code, for every hit you will get a result object. Because psl can have several hits for each result (different fragments of the same result), you will get several 'hit' objects for each result. It is not the most beautiful code, but it shows the point. I think it is easier this way than parsing the file, because you don't have to be bothered with which column has which meaning. Moreover it handles the different hits per query result, which you would otherwise have to do yourself. Greetings, Henk ---- snip ---- #!/usr/bin/perl use strict; use warnings; use Bio::SearchIO; use Error qw(:try); if (!defined $ARGV[0] || !-e $ARGV[0]) # Test if you have added a filename at the command line { die ("Usage: $0 filename.psl\n"); } my $pslfile = $ARGV[0]; my $parser = new Bio::SearchIO(-file => $pslfile, -format => 'psl'); my $result; while ($result = $parser->next_result()) { print $result->query_name()."\t"; print $result->query_length()."\t"; print $result->num_hits()."\n"; my $matches; foreach my $hit ($result->hits()) { print "\t".$hit->name()."\t"; try { $matches = $hit->matches('identities'); } catch Bio::Root::Exception with { no warnings 'all'; $matches = "ERROR"; }; print $matches."\t"; print $hit->score()."\n"; } } -----Original Message----- From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-bounces@portal.open-bio.org] On Behalf Of Sean Davis Sent: 29 November 2005 18:19 To: bioperl-ml List Subject: Re: [Bioperl-l] need BLAT parse code Neeti, You could simply put the file in a text editor and take out the header. Alternatively, type: blat without any arguments. You will notice that there are many options to blat, one of which is -noHead, which suppresses the header. Or, look at only lines that begin with a number using a regular expression. Ultimately, I think that it will serve you well to read a perl book, though, as parsing a text file is an important and basic topic to grasp if you want to use perl for data analysis. Sean On 11/29/05 9:43 AM, "Jason Stajich" wrote: > > > Begin forwarded message: > >> From: neeti somaiya >> Date: November 29, 2005 1:27:27 AM EST >> To: Jason Stajich >> Subject: Re: [Bioperl-l] need BLAT parse code >> >> I use the following code : >> >> open(FH,"output.psl"); >> while() >> { >> if( /^psLayout/ ) >> { >> for( 1..4 ) { <> } >> } >> my @line = split; >> my ( $matches,$mismatches,$rep_matches,$n_count, >> $q_num_insert,$q_base_insert, >> $t_num_insert, $t_base_insert, >> $strand, $q_name, $q_length, $q_start, >> $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, >> $block_sizes, $q_starts, $t_starts >> ) = split; >> >> >> print $t_start; >> print "\n"; >> print $t_end; >> >> } >> >> for output.psl file : >> >> match mis- rep. N's Q gap Q gap T gap T gap >> strand Q Q Q Q T >> T T T block blockSizes qStarts tStarts >> match match count bases count >> bases name size start end >> name size start end count >> --------------------------------------------------------------------- >> - >> --------------------------------------------------------------------- >> - >> ------------------- >> 27025 0 0 0 0 0 0 0 >> + query_sequence3 27025 0 27025 >> database_sequence3 57701691 132995 160020 1 >> 27025, 0, 132995, >> ~ >> >> >> It gave me output : >> >> Q >> Q >> >> 132995 >> 160020 >> >> What is the Q? Cant I obtain the coordinates (132995, 160020) alone? >> >> Please let me know. >> Thanks. >> >> On 11/28/05, Jason Stajich wrote: >> Bio::SearchIO::psl can parse psl output. >> >> or more simply: >> >> while(<>) { >> if( /^psLayout/ ) { # if there is a header >> for( 1..4 ) { <> } # take next 4 lines to skip the header >> } >> my @line = split; >> my ( $matches,$mismatches,$rep_matches,$n_count, >> $q_num_insert,$q_base_insert, >> $t_num_insert, $t_base_insert, >> $strand, $q_name, $q_length, $q_start, >> $q_end, $t_name, $t_length,$t_start, $t_end, >> $block_count, >> $block_sizes, $q_starts, $t_starts >> ) = split; >> >> # query aln vals are $q_start, and $q_end values >> # hit aln vals are $t_start, $t_end } >> >> On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: >> >>> Hi, >>> >>> I am using BLAT in a project.I am having simple .psl output files >>> after running BLAT of a gene sequences against full chromosomal >>> sequences.Doesanyone have a simple BLAT parse code. I am only >>> interested in obtaining the alignment start and end positions on the >>> target. >>> -- >>> -Neeti >>> Even my blood says, B positive >>> >>> _______________________________________________ >>> Bioperl-l mailing list >>> Bioperl-l@portal.open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l >> >> -- >> Jason Stajich >> Duke University >> http://www.duke.edu/~jes12 >> >> >> >> >> >> -- >> -Neeti >> Even my blood says, B positive > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > _______________________________________________ Bioperl-l mailing list Bioperl-l@portal.open-bio.org http://portal.open-bio.org/mailman/listinfo/bioperl-l From chen_li3 at yahoo.com Wed Nov 30 06:44:52 2005 From: chen_li3 at yahoo.com (chen li) Date: Wed Nov 30 06:49:23 2005 Subject: [Bioperl-l] bioperl-db and MySQL again In-Reply-To: Message-ID: <20051130114452.62862.qmail@web31813.mail.mud.yahoo.com> Hi Himar, There are so many problems working with Perl under Windows XP so I have linux Fedora core 1 installed on my computer. I already install all necessary compoents on my computer without any problem. But when I install bioperl-db. I still have problems: the installation can't make test. The following is the message I got(sorry for the lengthy post). What is really going on here? It seems there are some configuration problems but I am sure how to fix it. Thanks, Li message from the screen: cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz CPAN: LWP::UserAgent loaded ok Fetching with LWP: ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz CPAN: Digest::MD5 loaded ok CPAN: Compress::Zlib loaded ok Checksum for /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz okScanning cache /root/.cpan/build for sizes Deleting from cache: /root/.cpan/build/DBI-1.49 (11.3>10.0 MB) bioperl-db-0.1/ bioperl-db-0.1/Bio/ bioperl-db-0.1/Bio/DB/ bioperl-db-0.1/Bio/DB/Map/ (many are deleted here for short) ................................................... ................................................... /usr/bin/make -- OK Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/comment..........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/comment..........dubious Test returned status 255 (wstat 65280, 0xff00) Scalar found where operator expected at (eval 155) line 1, near "'int' $__val" (Missing operator before $__val?) DIED. FAILED tests 1-6 Failed 6/6 tests, 0.00% okay t/dbadaptor........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/dbadaptor........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-3 Failed 3/3 tests, 0.00% okay t/dblink...........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/dblink...........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-7 Failed 7/7 tests, 0.00% okay t/ensembl..........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/ensembl..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-14 Failed 14/14 tests, 0.00% okay t/ePCRdb...........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/ePCRdb...........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-3 Failed 3/3 tests, 0.00% okay t/map..............DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/map..............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-6 Failed 6/6 tests, 0.00% okay t/marker...........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/marker...........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-19 Failed 19/19 tests, 0.00% okay t/remove...........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/remove...........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-22 Failed 22/22 tests, 0.00% okay t/seqfeature.......DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/seqfeature.......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-9 Failed 9/9 tests, 0.00% okay t/seqfeaturekey....DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/seqfeaturekey....dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-11 Failed 11/11 tests, 0.00% okay t/seqlocation......DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/seqlocation......dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-10 Failed 10/10 tests, 0.00% okay t/simpleseq........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/simpleseq........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-20 Failed 20/20 tests, 0.00% okay t/species..........DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/species..........dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-6 Failed 6/6 tests, 0.00% okay t/swiss............DBI connect('host=localhost;','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 186 (in cleanup) DBI connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481;host=localhost','root',...) failed: Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm line 212 t/swiss............dubious Test returned status 255 (wstat 65280, 0xff00) DIED. FAILED tests 1-16 Failed 16/16 tests, 0.00% okay Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/comment.t 255 65280 6 12 200.00% 1-6 t/dbadaptor.t 255 65280 3 6 200.00% 1-3 t/dblink.t 255 65280 7 14 200.00% 1-7 t/ePCRdb.t 255 65280 3 6 200.00% 1-3 t/ensembl.t 255 65280 14 28 200.00% 1-14 t/map.t 255 65280 6 12 200.00% 1-6 t/marker.t 255 65280 19 38 200.00% 1-19 t/remove.t 255 65280 22 44 200.00% 1-22 t/seqfeature.t 255 65280 9 18 200.00% 1-9 t/seqfeaturekey.t 255 65280 11 22 200.00% 1-11 t/seqlocation.t 255 65280 10 20 200.00% 1-10 t/simpleseq.t 255 65280 20 40 200.00% 1-20 t/species.t 255 65280 6 12 200.00% 1-6 t/swiss.t 255 65280 16 32 200.00% 1-16 Failed 14/14 test scripts, 0.00% okay. 152/152 subtests failed, 0.00% okay. make: *** [test_dynamic] Error 255 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From bmoore at genetics.utah.edu Wed Nov 30 10:31:39 2005 From: bmoore at genetics.utah.edu (Barry Moore) Date: Wed Nov 30 10:53:40 2005 Subject: [Bioperl-l] bioperl-db and MySQL again Message-ID: Chen- It looks to me like all your failed tests are due to the fact that the test scripts can't connect to your MySQL database as 'root'. You could su to an account that is set up for access to your database for make test and then back to root for make install, you give root a MySQL account, or you could just skip the tests and force the install (probably what I'd do since I'm lazy, and haven't gotten burned for not testing that group of modules yet). I think all of those options should work, and hopefully Hilmar or someone else will correct me if I've led you astray. Barry > -----Original Message----- > From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- > bounces@portal.open-bio.org] On Behalf Of chen li > Sent: Wednesday, November 30, 2005 4:45 AM > To: Hilmar Lapp > Cc: bioperl-l@bioperl.org > Subject: [Bioperl-l] bioperl-db and MySQL again > > Hi Himar, > > There are so many problems working with Perl under > Windows XP so I have linux Fedora core 1 installed on > my computer. I already install all necessary compoents > on my computer without any problem. But when I install > bioperl-db. I still have problems: the installation > can't make test. The following is the message I > got(sorry for the lengthy post). What is really going > on here? It seems there are some configuration > problems but I am sure how to fix it. > > > Thanks, > > Li > > message from the screen: > > > > cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz > Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz > CPAN: LWP::UserAgent loaded ok > Fetching with LWP: > > ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz > CPAN: Digest::MD5 loaded ok > CPAN: Compress::Zlib loaded ok > Checksum for > /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz > okScanning cache /root/.cpan/build for sizes > Deleting from cache: /root/.cpan/build/DBI-1.49 > (11.3>10.0 MB) > bioperl-db-0.1/ > bioperl-db-0.1/Bio/ > bioperl-db-0.1/Bio/DB/ > bioperl-db-0.1/Bio/DB/Map/ > > (many are deleted here for short) > ................................................... > ................................................... > > > /usr/bin/make -- OK > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl > "-MExtUtils::Command::MM" "-e" "test_harness(0, > 'blib/lib', 'blib/arch')" t/*.t > t/comment..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/comment..........dubious > Test returned status 255 (wstat 65280, 0xff00) > Scalar found where operator expected at (eval 155) > line 1, near "'int' $__val" > (Missing operator before $__val?) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/dbadaptor........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dbadaptor........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/dblink...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dblink...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-7 > Failed 7/7 tests, 0.00% okay > t/ensembl..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ensembl..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-14 > Failed 14/14 tests, 0.00% okay > t/ePCRdb...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ePCRdb...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/map..............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/map..............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/marker...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/marker...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-19 > Failed 19/19 tests, 0.00% okay > t/remove...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/remove...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-22 > Failed 22/22 tests, 0.00% okay > t/seqfeature.......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeature.......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-9 > Failed 9/9 tests, 0.00% okay > t/seqfeaturekey....DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeaturekey....dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-11 > Failed 11/11 tests, 0.00% okay > t/seqlocation......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqlocation......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-10 > Failed 10/10 tests, 0.00% okay > t/simpleseq........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/simpleseq........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-20 > Failed 20/20 tests, 0.00% okay > t/species..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/species..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/swiss............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481; ho > st=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/swiss............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-16 > Failed 16/16 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List > of Failed > ------------------------------------------------------------------------ -- > ----- > t/comment.t 255 65280 6 12 200.00% 1-6 > t/dbadaptor.t 255 65280 3 6 200.00% 1-3 > t/dblink.t 255 65280 7 14 200.00% 1-7 > t/ePCRdb.t 255 65280 3 6 200.00% 1-3 > t/ensembl.t 255 65280 14 28 200.00% 1-14 > t/map.t 255 65280 6 12 200.00% 1-6 > t/marker.t 255 65280 19 38 200.00% 1-19 > t/remove.t 255 65280 22 44 200.00% 1-22 > t/seqfeature.t 255 65280 9 18 200.00% 1-9 > t/seqfeaturekey.t 255 65280 11 22 200.00% 1-11 > t/seqlocation.t 255 65280 10 20 200.00% 1-10 > t/simpleseq.t 255 65280 20 40 200.00% 1-20 > t/species.t 255 65280 6 12 200.00% 1-6 > t/swiss.t 255 65280 16 32 200.00% 1-16 > Failed 14/14 test scripts, 0.00% okay. 152/152 > subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install > without force > > > > > > > > > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l From hlapp at gmx.net Wed Nov 30 12:22:07 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 30 12:26:33 2005 Subject: [Bioperl-l] bioperl-db and MySQL again In-Reply-To: <20051130114452.62862.qmail@web31813.mail.mud.yahoo.com> References: <20051130114452.62862.qmail@web31813.mail.mud.yahoo.com> Message-ID: Chen, you can't download bioperl-db from CPAN and have it work with the current BioSQL version (and possibly not even with the current Bioperl version - it's very old). Sorry for this inconvenience. Download from CVS the main trunk, then issue the usual triple of $ perl Makefile.PL $ make $ make test followed possibly by 'make install' if you do have root access on the machine. Otherwise point PERL5LIB at the directory to which you downloaded bioperl-db/ -hilmar On Nov 30, 2005, at 3:44 AM, chen li wrote: > Hi Himar, > > There are so many problems working with Perl under > Windows XP so I have linux Fedora core 1 installed on > my computer. I already install all necessary compoents > on my computer without any problem. But when I install > bioperl-db. I still have problems: the installation > can't make test. The following is the message I > got(sorry for the lengthy post). What is really going > on here? It seems there are some configuration > problems but I am sure how to fix it. > > > Thanks, > > Li > > message from the screen: > > > > cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz > Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz > CPAN: LWP::UserAgent loaded ok > Fetching with LWP: > > ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db > -0.1.tar.gz > CPAN: Digest::MD5 loaded ok > CPAN: Compress::Zlib loaded ok > Checksum for > /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz > okScanning cache /root/.cpan/build for sizes > Deleting from cache: /root/.cpan/build/DBI-1.49 > (11.3>10.0 MB) > bioperl-db-0.1/ > bioperl-db-0.1/Bio/ > bioperl-db-0.1/Bio/DB/ > bioperl-db-0.1/Bio/DB/Map/ > > (many are deleted here for short) > ................................................... > ................................................... > > > /usr/bin/make -- OK > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl > "-MExtUtils::Command::MM" "-e" "test_harness(0, > 'blib/lib', 'blib/arch')" t/*.t > t/comment..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/comment..........dubious > Test returned status 255 (wstat 65280, 0xff00) > Scalar found where operator expected at (eval 155) > line 1, near "'int' $__val" > (Missing operator before $__val?) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/dbadaptor........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dbadaptor........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/dblink...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dblink...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-7 > Failed 7/7 tests, 0.00% okay > t/ensembl..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ensembl..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-14 > Failed 14/14 tests, 0.00% okay > t/ePCRdb...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ePCRdb...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/map..............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/map..............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/marker...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/marker...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-19 > Failed 19/19 tests, 0.00% okay > t/remove...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/remove...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-22 > Failed 22/22 tests, 0.00% okay > t/seqfeature.......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeature.......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-9 > Failed 9/9 tests, 0.00% okay > t/seqfeaturekey....DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeaturekey....dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-11 > Failed 11/11 tests, 0.00% okay > t/seqlocation......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqlocation......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-10 > Failed 10/10 tests, 0.00% okay > t/simpleseq........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/simpleseq........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-20 > Failed 20/20 tests, 0.00% okay > t/species..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/species..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/swiss............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/swiss............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-16 > Failed 16/16 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List > of Failed > ----------------------------------------------------------------------- > -------- > t/comment.t 255 65280 6 12 200.00% 1-6 > t/dbadaptor.t 255 65280 3 6 200.00% 1-3 > t/dblink.t 255 65280 7 14 200.00% 1-7 > t/ePCRdb.t 255 65280 3 6 200.00% 1-3 > t/ensembl.t 255 65280 14 28 200.00% 1-14 > t/map.t 255 65280 6 12 200.00% 1-6 > t/marker.t 255 65280 19 38 200.00% 1-19 > t/remove.t 255 65280 22 44 200.00% 1-22 > t/seqfeature.t 255 65280 9 18 200.00% 1-9 > t/seqfeaturekey.t 255 65280 11 22 200.00% 1-11 > t/seqlocation.t 255 65280 10 20 200.00% 1-10 > t/simpleseq.t 255 65280 20 40 200.00% 1-20 > t/species.t 255 65280 6 12 200.00% 1-6 > t/swiss.t 255 65280 16 32 200.00% 1-16 > Failed 14/14 test scripts, 0.00% okay. 152/152 > subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install > without force > > > > > > > > > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Wed Nov 30 12:28:46 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 30 12:26:41 2005 Subject: [Bioperl-l] bioperl-db and MySQL again In-Reply-To: References: Message-ID: <545bf9a43c75b54463ffd2077e9b562e@gmx.net> Not astray - only that forcing the install won't help if the downloaded version is 0.1 from CPAN - it needs to be from CVS. Provided it is, then you might choose to force the install and go back to running the tests once you encounter errors running the load_{seqdatabase,ontology}.pl scripts or one of your own. -hilmar On Nov 30, 2005, at 7:31 AM, Barry Moore wrote: > Chen- > > It looks to me like all your failed tests are due to the fact that the > test scripts can't connect to your MySQL database as 'root'. You could > su to an account that is set up for access to your database for make > test and then back to root for make install, you give root a MySQL > account, or you could just skip the tests and force the install > (probably what I'd do since I'm lazy, and haven't gotten burned for not > testing that group of modules yet). > > I think all of those options should work, and hopefully Hilmar or > someone else will correct me if I've led you astray. > > Barry > >> -----Original Message----- >> From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l- >> bounces@portal.open-bio.org] On Behalf Of chen li >> Sent: Wednesday, November 30, 2005 4:45 AM >> To: Hilmar Lapp >> Cc: bioperl-l@bioperl.org >> Subject: [Bioperl-l] bioperl-db and MySQL again >> >> Hi Himar, >> >> There are so many problems working with Perl under >> Windows XP so I have linux Fedora core 1 installed on >> my computer. I already install all necessary compoents >> on my computer without any problem. But when I install >> bioperl-db. I still have problems: the installation >> can't make test. The following is the message I >> got(sorry for the lengthy post). What is really going >> on here? It seems there are some configuration >> problems but I am sure how to fix it. >> >> >> Thanks, >> >> Li >> >> message from the screen: >> >> >> >> cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz >> Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz >> CPAN: LWP::UserAgent loaded ok >> Fetching with LWP: >> >> > ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db > -0.1.tar.gz >> CPAN: Digest::MD5 loaded ok >> CPAN: Compress::Zlib loaded ok >> Checksum for >> /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz >> okScanning cache /root/.cpan/build for sizes >> Deleting from cache: /root/.cpan/build/DBI-1.49 >> (11.3>10.0 MB) >> bioperl-db-0.1/ >> bioperl-db-0.1/Bio/ >> bioperl-db-0.1/Bio/DB/ >> bioperl-db-0.1/Bio/DB/Map/ >> >> (many are deleted here for short) >> ................................................... >> ................................................... >> >> >> /usr/bin/make -- OK >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl >> "-MExtUtils::Command::MM" "-e" "test_harness(0, >> 'blib/lib', 'blib/arch')" t/*.t >> t/comment..........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/comment..........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> Scalar found where operator expected at (eval 155) >> line 1, near "'int' $__val" >> (Missing operator before $__val?) >> DIED. FAILED tests 1-6 >> Failed 6/6 tests, 0.00% okay >> t/dbadaptor........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/dbadaptor........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-3 >> Failed 3/3 tests, 0.00% okay >> t/dblink...........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/dblink...........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-7 >> Failed 7/7 tests, 0.00% okay >> t/ensembl..........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/ensembl..........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-14 >> Failed 14/14 tests, 0.00% okay >> t/ePCRdb...........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/ePCRdb...........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-3 >> Failed 3/3 tests, 0.00% okay >> t/map..............DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/map..............dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-6 >> Failed 6/6 tests, 0.00% okay >> t/marker...........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/marker...........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-19 >> Failed 19/19 tests, 0.00% okay >> t/remove...........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/remove...........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-22 >> Failed 22/22 tests, 0.00% okay >> t/seqfeature.......DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/seqfeature.......dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-9 >> Failed 9/9 tests, 0.00% okay >> t/seqfeaturekey....DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/seqfeaturekey....dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-11 >> Failed 11/11 tests, 0.00% okay >> t/seqlocation......DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/seqlocation......dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-10 >> Failed 10/10 tests, 0.00% okay >> t/simpleseq........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/simpleseq........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-20 >> Failed 20/20 tests, 0.00% okay >> t/species..........DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/species..........dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-6 >> Failed 6/6 tests, 0.00% okay >> t/swiss............DBI >> connect('host=localhost;','root',...) failed: Can't >> connect to local MySQL server through socket >> '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm >> line 186 >> (in cleanup) DBI >> > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481 > ; > ho >> st=localhost','root',...) >> failed: Can't connect to local MySQL server through >> socket '/var/lib/mysql/mysql.sock' (2) at >> t/DBTestHarness.pm line 212 >> t/swiss............dubious >> Test returned status 255 (wstat 65280, 0xff00) >> DIED. FAILED tests 1-16 >> Failed 16/16 tests, 0.00% okay >> Failed Test Stat Wstat Total Fail Failed List >> of Failed >> > ----------------------------------------------------------------------- > - > -- >> ----- >> t/comment.t 255 65280 6 12 200.00% 1-6 >> t/dbadaptor.t 255 65280 3 6 200.00% 1-3 >> t/dblink.t 255 65280 7 14 200.00% 1-7 >> t/ePCRdb.t 255 65280 3 6 200.00% 1-3 >> t/ensembl.t 255 65280 14 28 200.00% 1-14 >> t/map.t 255 65280 6 12 200.00% 1-6 >> t/marker.t 255 65280 19 38 200.00% 1-19 >> t/remove.t 255 65280 22 44 200.00% 1-22 >> t/seqfeature.t 255 65280 9 18 200.00% 1-9 >> t/seqfeaturekey.t 255 65280 11 22 200.00% 1-11 >> t/seqlocation.t 255 65280 10 20 200.00% 1-10 >> t/simpleseq.t 255 65280 20 40 200.00% 1-20 >> t/species.t 255 65280 6 12 200.00% 1-6 >> t/swiss.t 255 65280 16 32 200.00% 1-16 >> Failed 14/14 test scripts, 0.00% okay. 152/152 >> subtests failed, 0.00% okay. >> make: *** [test_dynamic] Error 255 >> /usr/bin/make test -- NOT OK >> Running make install >> make test had returned bad status, won't install >> without force >> >> >> >> >> >> >> >> >> >> >> >> >> __________________________________ >> Yahoo! Mail - PC Magazine Editors' Choice 2005 >> http://mail.yahoo.com >> _______________________________________________ >> Bioperl-l mailing list >> Bioperl-l@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioperl-l > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From hlapp at gmx.net Wed Nov 30 12:25:21 2005 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed Nov 30 12:30:49 2005 Subject: [Bioperl-l] bioperl-db and MySQL again In-Reply-To: <20051130114452.62862.qmail@web31813.mail.mud.yahoo.com> References: <20051130114452.62862.qmail@web31813.mail.mud.yahoo.com> Message-ID: <8922965768d2faa8e7f320f574fd477a@gmx.net> In fact it also appears the connection attempt to mysql already fails. Make sure you have the Biosql instance instantiated, and make sure you followed the instructions and copied t/DBHarness.conf.example to t/DBHarness.biosql.conf while editing it to reflect your setup, username, and password. This is another reason why using the CPAN shell won't work for bioperl-db. -hilmar On Nov 30, 2005, at 3:44 AM, chen li wrote: > Hi Himar, > > There are so many problems working with Perl under > Windows XP so I have linux Fedora core 1 installed on > my computer. I already install all necessary compoents > on my computer without any problem. But when I install > bioperl-db. I still have problems: the installation > can't make test. The following is the message I > got(sorry for the lengthy post). What is really going > on here? It seems there are some configuration > problems but I am sure how to fix it. > > > Thanks, > > Li > > message from the screen: > > > > cpan> install B/BI/BIRNEY/bioperl-db-0.1.tar.gz > Running make for B/BI/BIRNEY/bioperl-db-0.1.tar.gz > CPAN: LWP::UserAgent loaded ok > Fetching with LWP: > > ftp://ftp.perl.org/pub/CPAN/authors/id/B/BI/BIRNEY/bioperl-db > -0.1.tar.gz > CPAN: Digest::MD5 loaded ok > CPAN: Compress::Zlib loaded ok > Checksum for > /root/.cpan/sources/authors/id/B/BI/BIRNEY/bioperl-db-0.1.tar.gz > okScanning cache /root/.cpan/build for sizes > Deleting from cache: /root/.cpan/build/DBI-1.49 > (11.3>10.0 MB) > bioperl-db-0.1/ > bioperl-db-0.1/Bio/ > bioperl-db-0.1/Bio/DB/ > bioperl-db-0.1/Bio/DB/Map/ > > (many are deleted here for short) > ................................................... > ................................................... > > > /usr/bin/make -- OK > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl > "-MExtUtils::Command::MM" "-e" "test_harness(0, > 'blib/lib', 'blib/arch')" t/*.t > t/comment..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42351 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/comment..........dubious > Test returned status 255 (wstat 65280, 0xff00) > Scalar found where operator expected at (eval 155) > line 1, near "'int' $__val" > (Missing operator before $__val?) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/dbadaptor........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42361 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dbadaptor........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/dblink...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42371 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/dblink...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-7 > Failed 7/7 tests, 0.00% okay > t/ensembl..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42381 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ensembl..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-14 > Failed 14/14 tests, 0.00% okay > t/ePCRdb...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42391 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/ePCRdb...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-3 > Failed 3/3 tests, 0.00% okay > t/map..............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42401 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/map..............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/marker...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42411 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/marker...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-19 > Failed 19/19 tests, 0.00% okay > t/remove...........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42421 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/remove...........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-22 > Failed 22/22 tests, 0.00% okay > t/seqfeature.......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42431 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeature.......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-9 > Failed 9/9 tests, 0.00% okay > t/seqfeaturekey....DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42441 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqfeaturekey....dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-11 > Failed 11/11 tests, 0.00% okay > t/seqlocation......DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42451 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/seqlocation......dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-10 > Failed 10/10 tests, 0.00% okay > t/simpleseq........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42461 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/simpleseq........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-20 > Failed 20/20 tests, 0.00% okay > t/species..........DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42471 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/species..........dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-6 > Failed 6/6 tests, 0.00% okay > t/swiss............DBI > connect('host=localhost;','root',...) failed: Can't > connect to local MySQL server through socket > '/var/lib/mysql/mysql.sock' (2) at t/DBTestHarness.pm > line 186 > (in cleanup) DBI > connect('database=_test_db_cpe_65_189_147_198_columbus_res_rr_com_42481 > ;host=localhost','root',...) > failed: Can't connect to local MySQL server through > socket '/var/lib/mysql/mysql.sock' (2) at > t/DBTestHarness.pm line 212 > t/swiss............dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 1-16 > Failed 16/16 tests, 0.00% okay > Failed Test Stat Wstat Total Fail Failed List > of Failed > ----------------------------------------------------------------------- > -------- > t/comment.t 255 65280 6 12 200.00% 1-6 > t/dbadaptor.t 255 65280 3 6 200.00% 1-3 > t/dblink.t 255 65280 7 14 200.00% 1-7 > t/ePCRdb.t 255 65280 3 6 200.00% 1-3 > t/ensembl.t 255 65280 14 28 200.00% 1-14 > t/map.t 255 65280 6 12 200.00% 1-6 > t/marker.t 255 65280 19 38 200.00% 1-19 > t/remove.t 255 65280 22 44 200.00% 1-22 > t/seqfeature.t 255 65280 9 18 200.00% 1-9 > t/seqfeaturekey.t 255 65280 11 22 200.00% 1-11 > t/seqlocation.t 255 65280 10 20 200.00% 1-10 > t/simpleseq.t 255 65280 20 40 200.00% 1-20 > t/species.t 255 65280 6 12 200.00% 1-6 > t/swiss.t 255 65280 16 32 200.00% 1-16 > Failed 14/14 test scripts, 0.00% okay. 152/152 > subtests failed, 0.00% okay. > make: *** [test_dynamic] Error 255 > /usr/bin/make test -- NOT OK > Running make install > make test had returned bad status, won't install > without force > > > > > > > > > > > > > __________________________________ > Yahoo! Mail - PC Magazine Editors' Choice 2005 > http://mail.yahoo.com > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From qfdong at iastate.edu Wed Nov 30 16:46:24 2005 From: qfdong at iastate.edu (Qunfeng) Date: Wed Nov 30 16:56:48 2005 Subject: [Bioperl-l] Deep recursion on subroutine Message-ID: <6.1.2.0.2.20051130154054.04161190@qfdong.mail.iastate.edu> Hi, I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick format, generated by PHYLIP). My code works well on a small tree. However, when I applied it to a big (ugly) tree, it produces the following error msg. Has anybody encountered a similar problem? Is this triggered by any invalid part of my tree? Thanks! Qunfeng ===========Error message begins ===================== Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. =========Error msg ends============================================== From jason.stajich at duke.edu Wed Nov 30 17:10:01 2005 From: jason.stajich at duke.edu (Jason Stajich) Date: Wed Nov 30 17:07:58 2005 Subject: [Bioperl-l] Deep recursion on subroutine In-Reply-To: <6.1.2.0.2.20051130154054.04161190@qfdong.mail.iastate.edu> References: <6.1.2.0.2.20051130154054.04161190@qfdong.mail.iastate.edu> Message-ID: <5825BB54-53CC-4EA5-8D3F-0EACA444A0E5@duke.edu> Without an actual example tree it is hard to really help you very much. A simple code example which can reproduce the problem and the offending tree should be submitted (please attach and don't just paste the datafile into the comment) as part of the bug report. http://bugzilla.open-bio.org/ You should also mention what version of Bioperl you are using. -jason On Nov 30, 2005, at 4:46 PM, Qunfeng wrote: > Hi, > > I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick > format, generated by PHYLIP). My code works well on a small tree. > However, when I applied it to a big (ugly) tree, it produces the > following error msg. Has anybody encountered a similar problem? Is > this triggered by any invalid part of my tree? Thanks! > > Qunfeng > ===========Error message begins ===================== > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at / > usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at / > usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at / > usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at / > usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at / > usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine > "Bio::Tree::NodeI::get_all_Descendents" at /usr/lib/perl5/site_perl/ > 5.8.0/Bio/Tree/NodeI.pm line 172, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at /usr/lib/ > perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > =========Error msg ends============================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Jason Stajich Duke University http://www.duke.edu/~jes12 From olenka.m at gmail.com Tue Nov 29 17:33:55 2005 From: olenka.m at gmail.com (Olena Morozova) Date: Wed Nov 30 17:52:41 2005 Subject: [Bioperl-l] clustalw.pm: could not open sequence file error Message-ID: <259a224c0511291433r2455a9afv76658ba3409e632f@mail.gmail.com> Hi all, I am trying to use this script use Bio::Tools::Run::Alignment::Clustalw; $ENV{CLUSTALDIR} = 'C:/perl/clustalw1.8/'; my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 'outfile'=> 'al_mouse.txt'); my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params); $inputfilename = 'c:/perl/mouse_unique.txt'; my $aln = $factory->align($inputfilename); to do a MSA, and it works for a test file with 2 or 3 sequences. However, when I try to run it on my actual file (has 97 sequences) which is in exactly the same format as the test file (fasta), I get a "could not open the sequence file" error. Is this because the file is too big and is there a way to fix this? Thanks a lot for your help! Olena On 11/29/05, Jason Stajich wrote: > > > Begin forwarded message: > > > From: neeti somaiya > > Date: November 29, 2005 1:27:27 AM EST > > To: Jason Stajich > > Subject: Re: [Bioperl-l] need BLAT parse code > > > > I use the following code : > > > > open(FH,"output.psl"); > > while() > > { > > if( /^psLayout/ ) > > { > > for( 1..4 ) { <> } > > } > > my @line = split; > > my ( $matches,$mismatches,$rep_matches,$n_count, > > $q_num_insert,$q_base_insert, > > $t_num_insert, $t_base_insert, > > $strand, $q_name, $q_length, $q_start, > > $q_end, $t_name, $t_length,$t_start, $t_end, $block_count, > > $block_sizes, $q_starts, $t_starts > > ) = split; > > > > > > print $t_start; > > print "\n"; > > print $t_end; > > > > } > > > > for output.psl file : > > > > match mis- rep. N's Q gap Q gap T gap T gap > > strand Q Q Q Q T > > T T T block blockSizes qStarts tStarts > > match match count bases count > > bases name size start end > > name size start end count > > ---------------------------------------------------------------------- > > ---------------------------------------------------------------------- > > ------------------- > > 27025 0 0 0 0 0 0 0 > > + query_sequence3 27025 0 27025 > > database_sequence3 57701691 132995 160020 1 > > 27025, 0, 132995, > > ~ > > > > > > It gave me output : > > > > Q > > Q > > > > 132995 > > 160020 > > > > What is the Q? Cant I obtain the coordinates (132995, 160020) alone? > > > > Please let me know. > > Thanks. > > > > On 11/28/05, Jason Stajich wrote: > > Bio::SearchIO::psl can parse psl output. > > > > or more simply: > > > > while(<>) { > > if( /^psLayout/ ) { # if there is a header > > for( 1..4 ) { <> } # take next 4 lines to skip the header > > } > > my @line = split; > > my ( $matches,$mismatches,$rep_matches,$n_count, > > $q_num_insert,$q_base_insert, > > $t_num_insert, $t_base_insert, > > $strand, $q_name, $q_length, $q_start, > > $q_end, $t_name, $t_length,$t_start, $t_end, > > $block_count, > > $block_sizes, $q_starts, $t_starts > > ) = split; > > > > # query aln vals are $q_start, and $q_end values > > # hit aln vals are $t_start, $t_end > > } > > > > On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote: > > > > > Hi, > > > > > > I am using BLAT in a project.I am having simple .psl output files > > > after > > > running BLAT of a gene sequences against full chromosomal > > > sequences.Doesanyone have a simple BLAT parse code. I am only > > > interested in obtaining the > > > alignment start and end positions on the target. > > > -- > > > -Neeti > > > Even my blood says, B positive > > > > > > _______________________________________________ > > > Bioperl-l mailing list > > > Bioperl-l@portal.open-bio.org > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l > > > > -- > > Jason Stajich > > Duke University > > http://www.duke.edu/~jes12 > > > > > > > > > > > > -- > > -Neeti > > Even my blood says, B positive > > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l > From jarthur at med.usyd.edu.au Wed Nov 30 17:39:41 2005 From: jarthur at med.usyd.edu.au (Jonathan Arthur) Date: Wed Nov 30 17:54:47 2005 Subject: [Bioperl-l] Deep recursion on subroutine In-Reply-To: <6.1.2.0.2.20051130154054.04161190@qfdong.mail.iastate.edu> References: <6.1.2.0.2.20051130154054.04161190@qfdong.mail.iastate.edu> Message-ID: <438E2A2D.6010305@med.usyd.edu.au> Hello Qunfeng, I have not seen this specifically with bioperl, but have had it occur once or twice in my own code and have always traced the problem back to an error in the tree where one node is its own ancestor, thereby causing an infinite recursion when you attempt to find all descendants from that node. If each node has a unique identifier, and if the tree is not too large, you could find the offedning node with a small script to traverse the tree, testing the unique identifer of each node against a list of all the nodes seen before and dying when it sees offending node again. Cheers, Jonathan Qunfeng wrote: > Hi, > > I am using bioperl (5.8.0, linux) to work on a UPGMA tree (newick > format, generated by PHYLIP). My code works well on a small tree. > However, when I applied it to a big (ugly) tree, it produces the > following error msg. Has anybody encountered a similar problem? Is > this triggered by any invalid part of my tree? Thanks! > > Qunfeng > ===========Error message begins ===================== > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::each_Descendent" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 495, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 201, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::Node::height" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/Node.pm line 496, line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Tree::NodeI::get_all_Descendents" > at /usr/lib/perl5/site_perl/5.8.0/Bio/Tree/NodeI.pm line 172, > line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > Deep recursion on subroutine "Bio::Root::Root::DESTROY" at > /usr/lib/perl5/site_perl/5.8.0/Bio/Root/Root.pm line 407, line 1. > =========Error msg ends============================================== > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- Dr Jonathan Arthur Sesqui Lecturer in Bioinformatics Central Clinical School, Faculty of Medicine and SUBIT Medical Foundation Building, K25 University of Sydney Ph: +61 2 9036 3132 Email: jarthur@med.usyd.edu.au From smarkel at scitegic.com Wed Nov 30 20:05:17 2005 From: smarkel at scitegic.com (Scott Markel) Date: Wed Nov 30 20:15:23 2005 Subject: [Bioperl-l] clustalw.pm: could not open sequence file error In-Reply-To: <259a224c0511291433r2455a9afv76658ba3409e632f@mail.gmail.com> References: <259a224c0511291433r2455a9afv76658ba3409e632f@mail.gmail.com> Message-ID: <438E4C4D.8070902@scitegic.com> Olena, Are you getting a BioPerl error or a ClustalW error? What happens if you invoke ClustalW directly on your input file, i.e., without using BioPerl? Scott Olena Morozova wrote: > Hi all, > > I am trying to use this script > > use Bio::Tools::Run::Alignment::Clustalw; > > $ENV{CLUSTALDIR} = 'C:/perl/clustalw1.8/'; > my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', > > 'outfile'=> 'al_mouse.txt'); > my $factory = > > Bio::Tools::Run::Alignment::Clustalw->new(@params); > $inputfilename = 'c:/perl/mouse_unique.txt'; > my $aln = $factory->align($inputfilename); > > to do a MSA, and it works for a test file with 2 or 3 sequences. > However, when I try to run it on my actual file (has 97 sequences) > which is in exactly the same format as the test file (fasta), I get a > "could not open the sequence file" error. > Is this because the file is too big and is there a way to fix this? > Thanks a lot for your help! > > Olena -- Scott Markel, Ph.D. Principal Bioinformatics Architect email: smarkel@scitegic.com SciTegic Inc. mobile: +1 858 205 3653 9665 Chesapeake Drive, Suite 401 voice: +1 858 279 8800, ext. 253 San Diego, CA 92123 fax: +1 858 279 8804 USA web: http://www.scitegic.com