From heikki at ebi.ac.uk Wed Oct 1 12:30:47 2003 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Wed Oct 1 12:28:42 2003 Subject: [Bioperl-l] Bioperl Developer snapshot 1.3.01 Message-ID: <1065025847.2553.112.camel@localhost> Bioperl developer snap shot 1.3.01 ----------------------------------- This is the first developer snap shot from the BioPerl CVS head that will eventually lead to release 1.4. Note that this is called snap shot rather than release. Number of things are guarantied to fail. The meaning of the snapshot is get more people to move from 1.2 series into using the latest code base to have enough momentum to put together a solid release. 1.3 series will be available only from the BioPerl FTP site and its mirrors, not from CPAN. Depending on developer activity new snapshots will be made available weekly or forth-nightly. These snap shots will be taken from the CVS head until there is a good reason to branch. http://bioperl.org/DIST/current_core_unstable.tar.gz http://bioperl.org/DIST/bioperl-1.3.01.tar.gz New things is featured for the first time in 1.3 which will be relaesed in 1.4 include: - installable scripts - Bio::Popgen - Bio::Restriction - Bio::Tools::Analysis - web based DNA and Protein analysis tools - Bio::Seq::Meta - per residue annotable sequences - Bio::Matrix::IO - improved Bio::Tools::Genewise - Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA - Bio::SeqFeature::Tools - seqFeature mapping tools - Bio::Tools::dpAlign - pure perl dynamic programming sequence alignment - new Bio::SearchIO formats - new parsers in Bio::Tools: Blat, Geneid, Lagan, Mdust, Promoterwise,PrositeScan, - hundreds of new and improved files Start these now! All feed back to bioperl-l@bioperl.org -Heikki -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From bmadsen at mathworks.com Wed Oct 1 18:25:06 2003 From: bmadsen at mathworks.com (Brian Madsen) Date: Wed Oct 1 18:22:57 2003 Subject: [Bioperl-l] Installation Problems Message-ID: I'm new to Bioperl and am trying to complete an installation. The company has a Solaris server, and I don't have write privileges to the perl5/site_perl source area, so I followed the instructions to install to a personal module area. In addition to the bioperl-1.2.3 tar file, I also ran installations for bioperl-ext-06, Bundle-BioPerl-2.05 and a separate installation for IO-String-1.02. In every case, I used: PREFIX=/home/bmadsen/bjm_perl as a parameter in building the makefile, and all of the installations were successful. Still, when I run the bptutorial.pl file, I get the error: "Can't locate IO/String.pm in @INC (@INC contains: ..." followed by a half-dozen notices about failed compilation. I've even tried copy the String.pm file into the bioperl-1.2.3 directory, but it doesn't help. I have already printed bptutorial.pl and am reading through it, but I had hoped to run it interactively. Any advice? Thanks -Brian From cjm at fruitfly.org Wed Oct 1 20:12:06 2003 From: cjm at fruitfly.org (Chris Mungall) Date: Wed Oct 1 19:26:27 2003 Subject: [Bioperl-l] Bio::Tools::GFF GFF3 parsing In-Reply-To: <200309261144.22482.lstein@cshl.edu> Message-ID: The main thing it seems to be missing is use of the ID and Parent tags to indicate the relationship of features to one another. I'm not really sure how best to do this, as this requires generating a unique identifier for any feature that contains other features. The code on the freaky-dev branch had a way of dealing with this, didn't it? I seem to recall this would require some big changes to the core model. Otherwise it looks great! On Fri, 26 Sep 2003, Lincoln Stein wrote: > Hi Jason, > > This is very good and I'm looking it over now. Does it handle the CIGAR lines > for gapped alignments? > > Lincoln > > On Thursday 18 September 2003 07:02 pm, Jason Stajich wrote: > > I added support for GFF3 parsing to Bio::Tools::GFF and added some simple > > tests. I'm not 100% I have GFF3 output correct so Chris Mungall, Lincoln > > if you don't mind giving it a look over that would be great. If I've > > duplicated functionality from somewhere else let me know, but I think > > Bio::Tools::GFF needs to be able to parse in GFF3 format at some point. > > > > The GFF3 parsing seems to work fine for processing the BGDP annotations so > > I feel confident it is working correctly, but more testing is welcomed! > > > > This is no real support for Unicode type output, the simpliest solution > > would be to rely on HTML::Entities for encoding non-ASCII codes. I wasn't > > sure I wanted to make Tools::GFF depend on this right now so I've just > > implemented a simple encoding for '=,;'. Feel free to fix this if it > > needs to be more aggresive. > > > > -jason > > From heikki at ebi.ac.uk Thu Oct 2 06:00:57 2003 From: heikki at ebi.ac.uk (Heikki Lehvaslaiho) Date: Thu Oct 2 05:58:51 2003 Subject: [Bioperl-l] Installation Problems In-Reply-To: References: Message-ID: <1065088856.4556.49.camel@localhost> Brian, Have you set up environmental variable PERL5LIB? Here is a command line example (which is best put into shell resource file): bash: % export PERL5LIB='$HOME/src/bioperl' tcsh: % setenv PERL5LIB '$HOME/src/bioperl' Using ':' as a separator you can add more than one directory. In your case for perl to find IO::String, PERL5LIB should contain '/home/bmadsen/bjm_perl' and in that directory you should have directory 'IO' with file 'String.pm' Hope this helps, -Heikki On Wed, 2003-10-01 at 23:25, Brian Madsen wrote: > I'm new to Bioperl and am trying to complete an installation. The > company has a Solaris server, and I don't have write privileges to the > perl5/site_perl source area, so I followed the instructions to install > to a personal module area. > In addition to the bioperl-1.2.3 tar file, I also ran installations for > bioperl-ext-06, Bundle-BioPerl-2.05 and a separate installation for > IO-String-1.02. In every case, I used: PREFIX=/home/bmadsen/bjm_perl as > a parameter in building the makefile, and all of the installations were > successful. > Still, when I run the bptutorial.pl file, I get the error: "Can't locate > IO/String.pm in @INC (@INC contains: ..." followed by a half-dozen > notices about failed compilation. I've even tried copy the String.pm > file into the bioperl-1.2.3 directory, but it doesn't help. > I have already printed bptutorial.pl and am reading through it, but I > had hoped to run it interactively. Any advice? > Thanks > -Brian > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioperl-l -- ______ _/ _/_____________________________________________________ _/ _/ http://www.ebi.ac.uk/mutations/ _/ _/ _/ Heikki Lehvaslaiho heikki_at_ebi ac uk _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute _/ _/ _/ Wellcome Trust Genome Campus, Hinxton _/ _/ _/ Cambs. CB10 1SD, United Kingdom _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468 ___ _/_/_/_/_/________________________________________________________ From e_lyn_goh at yahoo.com Thu Oct 2 01:36:53 2003 From: e_lyn_goh at yahoo.com (Eileen goh) Date: Thu Oct 2 08:22:37 2003 Subject: [Bioperl-l] Can't locate loadable object for module GD Message-ID: <20031002053653.6202.qmail@web40505.mail.yahoo.com> hi, i am trying create graphics for my output but i encounter the following exception : Can't locate loadable object for module GD in @INC (@INC contains: C:/Perl/lib C :/Perl/site/lib .) at C:/Perl/site/lib/Bio/Graphics/Glyph/Factory.pm line 55 Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Glyph/Factory.pm line 55. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics/Glyph/Factory .pm line 55. Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Panel.pm line 4. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics/Panel.pm line 4. Compilation failed in require at C:/Perl/site/lib/Bio/Graphics.pm line 3. BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics.pm line 3. Compilation failed in require at chart.pl line 4. BEGIN failed--compilation aborted at chart.pl line 4. i have downloaded and installed the module GD but i doesnt work. could it be i installed wrongly? my codes: #!/usr/bin/perl use strict; use Bio::Graphics; use Bio::SeqFeature::Generic; my $panel = Bio::Graphics::Panel->new(-length => 1000,-width => 800); my $track = $panel->add_track(-glyph => 'generic',-label =>1); while(<>) { chomp; next if /^\#/; my($name, $score, $start, $end) = spilt/\t+/; my $feature = Bio::SeqFeature::Generic->new(-display_name=>$name,-score=>$score, -start=>$start, -end=>$end); $tracj->add_feature($feature); } print $panel->png; Thanks blur queen --------------------------------- Do you Yahoo!? The New Yahoo! Shopping - with improved product search From jason at cgt.duhs.duke.edu Thu Oct 2 09:01:31 2003 From: jason at cgt.duhs.duke.edu (Jason Stajich) Date: Thu Oct 2 08:59:43 2003 Subject: [Bioperl-l] RE: problem connecting to remote blast In-Reply-To: References: Message-ID: I really don't know - i don't really have time to debug this for you I'm sorry - please post your question to the bioperl list. On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote: > hi, > i have already remove the entrez query part but i still encountered the same > warning. > > my codes: > > #!/usr/bin/perl -w > use Bio::SeqIO; > use Bio::Tools::Run::RemoteBlast; > use strict; > my $prog = 'blastn'; > my $db = 'ecoli.nt'; > my $e_val= '1e-10'; > my @params = ( '-prog' => $prog, > '-data' => $db, > '-expect' => $e_val, > '-readmethod' => 'SearchIO' ); > my $factory = Bio::Tools::Run::RemoteBlast->new(@params); > > #delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'}; > my $v = 1; > > my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' ); > while (my $input = $str->next_seq()){ > > #my $r = $factory->submit_blast($input); > my $r = $factory->submit_blast('test.txt'); > print STDERR "waiting..." if( $v > 0 ); > while ( my @rids = $factory->each_rid ) { > foreach my $rid ( @rids ) { > my $rc = $factory->retrieve_blast($rid); > if( !ref($rc) ) { > if( $rc < 0 ) { > $factory->remove_rid($rid); > } > print STDERR "." if ( $v > 0 ); > sleep 5; > } else { > my $result = $rc->next_result(); > #save the output > my $filename = $result->query_name()."\.out"; > $factory->save_output($filename); > $factory->remove_rid($rid); > print "\nQuery Name: ", $result->query_name(), "\n"; > while ( my $hit = $result->next_hit ) { > next unless ( $v > 0); > print "\thit name is ", $hit->name, "\n"; > while( my $hsp = $hit->next_hsp ) { > print "\t\tscore is ", $hsp->score, "\n"; > } > } > } > } > } > } > > -------------------- WARNING --------------------- > MSG:

> INFO: [blastsrv4.REAL]: Error: Segmentation violation > (or m > emory usage limit was exceeded) SIGSEGV (11). >

> 

> BLASTN 2.2.6 [Apr-09-2003]
>
> 
RID: 1064815728-21972-271666.BLASTQ3
> Query= Test
>          (560 letters)
>
> No significant similarity found. For reasons why,  "/blast/blast
> _FAQs.html#no hits">click here.


>
>
> ---------------------------------------------------
>
>
>
>
> -----Original Message-----
> From:	Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
> Sent:	Mon 9/29/2003 9:32 AM
> To:	010381P GOH PHUAY CHENG
> Cc:
> Subject:	Re: problem connecting to remote blast
>
> I suppose it might be because you specified an entrez query for homo
> sapiens on the ecoli db - that is not going to return any hits.  remove
> the entrez query part perhaps.
>
> please post your questions to the bioperl list in the future -
> bioperl-l@bioperl.org
>
> Thanks,
> -jason
>
> On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:
>
> > hi Jason,
> > i encountered some problems running the remote blast.could u please check
> for
> > me wats wrong with my codes. Thanks.
> >
> > phuay cheng
> >
> > -------------------- WARNING ---------------------
> > MSG: 

> > INFO: [blastsrv4.REAL]: Error: Segmentation violation
> > (or m
> > emory usage limit was exceeded) SIGSEGV (11).
> > 

> > 
> > BLASTN 2.2.6 [Apr-09-2003]
> >
> > 
RID: 1064796976-1676-2574126.BLASTQ3
> > Query= Test
> >          (560 letters)
> >
> > No significant similarity found. For reasons why,  > "/blast/blast
> > _FAQs.html#no hits">click here.


> >
> >
> > ---------------------------------------------------
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > use Bio::Tools::Run::RemoteBlast;
> >   use strict;
> >   my $prog = 'blastn';
> >   my $db   = 'ecoli.nt';
> >   #my $e_val= '1e-10';
> >   my @params = ( '-prog' => $prog,
> >          '-data' => $db,
> >          '-readmethod' => 'SearchIO' );
> >   my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >
> >   $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> > [ORGN]';
> >
> >   delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
> >   my $v = 1;
> >
> >   my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
> >   while (my $input = $str->next_seq()){
> >
> >     #my $r = $factory->submit_blast($input);
> >     my $r = $factory->submit_blast('test.txt');
> >     print STDERR "waiting..." if( $v > 0 );
> >     while ( my @rids = $factory->each_rid ) {
> >       foreach my $rid ( @rids ) {
> >         my $rc = $factory->retrieve_blast($rid);
> >         if( !ref($rc) ) {
> >           if( $rc < 0 ) {
> >             $factory->remove_rid($rid);
> >           }
> >           print STDERR "." if ( $v > 0 );
> >           sleep 5;
> >         } else {
> >           my $result = $rc->next_result();
> >           #save the output
> >           my $filename = $result->query_name()."\.out";
> >           $factory->save_output($filename);
> >           $factory->remove_rid($rid);
> >           print "\nQuery Name: ", $result->query_name(), "\n";
> >           while ( my $hit = $result->next_hit ) {
> >             next unless ( $v > 0);
> >             print "\thit name is ", $hit->name, "\n";
> >             while( my $hsp = $hit->next_hsp ) {
> >               print "\t\tscore is ", $hsp->score, "\n";
> >             }
> >           }
> >         }
> >       }
> >     }
> >   }
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From skirov at utk.edu  Thu Oct  2 10:20:59 2003
From: skirov at utk.edu (Stefan Kirov)
Date: Thu Oct  2 10:19:13 2003
Subject: [Bioperl-l] RE: problem connecting to remote blast
In-Reply-To: 
References: 
	
Message-ID: <3F7C344B.30404@utk.edu>

Did you try to run your search from the web interface as well? Did it 
work? Looking at the error you get I guess something might be wrong with 
your test.txt file: format violation, size, etc. Try it from the web 
interface (or if you have the db and blastn locally) to validate the input.
Good luck
Stefan

Jason Stajich wrote:

>I really don't know - i don't really have time to debug this for you I'm
>sorry - please post your question to the bioperl list.
>
>On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:
>
>  
>
>>hi,
>>i have already remove the entrez query part but i still encountered the same
>>warning.
>>
>>my codes:
>>
>>#!/usr/bin/perl -w
>>use Bio::SeqIO;
>>use Bio::Tools::Run::RemoteBlast;
>>use strict;
>>  my $prog = 'blastn';
>>  my $db   = 'ecoli.nt';
>>  my $e_val= '1e-10';
>>  my @params = ( '-prog' => $prog,
>>         '-data' => $db,
>>         '-expect' => $e_val,
>>         '-readmethod' => 'SearchIO' );
>>  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>
>>  #delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>>  my $v = 1;
>>
>>  my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
>>  while (my $input = $str->next_seq()){
>>
>>    #my $r = $factory->submit_blast($input);
>>    my $r = $factory->submit_blast('test.txt');
>>    print STDERR "waiting..." if( $v > 0 );
>>    while ( my @rids = $factory->each_rid ) {
>>      foreach my $rid ( @rids ) {
>>        my $rc = $factory->retrieve_blast($rid);
>>        if( !ref($rc) ) {
>>          if( $rc < 0 ) {
>>            $factory->remove_rid($rid);
>>          }
>>          print STDERR "." if ( $v > 0 );
>>          sleep 5;
>>        } else {
>>          my $result = $rc->next_result();
>>          #save the output
>>          my $filename = $result->query_name()."\.out";
>>          $factory->save_output($filename);
>>          $factory->remove_rid($rid);
>>          print "\nQuery Name: ", $result->query_name(), "\n";
>>          while ( my $hit = $result->next_hit ) {
>>            next unless ( $v > 0);
>>            print "\thit name is ", $hit->name, "\n";
>>            while( my $hsp = $hit->next_hsp ) {
>>              print "\t\tscore is ", $hsp->score, "\n";
>>            }
>>          }
>>        }
>>      }
>>    }
>>  }
>>
>>-------------------- WARNING ---------------------
>>MSG: 

>>INFO: [blastsrv4.REAL]: Error: Segmentation violation
>>(or m
>>emory usage limit was exceeded) SIGSEGV (11).
>>

>>
>>BLASTN 2.2.6 [Apr-09-2003]
>>
>>
RID: 1064815728-21972-271666.BLASTQ3
>>Query= Test
>>         (560 letters)
>>
>>No significant similarity found. For reasons why, >"/blast/blast
>>_FAQs.html#no hits">click here.


>>
>>
>>---------------------------------------------------
>>
>>
>>
>>
>>-----Original Message-----
>>From:	Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
>>Sent:	Mon 9/29/2003 9:32 AM
>>To:	010381P GOH PHUAY CHENG
>>Cc:
>>Subject:	Re: problem connecting to remote blast
>>
>>I suppose it might be because you specified an entrez query for homo
>>sapiens on the ecoli db - that is not going to return any hits.  remove
>>the entrez query part perhaps.
>>
>>please post your questions to the bioperl list in the future -
>>bioperl-l@bioperl.org
>>
>>Thanks,
>>-jason
>>
>>On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:
>>
>>    
>>
>>>hi Jason,
>>>i encountered some problems running the remote blast.could u please check
>>>      
>>>
>>for
>>    
>>
>>>me wats wrong with my codes. Thanks.
>>>
>>>phuay cheng
>>>
>>>-------------------- WARNING ---------------------
>>>MSG: 

>>>INFO: [blastsrv4.REAL]: Error: Segmentation violation
>>>(or m
>>>emory usage limit was exceeded) SIGSEGV (11).
>>>

>>>
>>>BLASTN 2.2.6 [Apr-09-2003]
>>>
>>>
RID: 1064796976-1676-2574126.BLASTQ3
>>>Query= Test
>>>         (560 letters)
>>>
>>>No significant similarity found. For reasons why, >>"/blast/blast
>>>_FAQs.html#no hits">click here.


>>>
>>>
>>>---------------------------------------------------
>>>
>>>#!/usr/bin/perl -w
>>>use Bio::SeqIO;
>>>use Bio::Tools::Run::RemoteBlast;
>>>  use strict;
>>>  my $prog = 'blastn';
>>>  my $db   = 'ecoli.nt';
>>>  #my $e_val= '1e-10';
>>>  my @params = ( '-prog' => $prog,
>>>         '-data' => $db,
>>>         '-readmethod' => 'SearchIO' );
>>>  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>>>
>>>  $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
>>>[ORGN]';
>>>
>>>  delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>>>  my $v = 1;
>>>
>>>  my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
>>>  while (my $input = $str->next_seq()){
>>>
>>>    #my $r = $factory->submit_blast($input);
>>>    my $r = $factory->submit_blast('test.txt');
>>>    print STDERR "waiting..." if( $v > 0 );
>>>    while ( my @rids = $factory->each_rid ) {
>>>      foreach my $rid ( @rids ) {
>>>        my $rc = $factory->retrieve_blast($rid);
>>>        if( !ref($rc) ) {
>>>          if( $rc < 0 ) {
>>>            $factory->remove_rid($rid);
>>>          }
>>>          print STDERR "." if ( $v > 0 );
>>>          sleep 5;
>>>        } else {
>>>          my $result = $rc->next_result();
>>>          #save the output
>>>          my $filename = $result->query_name()."\.out";
>>>          $factory->save_output($filename);
>>>          $factory->remove_rid($rid);
>>>          print "\nQuery Name: ", $result->query_name(), "\n";
>>>          while ( my $hit = $result->next_hit ) {
>>>            next unless ( $v > 0);
>>>            print "\thit name is ", $hit->name, "\n";
>>>            while( my $hsp = $hit->next_hsp ) {
>>>              print "\t\tscore is ", $hsp->score, "\n";
>>>            }
>>>          }
>>>        }
>>>      }
>>>    }
>>>  }
>>>
>>>      
>>>
>>--
>>Jason Stajich
>>Duke University
>>jason at cgt.mc.duke.edu
>>
>>
>>
>>
>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
fax +865 241 1965
e-mail: skirov@utk.edu
sao@ornl.gov


From scamargo at inf.ufrgs.br  Thu Oct  2 12:45:03 2003
From: scamargo at inf.ufrgs.br (Sandro da Silva Camargo)
Date: Thu Oct  2 12:45:25 2003
Subject: [Bioperl-l] Remote Blast
Message-ID: <1065113103.3f7c560fbc1a1@webmail.inf.ufrgs.br>

Hi,

I am trying to connect to the remote blast, but i got the following
error. 

waiting...Error in tempfile() using /tmp/XXXXXXXXXX: Have exceeded the maximum
number of attempts (10) to open temp file/dir at
/usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Root/IO.pm line 659

Can somebody help me?

Thanks in advance.

Sandro

Sandro da Silva Camargo
Instituto de Informatica - Universidade Federal do Rio Grande do Sul
E-mail: scamargo@inf.ufrgs.br
URL: www.inf.ufrgs.br/~scamargo

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
From jason at cgt.duhs.duke.edu  Thu Oct  2 12:51:19 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Oct  2 12:49:23 2003
Subject: [Bioperl-l] help (fwd)
Message-ID: 


---------- Forwarded message ----------
Date: Thu, 02 Oct 2003 18:47:46 +0200
From: "[iso-8859-1] Antonio Ramos Fern?ndez" 
Subject: help

Help ! Help please !

Sorry about this question (it could seem some silly)  but I have some doubts
about bioperl installation and I don?t know anybody who could help me (I?ve
read the installation info at README, INSTALL, INSTALL_WIN, and bptutorial
core documentation files, but i think it?s not clear enough for me). I have
downloaded the zip-compressed 1.2.3 bioperl release, and my Win98 has the
5.8.0 Activestate Perl binary distribution installed. I have unzipped the
file and the directory tree is intact. I guess I have to move the ?Bio?
folder to c:\perl\lib (I?ve read in INSTALL_WIN that the other stuff is
useful but not recommended to install). To install it, I understand I have
to execute the makefile.pl script, but if i move it out its original folder
it gives error messages about ?tests?. If I move the full content of the
zip.file (decompressed) ot the c:\perl\lib folder makefile.pl runs and
prints info about external module requirements for some of the bioperl
modules (and does not seem to do anythhing else). It also prints:

Enjoy the rest of bioperl, which you can use after going 'make install'
Writing Makefile for Bio

I dont? understand the steps I have to follow to install bioperl. MS-DOS
does not recognise these commands (I refer to the three steps make- make
install-make tests) and makefile.pl does not run without other files in the
zip ?root directory?. I don?t know what I have to do exactly with the zip
content. I don?t remember all the command combinations and folders I?ve
tested, but I?ve noticed I don?t know what the hell I?m doing. I think three
new files have appeared in the perl\lib folder after running makefile.pl:
?bioperl.conf?,  ?makefile? and ?&1? (have I to erase them to try again?
-I?ve removed the bio folder from perl\lib after getting tired of all this).
Perl only notices the presence o specific modules when I include in my
scripts the statement [ use lib ?c:\perl\lib\bio\module_name?;   ], but I
don?t think this is the best way to use the modules. Sorry, I started with
perl some months ago and I?m not a skilled programmer (and I have never been
the best friend of my computer). Buff!!! I know I need a makefile utility
(?makefile.pl?), but I don?t know what exactly it is and how does it work.
Thanks a lot if you can help me. Sorry for possible disturbances/time
wasted/economical losses/etc etc. Long life for bioperl.

NOTE: I?ve noticed that modules generally aren?t bigger than 100Kb. Should I
search for and install additional modules using the activestate perl package
manager? (I haven?t done it for bioperl because of its size. I have a 56K
modem and sometimes connection is interrupted by phone calls, so I used a
download manager program called Go!zilla).

Antonio Ramos Fern?ndez, Girona, Spain.

_________________________________________________________________
Localiza y ponte en contacto con tus antiguos compa?eros de clase en MSN
Compa?eros.  http://mipasado.msn.es/

From birney at ebi.ac.uk  Thu Oct  2 13:11:56 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Thu Oct  2 13:09:51 2003
Subject: [Bioperl-l] Remote Blast
In-Reply-To: <1065113103.3f7c560fbc1a1@webmail.inf.ufrgs.br>
Message-ID: 

On Thu, 2 Oct 2003, Sandro da Silva Camargo wrote:

> Hi,
> 
> I am trying to connect to the remote blast, but i got the following
> error. 
> 
> waiting...Error in tempfile() using /tmp/XXXXXXXXXX: Have exceeded the maximum
> number of attempts (10) to open temp file/dir at
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Root/IO.pm line 659
> 
> Can somebody help me?

Which version of bioperl are you using - I think this bug has been 
squashed in 1.2.2 onwards



> 
> Thanks in advance.
> 
> Sandro
> 
> Sandro da Silva Camargo
> Instituto de Informatica - Universidade Federal do Rio Grande do Sul
> E-mail: scamargo@inf.ufrgs.br
> URL: www.inf.ufrgs.br/~scamargo
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
. 
-----------------------------------------------------------------

From birney at ebi.ac.uk  Thu Oct  2 13:12:46 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Thu Oct  2 13:10:41 2003
Subject: [Bioperl-l] Remote Blast
In-Reply-To: <1065113103.3f7c560fbc1a1@webmail.inf.ufrgs.br>
Message-ID: 

On Thu, 2 Oct 2003, Sandro da Silva Camargo wrote:

> Hi,
> 
> I am trying to connect to the remote blast, but i got the following
> error. 
> 
> waiting...Error in tempfile() using /tmp/XXXXXXXXXX: Have exceeded the maximum
> number of attempts (10) to open temp file/dir at
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Root/IO.pm line 659

Also - what system are you running on?


> 
> Can somebody help me?
> 
> Thanks in advance.
> 
> Sandro
> 
> Sandro da Silva Camargo
> Instituto de Informatica - Universidade Federal do Rio Grande do Sul
> E-mail: scamargo@inf.ufrgs.br
> URL: www.inf.ufrgs.br/~scamargo
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
. 
-----------------------------------------------------------------

From skirov at utk.edu  Thu Oct  2 13:37:00 2003
From: skirov at utk.edu (Stefan Kirov)
Date: Thu Oct  2 13:35:12 2003
Subject: [Bioperl-l] help (fwd)
In-Reply-To: 
References: 
Message-ID: <3F7C623C.9000508@utk.edu>

Use the ActiveState Perl PPM3:
(MS-DOS console):

C:\ppm3

PPM>repository add Bioperl http://bioperl.org/DIST/

PPM>search bioperl

PPM>install 

(for example install 1).
This should be in the documentation somewhere I believe- read carefully 
again.

Jason Stajich wrote:

>---------- Forwarded message ----------
>Date: Thu, 02 Oct 2003 18:47:46 +0200
>From: "[iso-8859-1] Antonio Ramos Fern?ndez" 
>Subject: help
>
>Help ! Help please !
>
>Sorry about this question (it could seem some silly)  but I have some doubts
>about bioperl installation and I don?t know anybody who could help me (I?ve
>read the installation info at README, INSTALL, INSTALL_WIN, and bptutorial
>core documentation files, but i think it?s not clear enough for me). I have
>downloaded the zip-compressed 1.2.3 bioperl release, and my Win98 has the
>5.8.0 Activestate Perl binary distribution installed. I have unzipped the
>file and the directory tree is intact. I guess I have to move the ?Bio?
>folder to c:\perl\lib (I?ve read in INSTALL_WIN that the other stuff is
>useful but not recommended to install). To install it, I understand I have
>to execute the makefile.pl script, but if i move it out its original folder
>it gives error messages about ?tests?. If I move the full content of the
>zip.file (decompressed) ot the c:\perl\lib folder makefile.pl runs and
>prints info about external module requirements for some of the bioperl
>modules (and does not seem to do anythhing else). It also prints:
>
>Enjoy the rest of bioperl, which you can use after going 'make install'
>Writing Makefile for Bio
>
>I dont? understand the steps I have to follow to install bioperl. MS-DOS
>does not recognise these commands (I refer to the three steps make- make
>install-make tests) and makefile.pl does not run without other files in the
>zip ?root directory?. I don?t know what I have to do exactly with the zip
>content. I don?t remember all the command combinations and folders I?ve
>tested, but I?ve noticed I don?t know what the hell I?m doing. I think three
>new files have appeared in the perl\lib folder after running makefile.pl:
>?bioperl.conf?,  ?makefile? and ?&1? (have I to erase them to try again?
>-I?ve removed the bio folder from perl\lib after getting tired of all this).
>Perl only notices the presence o specific modules when I include in my
>scripts the statement [ use lib ?c:\perl\lib\bio\module_name?;   ], but I
>don?t think this is the best way to use the modules. Sorry, I started with
>perl some months ago and I?m not a skilled programmer (and I have never been
>the best friend of my computer). Buff!!! I know I need a makefile utility
>(?makefile.pl?), but I don?t know what exactly it is and how does it work.
>Thanks a lot if you can help me. Sorry for possible disturbances/time
>wasted/economical losses/etc etc. Long life for bioperl.
>
>NOTE: I?ve noticed that modules generally aren?t bigger than 100Kb. Should I
>search for and install additional modules using the activestate perl package
>manager? (I haven?t done it for bioperl because of its size. I have a 56K
>modem and sometimes connection is interrupted by phone calls, so I used a
>download manager program called Go!zilla).
>
>Antonio Ramos Fern?ndez, Girona, Spain.
>
>_________________________________________________________________
>Localiza y ponte en contacto con tus antiguos compa?eros de clase en MSN
>Compa?eros.  http://mipasado.msn.es/
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
USA
tel +865 576 5120
fax +865 241 1965
e-mail: skirov@utk.edu
sao@ornl.gov


From bmadsen at mathworks.com  Thu Oct  2 14:56:40 2003
From: bmadsen at mathworks.com (Brian Madsen)
Date: Thu Oct  2 14:54:31 2003
Subject: [Bioperl-l] Installation Problems
Message-ID: 

Thanks for the help. I moved everything to home/bmadsen/bioperl and was
able to set the variable by adding:
setenv PERL5LIB '$HOME/bmadsen/bioperl'
to .login and:
DTSOURCEPROFILE=true
to .dtprofile

-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk] 
Sent: Thursday, October 02, 2003 6:01 AM
To: Brian Madsen
Cc: Bioperl
Subject: Re: [Bioperl-l] Installation Problems

Brian,

Have you set up environmental variable PERL5LIB? 

Here is a command line example (which is best put into shell resource
file):

   bash: % export PERL5LIB='$HOME/src/bioperl'
   tcsh: % setenv PERL5LIB '$HOME/src/bioperl'

Using ':' as a separator you can add more than one directory.

In your case for perl to find IO::String, PERL5LIB should contain
'/home/bmadsen/bjm_perl' and in that directory you should have directory
'IO' with file 'String.pm'

Hope this helps,

	-Heikki



On Wed, 2003-10-01 at 23:25, Brian Madsen wrote:
> I'm new to Bioperl and am trying to complete an installation. The
> company has a Solaris server, and I don't have write privileges to the
> perl5/site_perl source area, so I followed the instructions to install
> to a personal module area.
> In addition to the bioperl-1.2.3 tar file, I also ran installations
for
> bioperl-ext-06, Bundle-BioPerl-2.05 and a separate installation for
> IO-String-1.02. In every case, I used: PREFIX=/home/bmadsen/bjm_perl
as
> a parameter in building the makefile, and all of the installations
were
> successful.
> Still, when I run the bptutorial.pl file, I get the error: "Can't
locate
> IO/String.pm in @INC (@INC contains: ..." followed by a half-dozen
> notices about failed compilation. I've even tried copy the String.pm
> file into the bioperl-1.2.3 directory, but it doesn't help.
> I have already printed bptutorial.pl and am reading through it, but I
> had hoped to run it interactively. Any advice?
> Thanks
> -Brian
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________


From brian_osborne at cognia.com  Thu Oct  2 15:29:14 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Thu Oct  2 15:31:18 2003
Subject: [Bioperl-l] Bioperl PPM for 1.2.3
Message-ID: 

bioperl-l,

>Cool. bioperl-1.2.3-ppm.tar.gz tested for installation on perl 5.6 and 5.8
>from the bioperl.org site. The PPM's are functional and everything (almost)
>seems to works.

>Nigam Shah

That one failed test is probably due to a missing module.

Thanks very much Nigam!


Brian O.


From ng at cs.usask.ca  Thu Oct  2 15:50:53 2003
From: ng at cs.usask.ca (Ambrose Ng)
Date: Thu Oct  2 22:07:51 2003
Subject: [Bioperl-l] something wrong with my code?
Message-ID: <200310021350.53962.ng@cs.usask.ca>

my code here:
		
my @s_ind = $hsp->seq_inds('hit', 'id', 1);
print "conserved=", my $s_ind = join (" ",@s_ind), "\n";

reports this:

conserved=7896-8225 8249-8949


but the numbers are different from the blast report.

Is it more likely to do with my code or is there something going on with the 
bioperl module compatibility with this blast report that I'm 
misunderstanding?

Ambrose

-------------- next part --------------
Query=  gnl|UG|Os#S16394561 Oryza sativa (japonica cultivar-group) cDNA clone:00
2-141-A12, full insert sequence /gb=AK108259 /gi=32993468 /ug=Os.4 /len=1031
        (1031 letters)

Database:  /fdf/coe05/gm0/0/rice_Chr1f.dna
           426 sequences; 63,195,892 total letters.
Searching.......................................................done.

                                                               Score     E
Sequences producing significant alignments:                    (bits)  Value

o_sativa|chr_1|OJ1116_H09|6985                                  1933  0.0

>o_sativa|chr_1|OJ1116_H09|6985
            Length = 110086

 Score = 1933 bits (975), Expect = 0.0
 Identities = 1031/1124 (91%)
 Strand = Plus / Plus


Query: 1    aagctagctcgcgcgcaaattaatcgccgatcgatcctacgatgaagcggaagcggccgg 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7826 aagctagctcgcgcgcaaattaatcgccgatcgatcctacgatgaagcggaagcggccgg 7885


Query: 61   cggcgctgcgcggcggggaggaggcggcggcggcggcgctgaagcgtgggccgtggacgc 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7886 cggcgctgcgcggcggggaggaggcggcggcggcggcgctgaagcgtgggccgtggacgc 7945


Query: 121  ccgaggaggacgaggtgctggcgcggttcgtggcgcgggaggggtgcgaccggtggcgca 180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 7946 ccgaggaggacgaggtgctggcgcggttcgtggcgcgggaggggtgcgaccggtggcgca 8005


Query: 181  cgctgccgcggcgcgcgggcctgctgcgctgcggcaagagctgccgcctccggtggatga 240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8006 cgctgccgcggcgcgcgggcctgctgcgctgcggcaagagctgccgcctccggtggatga 8065


Query: 241  actacctccgccccgacatcaagcgctgccccatcgccgacgacgaggaggacctcatcc 300
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8066 actacctccgccccgacatcaagcgctgccccatcgccgacgacgaggaggacctcatcc 8125


Query: 301  tccgcctccaccgcctcctcggcaaccggt---------------------------ggt 333
            ||||||||||||||||||||||||||||||                           |||
Sbjct: 8126 tccgcctccaccgcctcctcggcaaccggtaagca<--[8161:8243]-->taggtggt 8251


Query: 334  cgctgatcgccgggaggttgccggggcgcacggacaacgagatcaagaactactggaact 393
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8252 cgctgatcgccgggaggttgccggggcgcacggacaacgagatcaagaactactggaact 8311


Query: 394  cgcatctcagcaagaagctcatcgcgcagggcatcgacccgcggacgcacaagccgctga 453
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8312 cgcatctcagcaagaagctcatcgcgcagggcatcgacccgcggacgcacaagccgctga 8371


Query: 454  cggccgccgccgatcactccaacgccgccgctgccgtcgccgccacttcttacaagaagg 513
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8372 cggccgccgccgatcactccaacgccgccgctgccgtcgccgccacttcttacaagaagg 8431


Query: 514  cggtgccggccaagccgccgaggacggcatcctcgccggccgctggcattgagtgcagcg 573
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8432 cggtgccggccaagccgccgaggacggcatcctcgccggccgctggcattgagtgcagcg 8491


Query: 574  acgatcgtgcccgaccggccgacggtggcggtgacttcgcagcgatggtgagcgccgccg 633
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8492 acgatcgtgcccgaccggccgacggtggcggtgacttcgcagcgatggtgagcgccgccg 8551


Query: 634  atgccgagggattcgaaggaggatttggcgatcagttctgtgccgaggatgcagttcatg 693
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8552 atgccgagggattcgaaggaggatttggcgatcagttctgtgccgaggatgcagttcatg 8611


Query: 694  gtggcttcgacatgggttccgcttccgccatggtgggtgacgacgacttctcctcgtttc 753
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8612 gtggcttcgacatgggttccgcttccgccatggtgggtgacgacgacttctcctcgtttc 8671


Query: 754  ttgattctctgatcaacgacgagcagttaggcgatctcttcgtcgtcgagggcaacgatc 813
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8672 ttgattctctgatcaacgacgagcagttaggcgatctcttcgtcgtcgagggcaacgatc 8731


Query: 814  acgagcatggcaatggtgagattggtcatggagacgtcatggaatccaaacagtaatctt 873
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8732 acgagcatggcaatggtgagattggtcatggagacgtcatggaatccaaacagtaatctt 8791


Query: 874  tcgggagattgatcagggaataagttgaccatgagaaaacatgtaagaacagcttgtctg 933
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8792 tcgggagattgatcagggaataagttgaccatgagaaaacatgtaagaacagcttgtctg 8851


Query: 934  ctgagtcatgaccggtgatgtgtatgtgatggaagaaaacgtatgtacgacttaatgctt 993
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 8852 ctgagtcatgaccggtgatgtgtatgtgatggaagaaaacgtatgtacgacttaatgctt 8911


Query: 994  gcacctatactactgctgtgtgcattattcgagtgatc 1031
            ||||||||||||||||||||||||||||||||||||||
Sbjct: 8912 gcacctatactactgctgtgtgcattattcgagtgatc 8949
From jason at cgt.duhs.duke.edu  Fri Oct  3 09:42:31 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct  3 09:40:37 2003
Subject: [Bioperl-l] something wrong with my code?
In-Reply-To: <200310021350.53962.ng@cs.usask.ca>
References: <200310021350.53962.ng@cs.usask.ca>
Message-ID: 

Looks like a bug alright, but it has to do with this part of the
alignment in your report.

Query: 301  tccgcctccaccgcctcctcggcaaccggt---------------------------ggt 333
            ||||||||||||||||||||||||||||||                           |||
Sbjct: 8126 tccgcctccaccgcctcctcggcaaccggtaagca<--[8161:8243]-->taggtggt 8251

We currently can't parse that an turn it into anything appropriate - does
it mean there is a gap there or should those bases be 'N's?

Can you report it to http://bugzilla.open-bio.org for the time being.

-jason
On Thu, 2 Oct 2003, Ambrose Ng wrote:

> my code here:
>
> my @s_ind = $hsp->seq_inds('hit', 'id', 1);
> print "conserved=", my $s_ind = join (" ",@s_ind), "\n";
>
> reports this:
>
> conserved=7896-8225 8249-8949
>
>
> but the numbers are different from the blast report.
>
> Is it more likely to do with my code or is there something going on with the
> bioperl module compatibility with this blast report that I'm
> misunderstanding?
>
> Ambrose
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From scamargo at inf.ufrgs.br  Fri Oct  3 12:25:27 2003
From: scamargo at inf.ufrgs.br (Sandro da Silva Camargo)
Date: Fri Oct  3 12:25:03 2003
Subject: [Bioperl-l] Remote Blast
Message-ID: <1065198327.3f7da2f7d030c@webmail.inf.ufrgs.br>

Hi,

I am using:

Solaris 8
ActivePerl 5.8
BioPerl 1.2.3

Thanks,

Sandro


----- Mensagem encaminhada de Ewan Birney  -----
    Data: Thu, 2 Oct 2003 18:12:46 +0100 (BST)
      De: Ewan Birney 
Reponder para: Ewan Birney 
 Assunto: Re: [Bioperl-l] Remote Blast
    Para: Sandro da Silva Camargo 

On Thu, 2 Oct 2003, Sandro da Silva Camargo wrote:

> Hi,
> 
> I am trying to connect to the remote blast, but i got the following
> error. 
> 
> waiting...Error in tempfile() using /tmp/XXXXXXXXXX: Have exceeded the
maximum
> number of attempts (10) to open temp file/dir at
> /usr/local/ActivePerl-5.8/lib/site_perl/5.8.0/Bio/Root/IO.pm line 659

Also - what system are you running on?


> 
> Can somebody help me?
> 
> Thanks in advance.
> 
> Sandro
> 
> Sandro da Silva Camargo
> Instituto de Informatica - Universidade Federal do Rio Grande do Sul
> E-mail: scamargo@inf.ufrgs.br
> URL: www.inf.ufrgs.br/~scamargo
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
. 
-----------------------------------------------------------------

----- Finalizar mensagem encaminhada -----


Sandro da Silva Camargo
Instituto de Informatica - Universidade Federal do Rio Grande do Sul
Porto Alegre - RS - Brasil
E-mail: scamargo@inf.ufrgs.br
URL: www.inf.ufrgs.br/~scamargo

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.
From lstein at cshl.edu  Fri Oct  3 12:27:37 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri Oct  3 12:26:20 2003
Subject: [Bioperl-l] Bio::Graphics output
In-Reply-To: <200309122139.47541.nel@birc.dk>
References: 
	<200309122139.47541.nel@birc.dk>
Message-ID: <200310031227.37523.lstein@cshl.edu>

Then you have to generate a temporary file and point at it.

Lincoln

On Friday 12 September 2003 03:39 pm, Niels Larsen wrote:
> > You have to output the image to a file and make an html img tag pointing
> > to that file. HTH,
> > Marc
>
> Or have a script make it while the page is loaded,
>
> 
>
> That works good for few large images; many mall ones would
> slow the server.
>
> Niels L
>
> _______________________________________________
> 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From jnolan at tulane.edu  Fri Oct  3 17:06:02 2003
From: jnolan at tulane.edu (Jim Nolan)
Date: Fri Oct  3 17:05:20 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
Message-ID: 

I have been unable to install bioperl versions later than 1.2.1 on 
Mac OS X. The first error I get is during 'make test':
"The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
   '/Library/Perl'
If this is a CPAN/distributed module, you may need to reinstall it on your
system.
To allow Inline to compile the module in a temporary cache, simply remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
  at t/FootPrinter.t line 0"
and numerous other tests.

So I attempted to install bioperl-ext, which meant instaling the 
Staden io_lib, though I don't use Staden. This had the difficulty of 
errors caused by the locations of os.h and config.h 
(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html). 
I proceeded with the bioperl-ext install, using the directions at 
http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
(which worked great until recently) I did the -fPIC edit, I did the 
ranlib, but on make test for bioper-ext, I get:
/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl 
/System/Library/Perl/ExtUtils/xsubpp  -typemap 
/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv 
read.xsc read.c
cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden 
-I/usr/local/include/io_lib -g -pipe -pipe -fno-common 
-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE 
-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" 
-I/System/Library/Perl/darwin/CORE  read.c
In file included from /usr/local/include/io_lib/os.h:4,
                  from /usr/local/include/io_lib/Read.h:43,
                  from read.xs:5:
/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
read.c:1:1: warning: this is the location of the previous definition
In file included from /usr/local/include/io_lib/translate.h:20,
                  from /usr/local/include/io_lib/Read.h:227,
                  from read.xs:5:
/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
/usr/local/include/io_lib/expFileIO.h:42: warning: data definition 
has no type o"
and lots of similar warnings.

So it seems like there is still a problem with these libraries, 
though I copied them where the compiler seems to be looking for them.

Can someone point me in the right direction?


It would be great if there was a way to get rid of the dependency on 
installing bioperl-ext to get bioperl to work. Even if the solution 
for my particular problem is simple, the need to install additional 
layers of dependencies takes a lot of the fun out of it for us lame 
biological types ;-)
.

Thanks.
Jim
-- 
---------------------------------------------------------
Jim Nolan			email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
From jason at cgt.duhs.duke.edu  Fri Oct  3 17:40:27 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct  3 17:39:07 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
Message-ID: 

And you've tried with bioperl 1.2.3?

But I'm a little confused -

 a) you do not need bioperl-ext unless you want to use the specialized
    stuff in there (c-extensions to bioperl modules).

 b) What test is giving you the warnings about IO::Staden - I can
    find no reference to it in any of the tests.  Very weird error
    t/FootPrinter.t has nothing to do with Staden.

We have tried very hard (or at least I advocate it very strongly) not to
have a lot of dependancies, I think we are using a bare minimum of them,
IO::String being one of the most essential. Lincoln even wrote
his own socket based HTTP access to begin to remove LWP as a dependancy.

What people need to remember is when it warns you about extra modules when
you run perl Makefile.PL you don't HAVE To install all of those things,
only those which are dependancies for functionality you want.


-jason
On Fri, 3 Oct 2003, Jim Nolan wrote:

> I have been unable to install bioperl versions later than 1.2.1 on
> Mac OS X. The first error I get is during 'make test':
> "The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
>    '/Library/Perl'
> If this is a CPAN/distributed module, you may need to reinstall it on your
> system.
> To allow Inline to compile the module in a temporary cache, simply remove the
> Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>   at t/FootPrinter.t line 0"
> and numerous other tests.
>
> So I attempted to install bioperl-ext, which meant instaling the
> Staden io_lib, though I don't use Staden. This had the difficulty of
> errors caused by the locations of os.h and config.h
> (http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
> I proceeded with the bioperl-ext install, using the directions at
> http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
> (which worked great until recently) I did the -fPIC edit, I did the
> ranlib, but on make test for bioper-ext, I get:
> /usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
> /System/Library/Perl/ExtUtils/xsubpp  -typemap
> /System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
> read.xsc read.c
> cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
> -I/usr/local/include/io_lib -g -pipe -pipe -fno-common
> -no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
> -fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
> -I/System/Library/Perl/darwin/CORE  read.c
> In file included from /usr/local/include/io_lib/os.h:4,
>                   from /usr/local/include/io_lib/Read.h:43,
>                   from read.xs:5:
> /usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
> read.c:1:1: warning: this is the location of the previous definition
> In file included from /usr/local/include/io_lib/translate.h:20,
>                   from /usr/local/include/io_lib/Read.h:227,
>                   from read.xs:5:
> /usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
> /usr/local/include/io_lib/expFileIO.h:42: warning: data definition
> has no type o"
> and lots of similar warnings.
>
> So it seems like there is still a problem with these libraries,
> though I copied them where the compiler seems to be looking for them.
>
> Can someone point me in the right direction?
>
>
> It would be great if there was a way to get rid of the dependency on
> installing bioperl-ext to get bioperl to work. Even if the solution
> for my particular problem is simple, the need to install additional
> layers of dependencies takes a lot of the fun out of it for us lame
> biological types ;-)
> .
>
> Thanks.
> Jim
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From brian_osborne at cognia.com  Fri Oct  3 18:08:10 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Fri Oct  3 18:11:30 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
Message-ID: 

Jim,

> It would be great if there was a way to get rid of the dependency on
installing bioperl-ext to get bioperl to work.

This is odd. I've done 'make install' many, many times but I've never
installed nor used the bioperl-ext library. Ever. Do you think you could
have done something unconventional to see the behavior you're seeing?

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
Sent: Friday, October 03, 2003 5:06 PM
To: bioperl-l@portal.open-bio.org
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems

I have been unable to install bioperl versions later than 1.2.1 on
Mac OS X. The first error I get is during 'make test':
"The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
   '/Library/Perl'
If this is a CPAN/distributed module, you may need to reinstall it on your
system.
To allow Inline to compile the module in a temporary cache, simply remove
the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
  at t/FootPrinter.t line 0"
and numerous other tests.

So I attempted to install bioperl-ext, which meant instaling the
Staden io_lib, though I don't use Staden. This had the difficulty of
errors caused by the locations of os.h and config.h
(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
I proceeded with the bioperl-ext install, using the directions at
http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
(which worked great until recently) I did the -fPIC edit, I did the
ranlib, but on make test for bioper-ext, I get:
/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
/System/Library/Perl/ExtUtils/xsubpp  -typemap
/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
read.xsc read.c
cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
-I/System/Library/Perl/darwin/CORE  read.c
In file included from /usr/local/include/io_lib/os.h:4,
                  from /usr/local/include/io_lib/Read.h:43,
                  from read.xs:5:
/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
read.c:1:1: warning: this is the location of the previous definition
In file included from /usr/local/include/io_lib/translate.h:20,
                  from /usr/local/include/io_lib/Read.h:227,
                  from read.xs:5:
/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
has no type o"
and lots of similar warnings.

So it seems like there is still a problem with these libraries,
though I copied them where the compiler seems to be looking for them.

Can someone point me in the right direction?


It would be great if there was a way to get rid of the dependency on
installing bioperl-ext to get bioperl to work. Even if the solution
for my particular problem is simple, the need to install additional
layers of dependencies takes a lot of the fun out of it for us lame
biological types ;-)
.

Thanks.
Jim
--
---------------------------------------------------------
Jim Nolan                       email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.                Phone: (504)-584-2453
New Orleans, LA 70112-2699      FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
_______________________________________________
Bioperl-l mailing list
Bioperl-l@portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


From jnolan at tulane.edu  Fri Oct  3 18:54:29 2003
From: jnolan at tulane.edu (Jim Nolan)
Date: Fri Oct  3 18:52:41 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
Message-ID: 

I sent the full list of test errors to Jason, but I got 29 errors 
looking for Staden::read when I tested Bioperl 1.2.3.
These were the tests that asked for it:
BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator, 
Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO, 
Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game, 
largefas, multiple, phd, primaryq, qual, scf, splicedseq

I think I get even more for the CVS version.
I guess it must be something specific to my machine, since nobody's 
heard of this one. When I saw the Staden::read errors, then I figured 
I had to have bioperl-ext.
Sorry I whined, I thought that it was just a new dependency that 
wasn't as much of a hassle for most machines as it is for mine.

If anyone has any clues as to what I did wrong, I'd be glad to hear them.

Thanks
Jim

>Jim,
>
>>  It would be great if there was a way to get rid of the dependency on
>installing bioperl-ext to get bioperl to work.
>
>This is odd. I've done 'make install' many, many times but I've never
>installed nor used the bioperl-ext library. Ever. Do you think you could
>have done something unconventional to see the behavior you're seeing?
>
>Brian O.
>
>-----Original Message-----
>From: bioperl-l-bounces@portal.open-bio.org
>[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
>Sent: Friday, October 03, 2003 5:06 PM
>To: bioperl-l@portal.open-bio.org
>Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
>
>I have been unable to install bioperl versions later than 1.2.1 on
>Mac OS X. The first error I get is during 'make test':
>"The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
>    '/Library/Perl'
>If this is a CPAN/distributed module, you may need to reinstall it on your
>system.
>To allow Inline to compile the module in a temporary cache, simply remove
>the
>Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>   at t/FootPrinter.t line 0"
>and numerous other tests.
>
>So I attempted to install bioperl-ext, which meant instaling the
>Staden io_lib, though I don't use Staden. This had the difficulty of
>errors caused by the locations of os.h and config.h
>(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
>I proceeded with the bioperl-ext install, using the directions at
>http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
>(which worked great until recently) I did the -fPIC edit, I did the
>ranlib, but on make test for bioper-ext, I get:
>/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
>/System/Library/Perl/ExtUtils/xsubpp  -typemap
>/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
>read.xsc read.c
>cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
>-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
>-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
>-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
>-I/System/Library/Perl/darwin/CORE  read.c
>In file included from /usr/local/include/io_lib/os.h:4,
>                   from /usr/local/include/io_lib/Read.h:43,
>                   from read.xs:5:
>/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
>read.c:1:1: warning: this is the location of the previous definition
>In file included from /usr/local/include/io_lib/translate.h:20,
>                   from /usr/local/include/io_lib/Read.h:227,
>                   from read.xs:5:
>/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
>/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
>has no type o"
>and lots of similar warnings.
>
>So it seems like there is still a problem with these libraries,
>though I copied them where the compiler seems to be looking for them.
>
>Can someone point me in the right direction?
>
>
>It would be great if there was a way to get rid of the dependency on
>installing bioperl-ext to get bioperl to work. Even if the solution
>for my particular problem is simple, the need to install additional
>layers of dependencies takes a lot of the fun out of it for us lame
>biological types ;-)
>.
>
>Thanks.
>Jim
>--
>---------------------------------------------------------
>Jim Nolan                       email:JNolan@tulane.edu
>Department of Biochemistry SL43
>Tulane University Health Sciences Center
>1430 Tulane Ave.                Phone: (504)-584-2453
>New Orleans, LA 70112-2699      FAX:   (504)-584-2739
>http://www.tulane.edu/~biochem/faculty/nolan.htm
>http://phage.bioc.tulane.edu
>The requirements said: Windows 2000 or better.
>So I got a Macintosh.
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
From vamsi at warta.bio.psu.edu  Fri Oct  3 20:48:25 2003
From: vamsi at warta.bio.psu.edu (Vamsi)
Date: Fri Oct  3 20:46:09 2003
Subject: [Bioperl-l] Bio::Root::IO possible bug?
Message-ID: <200310040048.h940mPN24316@warta.bio.psu.edu>

Hi,

After I upgraded to Bioperl 1.2.3 having problems with even
simple scripts.

For instance

--------------
use Bio::SeqIO;
my $in = Bio::SeqIO->new(-file => $ARGV[0], -format => 'Fasta');
$in->next_seq;
$in->close;
--------------

results in

Can't call method "isa" on unblessed reference at /usr/perl5/site_perl/5.005/Bio/Root/IO.pm line 487,  chunk 1.

Is there a bug in Bio::Root::IO.pm?

Thanks,
Vamsi

From 010381P at nyp.edu.sg  Fri Oct  3 21:35:43 2003
From: 010381P at nyp.edu.sg (010381P GOH PHUAY CHENG)
Date: Sat Oct  4 00:09:47 2003
Subject: [Bioperl-l] (no subject)
Message-ID: 

hi,
i am trying to use the GD module module but i encountered the following
error.. pls help me.. wat should i do.

GD object version 2.07 does not match $GD::VERSION 1.19 at
C:/Perl/lib/DynaLoade
r.pm line 249.
Compilation failed in require at
C:/Perl/site/lib/Bio/Graphics/Glyph/Factory.pm
line 55.
BEGIN failed--compilation aborted at
C:/Perl/site/lib/Bio/Graphics/Glyph/Factory
.pm line 55.
Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Panel.pm line
4.
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics/Panel.pm
line
 4.
Compilation failed in require at C:/Perl/site/lib/Bio/Graphics.pm line 3.
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics.pm line 3.
Compilation failed in require at chart.pl line 4.
BEGIN failed--compilation aborted at chart.pl line 4.

thanks 
blur queen
From jason at cgt.duhs.duke.edu  Sat Oct  4 08:37:23 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sat Oct  4 08:35:00 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems (fwd)
Message-ID: 



--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Fri, 3 Oct 2003 17:12:08 -0500
From: Jim Nolan 
To: Jason Stajich 
Subject: Re: [Bioperl-l] OS X bioperl, staden/read, install problems

I get 29  errors in 'make test' for bioperl 1.2.3, asking for staden:read.
Here is a truncated output from the tests. I removed all the "ok"s
and truncated this part of the error message for staden:read:
"If this is a CPAN/distributed module, you may need to reinstall it on your
rsystem.
To allow Inline to compile the module in a temporary cache, simply remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module."

I get this error when I try to run my old scripts now.

The rest of the test output is below:
t/AlignIO....................ok 67/67One or more DATA sections were
not processed by Inline.

t/Biblio_biofetch............ok 11/11One or more DATA sections were
not processed by Inline.

t/BioDBGFF...................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/BioDBGFF.t line 0
INIT failed--call queue aborted,  line 1.
t/BioDBGFF...................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-120
         Failed 120/120 tests, 0.00% okay
t/BioFetch_DB................ok 27/27One or more DATA sections were
not processed by Inline.

t/DB.........................ok 78/78One or more DATA sections were
not processed by Inline.

         1/78 skipped:
t/EMBL_DB....................ok 15/15One or more DATA sections were
not processed by Inline.

t/FootPrinter................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/FootPrinter.t line 0
INIT failed--call queue aborted,  line 1.
t/FootPrinter................dubious
         Test returned status 255 (wstat 65280, 0xff00)
         after all the subtests completed successfully
t/Genewise...................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Genewise.t line 0
INIT failed--call queue aborted,  line 1.
t/Genewise...................dubious
         Test returned status 255 (wstat 65280, 0xff00)
         after all the subtests completed successfully
t/Genpred....................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Genpred.t line 0
INIT failed--call queue aborted,  line 1.
t/Genpred....................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-35
         Failed 35/35 tests, 0.00% okay
t/Index......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Index.t line 0
INIT failed--call queue aborted,  line 1.
t/Index......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
         after all the subtests completed successfully
t/LiveSeq....................ok 48/48One or more DATA sections were
not processed by Inline.

t/LocusLink..................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/LocusLink.t line 0
INIT failed--call queue aborted,  line 1.
t/LocusLink..................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
         Failed 23/23 tests, 0.00% okay
t/Mutator....................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Mutator.t line 0
INIT failed--call queue aborted,  line 1.
t/Mutator....................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-13
         Failed 13/13 tests, 0.00% okay
t/Perl.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Perl.t line 0
INIT failed--call queue aborted,  line 1.
t/Perl.......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-14
         Failed 14/14 tests, 0.00% okay
t/RefSeq.....................ok 3/13sleeping for 3 seconds
One or more DATA sections were not processed by Inline.

t/RepeatMasker...............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/RepeatMasker.t line 0
INIT failed--call queue aborted,  line 1.
t/RepeatMasker...............dubious
         Test returned status 255 (wstat 65280, 0xff00)
         after all the subtests completed successfully
t/RootI......................ok 10/10One or more DATA sections were
not processed by Inline.

t/SeqAnalysisParser..........The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SeqAnalysisParser.t line 0
INIT failed--call queue aborted,  line 1.
t/SeqAnalysisParser..........dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-11
         Failed 11/11 tests, 0.00% okay
t/SeqBuilder.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SeqBuilder.t line 0
INIT failed--call queue aborted,  line 1.
t/SeqBuilder.................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-101
         Failed 101/101 tests, 0.00% okay
t/SeqFeatCollection..........The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SeqFeatCollection.t line 0
INIT failed--call queue aborted,  line 1.
t/SeqFeatCollection..........dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-428
         Failed 428/428 tests, 0.00% okay
t/SeqFeature.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SeqFeature.t line 0
INIT failed--call queue aborted,  line 1.
t/SeqFeature.................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-62
         Failed 62/62 tests, 0.00% okay
t/SeqIO......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SeqIO.t line 0
INIT failed--call queue aborted,  line 1.
t/SeqIO......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-184
         Failed 184/184 tests, 0.00% okay
t/SequenceFamily.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SequenceFamily.t line 0
INIT failed--call queue aborted,  line 1.
t/SequenceFamily.............dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-17
         Failed 17/17 tests, 0.00% okay
t/SimilarityPair.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/SimilarityPair.t line 0
INIT failed--call queue aborted,  line 1.
t/SimilarityPair.............dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
         Failed 5/5 tests, 0.00% okay
t/StandAloneBlast............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/StandAloneBlast.t line 0
INIT failed--call queue aborted,  line 1.
t/StandAloneBlast............dubious
         Test returned status 255 (wstat 65280, 0xff00)
         after all the subtests completed successfully
t/Swiss......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Swiss.t line 0
INIT failed--call queue aborted,  line 1.
t/Swiss......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
         Failed 5/5 tests, 0.00% okay
t/Tools......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Tools.t line 0
INIT failed--call queue aborted,  line 1.
t/Tools......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-8
         Failed 8/8 tests, 0.00% okay
t/Variation_IO...............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/Variation_IO.t line 0
INIT failed--call queue aborted,  line 1.
t/Variation_IO...............dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-25
         Failed 25/25 tests, 0.00% okay
t/XEMBL_DB...................ok 2/9One or more DATA sections were not
processed by Inline.

t/ePCR.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/ePCR.t line 0
INIT failed--call queue aborted,  line 1.
t/ePCR.......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
         Failed 23/23 tests, 0.00% okay
t/flat.......................ok 11/11One or more DATA sections were
not processed by Inline.

t/game.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/game.t line 0
INIT failed--call queue aborted,  line 1.
t/game.......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-23
         Failed 23/23 tests, 0.00% okay
t/largefasta.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/largefasta.t line 0
INIT failed--call queue aborted,  line 1.
Use of uninitialized value in unlink at t/largefasta.t line 16,  line 1.
t/largefasta.................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-15
         Failed 15/15 tests, 0.00% okay
t/multiple_fasta.............The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/multiple_fasta.t line 0
INIT failed--call queue aborted,  line 1.
t/multiple_fasta.............dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-8
         Failed 8/8 tests, 0.00% okay
t/phd........................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/phd.t line 0
INIT failed--call queue aborted,  line 1.
t/phd........................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-5
         Failed 5/5 tests, 0.00% okay
t/primaryqual................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/primaryqual.t line 0
INIT failed--call queue aborted,  line 1.
t/primaryqual................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-31
         Failed 31/31 tests, 0.00% okay
t/qual.......................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/qual.t line 0
INIT failed--call queue aborted,  line 1.
t/qual.......................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-12
         Failed 12/12 tests, 0.00% okay
t/scf........................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/scf.t line 0
INIT failed--call queue aborted,  line 1.
t/scf........................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-15
         Failed 15/15 tests, 0.00% okay
t/splicedseq.................The extension 'Bio::SeqIO::staden::read'
is not properly installed in path:
   '/Library/Perl'
  at t/splicedseq.t line 0
INIT failed--call queue aborted,  line 1.
t/splicedseq.................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-9
         Failed 9/9 tests, 0.00% okay
Failed Test           Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/BioDBGFF.t           255 65280   120  240 200.00%  1-120
t/FootPrinter.t        255 65280    20    0   0.00%  ??
t/Genewise.t           255 65280    32    0   0.00%  ??
t/Genpred.t            255 65280    35   70 200.00%  1-35
t/Index.t              255 65280    32    0   0.00%  ??
t/LocusLink.t          255 65280    23   46 200.00%  1-23
t/Mutator.t            255 65280    13   26 200.00%  1-13
t/Perl.t               255 65280    14   28 200.00%  1-14
t/RepeatMasker.t       255 65280     6    0   0.00%  ??
t/SeqAnalysisParser.t  255 65280    11   22 200.00%  1-11
t/SeqBuilder.t         255 65280   101  202 200.00%  1-101
t/SeqFeatCollection.t  255 65280   428  856 200.00%  1-428
t/SeqFeature.t         255 65280    62  124 200.00%  1-62
t/SeqIO.t              255 65280   184  368 200.00%  1-184
t/SequenceFamily.t     255 65280    17   34 200.00%  1-17
t/SimilarityPair.t     255 65280     5   10 200.00%  1-5
t/StandAloneBlast.t    255 65280    10    0   0.00%  ??
t/Swiss.t              255 65280     5   10 200.00%  1-5
t/Tools.t              255 65280     8   16 200.00%  1-8
t/Variation_IO.t       255 65280    25   50 200.00%  1-25
t/ePCR.t               255 65280    23   46 200.00%  1-23
t/game.t               255 65280    23   46 200.00%  1-23
t/largefasta.t         255 65280    15   30 200.00%  1-15
t/multiple_fasta.t     255 65280     8   16 200.00%  1-8
t/phd.t                255 65280     5   10 200.00%  1-5
t/primaryqual.t        255 65280    31   62 200.00%  1-31
t/qual.t               255 65280    12   24 200.00%  1-12
t/scf.t                255 65280    15   30 200.00%  1-15
t/splicedseq.t         255 65280     9   18 200.00%  1-9
1 subtest skipped.
Failed 29/137 test scripts, 78.83% okay. 1192/6319 subtests failed,
81.14% okay.
make: *** [test_dynamic] Error 35

I never tried to install bioperl-ext before, but with all of these
errors, I figured it was a new dependency. some of the usual
dependencies I installed with fink, which mostly works OK (I
sometimes have to put a use/sw/libs/perl... line in scripts)

I appreciate your efforts to keep down the dependencies. Everything
was smooth for the last year or so on OS X.

Thanks again,
Jim

PS I was in the Duke Genetics Program, too.  I was in the same class
as Tai-ping Sun.
I enjoyed the dUPG web page

>And you've tried with bioperl 1.2.3?
>
>But I'm a little confused -
>
>  a) you do not need bioperl-ext unless you want to use the specialized
>     stuff in there (c-extensions to bioperl modules).
>
>  b) What test is giving you the warnings about IO::Staden - I can
>     find no reference to it in any of the tests.  Very weird error
>     t/FootPrinter.t has nothing to do with Staden.
>
>We have tried very hard (or at least I advocate it very strongly) not to
>have a lot of dependancies, I think we are using a bare minimum of them,
>IO::String being one of the most essential. Lincoln even wrote
>his own socket based HTTP access to begin to remove LWP as a dependancy.
>
>What people need to remember is when it warns you about extra modules when
>you run perl Makefile.PL you don't HAVE To install all of those things,
>only those which are dependancies for functionality you want.
>
>
>-jason
>On Fri, 3 Oct 2003, Jim Nolan wrote:
>
>>  I have been unable to install bioperl versions later than 1.2.1 on
>  > Mac OS X. The first error I get is during 'make test':
>  > "The extension 'Bio::SeqIO::staden::read' is not properly
>installed in path:
>  >    '/Library/Perl'
>>  If this is a CPAN/distributed module, you may need to reinstall it on your
>>  system.
>>  To allow Inline to compile the module in a temporary cache, simply
>>remove the
>>  Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>>    at t/FootPrinter.t line 0"
>>  and numerous other tests.
>>
>>  So I attempted to install bioperl-ext, which meant instaling the
>>  Staden io_lib, though I don't use Staden. This had the difficulty of
>>  errors caused by the locations of os.h and config.h
>>  (http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
>>  I proceeded with the bioperl-ext install, using the directions at
>>  http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
>>  (which worked great until recently) I did the -fPIC edit, I did the
>>  ranlib, but on make test for bioper-ext, I get:
>>  /usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
>>  /System/Library/Perl/ExtUtils/xsubpp  -typemap
>>  /System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
>>  read.xsc read.c
>>  cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
>>  -I/usr/local/include/io_lib -g -pipe -pipe -fno-common
>>  -no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
>>  -fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
>  > -I/System/Library/Perl/darwin/CORE  read.c
>  > In file included from /usr/local/include/io_lib/os.h:4,
>  >                   from /usr/local/include/io_lib/Read.h:43,
>>                    from read.xs:5:
>>  /usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
>>  read.c:1:1: warning: this is the location of the previous definition
>>  In file included from /usr/local/include/io_lib/translate.h:20,
>>                    from /usr/local/include/io_lib/Read.h:227,
>>                    from read.xs:5:
>>  /usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
>>  /usr/local/include/io_lib/expFileIO.h:42: warning: data definition
>>  has no type o"
>>  and lots of similar warnings.
>>
>>  So it seems like there is still a problem with these libraries,
>>  though I copied them where the compiler seems to be looking for them.
>>
>>  Can someone point me in the right direction?
>>
>>
>>  It would be great if there was a way to get rid of the dependency on
>>  installing bioperl-ext to get bioperl to work. Even if the solution
>>  for my particular problem is simple, the need to install additional
>>  layers of dependencies takes a lot of the fun out of it for us lame
>>  biological types ;-)
>>  .
>>
>>  Thanks.
>>  Jim
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
From jason at cgt.duhs.duke.edu  Sat Oct  4 08:48:23 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sat Oct  4 08:45:59 2003
Subject: [Bioperl-l] Bio::Root::IO possible bug?
In-Reply-To: <200310040048.h940mPN24316@warta.bio.psu.edu>
References: <200310040048.h940mPN24316@warta.bio.psu.edu>
Message-ID: 

This seems like a perl 5.005 bug I guess - we obviously did't see this
error in any of our tests.

You can try and add this to the logic in the if statement on line 487
which is causing you grief:

if( ref($self->{'_filehandle'}) =~ /GLOB/i  ||
    ! ref($self->{'_filehandle'}) ||
    ! $self->{'_filehandle'}->isa('IO::String') ) {
  close($self->{'_filehandle'});
}

-jason
On Fri, 3 Oct 2003, Vamsi wrote:

> Hi,
>
> After I upgraded to Bioperl 1.2.3 having problems with even
> simple scripts.
>
> For instance
>
> --------------
> use Bio::SeqIO;
> my $in = Bio::SeqIO->new(-file => $ARGV[0], -format => 'Fasta');
> $in->next_seq;
> $in->close;
> --------------
>
> results in
>
> Can't call method "isa" on unblessed reference at /usr/perl5/site_perl/5.005/Bio/Root/IO.pm line 487,  chunk 1.
>
> Is there a bug in Bio::Root::IO.pm?
>
> Thanks,
> Vamsi
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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Date: Sat Oct  4 08:47:22 2003
Subject: [Bioperl-l] Available; Government and private financing in Canada
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From jason at cgt.duhs.duke.edu  Sat Oct  4 08:55:51 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sat Oct  4 08:54:10 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
	
Message-ID: 

I would try to get things back to a simple state.

Are you using the system installed perl 5.6.0?

Hopefully you've made your changes on your system by adding things to
PERL5LIB so you can just reset it to a simple state.   If not, you'll be
picking out files and dirs from /Library/Perl I guess

Get rid of any of the bioperl-ext stuff from your paths, you don't need
them.

At a very minimum look at Bio::SeqIO.pm - you can comment out the
following lines and see if your warnings go away.

#sub BEGIN {
#    eval { require Bio::SeqIO::staden::read; };
#}

We've managed to have so many problems with this - I would just suggest
people comment it out from their local installs if they have problems
until Aaron or someone can get detailed, reproduceable problem reports
from folks.

I would really try and whittle things down to a bare minimum and then
try and run the tests.  You can always run a specific test by saying
% make test_FootPrinter
or
% perl -I. -w t/FootPrinter.t

to see more details and when the error is occuring.

-jason

On Fri, 3 Oct 2003, Jim Nolan wrote:

> I sent the full list of test errors to Jason, but I got 29 errors
> looking for Staden::read when I tested Bioperl 1.2.3.
> These were the tests that asked for it:
> BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator,
> Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO,
> Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game,
> largefas, multiple, phd, primaryq, qual, scf, splicedseq
>
> I think I get even more for the CVS version.
> I guess it must be something specific to my machine, since nobody's
> heard of this one. When I saw the Staden::read errors, then I figured
> I had to have bioperl-ext.
> Sorry I whined, I thought that it was just a new dependency that
> wasn't as much of a hassle for most machines as it is for mine.
>
> If anyone has any clues as to what I did wrong, I'd be glad to hear them.
>
> Thanks
> Jim
>
> >Jim,
> >
> >>  It would be great if there was a way to get rid of the dependency on
> >installing bioperl-ext to get bioperl to work.
> >
> >This is odd. I've done 'make install' many, many times but I've never
> >installed nor used the bioperl-ext library. Ever. Do you think you could
> >have done something unconventional to see the behavior you're seeing?
> >
> >Brian O.
> >
> >-----Original Message-----
> >From: bioperl-l-bounces@portal.open-bio.org
> >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
> >Sent: Friday, October 03, 2003 5:06 PM
> >To: bioperl-l@portal.open-bio.org
> >Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
> >
> >I have been unable to install bioperl versions later than 1.2.1 on
> >Mac OS X. The first error I get is during 'make test':
> >"The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
> >    '/Library/Perl'
> >If this is a CPAN/distributed module, you may need to reinstall it on your
> >system.
> >To allow Inline to compile the module in a temporary cache, simply remove
> >the
> >Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
> >   at t/FootPrinter.t line 0"
> >and numerous other tests.
> >
> >So I attempted to install bioperl-ext, which meant instaling the
> >Staden io_lib, though I don't use Staden. This had the difficulty of
> >errors caused by the locations of os.h and config.h
> >(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
> >I proceeded with the bioperl-ext install, using the directions at
> >http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
> >(which worked great until recently) I did the -fPIC edit, I did the
> >ranlib, but on make test for bioper-ext, I get:
> >/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
> >/System/Library/Perl/ExtUtils/xsubpp  -typemap
> >/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
> >read.xsc read.c
> >cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
> >-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
> >-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
> >-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
> >-I/System/Library/Perl/darwin/CORE  read.c
> >In file included from /usr/local/include/io_lib/os.h:4,
> >                   from /usr/local/include/io_lib/Read.h:43,
> >                   from read.xs:5:
> >/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
> >read.c:1:1: warning: this is the location of the previous definition
> >In file included from /usr/local/include/io_lib/translate.h:20,
> >                   from /usr/local/include/io_lib/Read.h:227,
> >                   from read.xs:5:
> >/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
> >/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
> >has no type o"
> >and lots of similar warnings.
> >
> >So it seems like there is still a problem with these libraries,
> >though I copied them where the compiler seems to be looking for them.
> >
> >Can someone point me in the right direction?
> >
> >
> >It would be great if there was a way to get rid of the dependency on
> >installing bioperl-ext to get bioperl to work. Even if the solution
> >for my particular problem is simple, the need to install additional
> >layers of dependencies takes a lot of the fun out of it for us lame
> >biological types ;-)
> >.
> >
> >Thanks.
> >Jim
> >--
> >---------------------------------------------------------
> >Jim Nolan                       email:JNolan@tulane.edu
> >Department of Biochemistry SL43
> >Tulane University Health Sciences Center
> >1430 Tulane Ave.                Phone: (504)-584-2453
> >New Orleans, LA 70112-2699      FAX:   (504)-584-2739
> >http://www.tulane.edu/~biochem/faculty/nolan.htm
> >http://phage.bioc.tulane.edu
> >The requirements said: Windows 2000 or better.
> >So I got a Macintosh.
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l@portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From vamsi at warta.bio.psu.edu  Sat Oct  4 13:46:43 2003
From: vamsi at warta.bio.psu.edu (Vamsi)
Date: Sat Oct  4 13:44:33 2003
Subject: [Bioperl-l] Bio::Root::IO possible bug?
In-Reply-To: 
	from "Jason Stajich" at Oct 04, 2003 08:48:23 AM
Message-ID: <200310041746.h94Hkh325784@warta.bio.psu.edu>

Yes, I rewrote the lines as

if ( ! ref($self->{'_filehandle'}) ||
     (ref($self->{'_filehandle'}) eq 'IO::String') ) {
   close($self->{'_filehandle'});
}

and it works fine. The trouble seems to be with the use of 'isa'

Thanks,
Vamsi
> 
> This seems like a perl 5.005 bug I guess - we obviously did't see this
> error in any of our tests.
> 
> You can try and add this to the logic in the if statement on line 487
> which is causing you grief:
> 
> if( ref($self->{'_filehandle'}) =~ /GLOB/i  ||
>     ! ref($self->{'_filehandle'}) ||
>     ! $self->{'_filehandle'}->isa('IO::String') ) {
>   close($self->{'_filehandle'});
> }
> 
> -jason
> On Fri, 3 Oct 2003, Vamsi wrote:
> 
> > Hi,
> >
> > After I upgraded to Bioperl 1.2.3 having problems with even
> > simple scripts.
> >
> > For instance
> >
> > --------------
> > use Bio::SeqIO;
> > my $in = Bio::SeqIO->new(-file => $ARGV[0], -format => 'Fasta');
> > $in->next_seq;
> > $in->close;
> > --------------
> >
> > results in
> >
> > Can't call method "isa" on unblessed reference at /usr/perl5/site_perl/5.005/Bio/Root/IO.pm line 487,  chunk 1.
> >
> > Is there a bug in Bio::Root::IO.pm?
> >
> > Thanks,
> > Vamsi
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

From lstein at cshl.edu  Sat Oct  4 14:18:54 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat Oct  4 14:16:51 2003
Subject: [Bioperl-l] Bio::Graphics segments problem
In-Reply-To: <200309291926.h8TJQik06123@warta.bio.psu.edu>
References: <200309291926.h8TJQik06123@warta.bio.psu.edu>
Message-ID: <200310041418.54706.lstein@cshl.edu>

Hi,

I know it looks weird, but a Bio::Graphics now defines the 1..2 as:

	1-------2-------3
        =========

That is, the width of the line will be exactly two units long.  The position 
of the dimensionless coordinate is to the left of the graphic.  In graphics 
terminology it is a "half open interval".  I know you would prefer this:

	1------2-------3
        =====

But this causes visual anomalies at high magnifications when the sequence is 
shown:

	0------1-----2------3
         A   GC?

I am willing to consider this alternative:

	0-----1------2------3
            ========

but it might be troublesome.

Lincoln

On Monday 29 September 2003 03:26 pm, Vamsi wrote:
> use Bio::Graphics::Panel;
> use Bio::SeqFeature::Generic;
>
> my $length = 100;
> my $seq = Bio::SeqFeature::Generic->new(-start => 1,
>                                         -end => $length);
>
> my $p = new Bio::Graphics::Panel(
>                                  -length => $length,
>                                  -width => 800,
>                                  );
> $p->add_track($seq,
>               -glyph => 'arrow',
>               -tick => 2,
>               -double => 1,
>               );
>
> #$p->add_track(segments => [[1,40],[61,90]]);
> my $g = $p->add_track();
> $g->add_group([[1,40],[61,90]]);
>
> open(F, '>b.png');
> binmode F;
> print F $p->png();
> close F;

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From jnolan at tulane.edu  Sat Oct  4 14:42:56 2003
From: jnolan at tulane.edu (Jim Nolan)
Date: Sat Oct  4 14:32:10 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
	
	
Message-ID: 

Yes, I am using the system perl 5.6.0. I will try your suggestions on 
Monday, and let you know if anything interesting happens.

Thanks!
Jim

At 8:55 AM -0400 10/4/03, Jason Stajich wrote:
>I would try to get things back to a simple state.
>
>Are you using the system installed perl 5.6.0?
>
>Hopefully you've made your changes on your system by adding things to
>PERL5LIB so you can just reset it to a simple state.   If not, you'll be
>picking out files and dirs from /Library/Perl I guess
>
>Get rid of any of the bioperl-ext stuff from your paths, you don't need
>them.
>
>At a very minimum look at Bio::SeqIO.pm - you can comment out the
>following lines and see if your warnings go away.
>
>#sub BEGIN {
>#    eval { require Bio::SeqIO::staden::read; };
>#}
>
>We've managed to have so many problems with this - I would just suggest
>people comment it out from their local installs if they have problems
>until Aaron or someone can get detailed, reproduceable problem reports
>from folks.
>
>I would really try and whittle things down to a bare minimum and then
>try and run the tests.  You can always run a specific test by saying
>% make test_FootPrinter
>or
>% perl -I. -w t/FootPrinter.t
>
>to see more details and when the error is occuring.
>
>-jason
>
>On Fri, 3 Oct 2003, Jim Nolan wrote:
>
>>  I sent the full list of test errors to Jason, but I got 29 errors
>>  looking for Staden::read when I tested Bioperl 1.2.3.
>>  These were the tests that asked for it:
>>  BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator,
>>  Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO,
>>  Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game,
>>  largefas, multiple, phd, primaryq, qual, scf, splicedseq
>>
>>  I think I get even more for the CVS version.
>>  I guess it must be something specific to my machine, since nobody's
>>  heard of this one. When I saw the Staden::read errors, then I figured
>>  I had to have bioperl-ext.
>>  Sorry I whined, I thought that it was just a new dependency that
>>  wasn't as much of a hassle for most machines as it is for mine.
>>
>>  If anyone has any clues as to what I did wrong, I'd be glad to hear them.
>>
>>  Thanks
>>  Jim
>>
>>  >Jim,
>>  >
>>  >>  It would be great if there was a way to get rid of the dependency on
>>  >installing bioperl-ext to get bioperl to work.
>>  >
>>  >This is odd. I've done 'make install' many, many times but I've never
>>  >installed nor used the bioperl-ext library. Ever. Do you think you could
>>  >have done something unconventional to see the behavior you're seeing?
>>  >
>>  >Brian O.
>>  >
>>  >-----Original Message-----
>>  >From: bioperl-l-bounces@portal.open-bio.org
>>  >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
>>  >Sent: Friday, October 03, 2003 5:06 PM
>>  >To: bioperl-l@portal.open-bio.org
>>  >Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
>>  >
>>  >I have been unable to install bioperl versions later than 1.2.1 on
>>  >Mac OS X. The first error I get is during 'make test':
>>  >"The extension 'Bio::SeqIO::staden::read' is not properly 
>>installed in path:
>>  >    '/Library/Perl'
>>  >If this is a CPAN/distributed module, you may need to reinstall it on your
>>  >system.
>>  >To allow Inline to compile the module in a temporary cache, simply remove
>>  >the
>>  >Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>>  >   at t/FootPrinter.t line 0"
>>  >and numerous other tests.
>>  >
>>  >So I attempted to install bioperl-ext, which meant instaling the
>>  >Staden io_lib, though I don't use Staden. This had the difficulty of
>>  >errors caused by the locations of os.h and config.h
>>  >(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
>>  >I proceeded with the bioperl-ext install, using the directions at
>>  >http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
>>  >(which worked great until recently) I did the -fPIC edit, I did the
>  > >ranlib, but on make test for bioper-ext, I get:
>>  >/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
>>  >/System/Library/Perl/ExtUtils/xsubpp  -typemap
>>  >/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
>>  >read.xsc read.c
>>  >cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
>>  >-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
>>  >-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
>>  >-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
>>  >-I/System/Library/Perl/darwin/CORE  read.c
>>  >In file included from /usr/local/include/io_lib/os.h:4,
>>  >                   from /usr/local/include/io_lib/Read.h:43,
>>  >                   from read.xs:5:
>>  >/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
>>  >read.c:1:1: warning: this is the location of the previous definition
>>  >In file included from /usr/local/include/io_lib/translate.h:20,
>>  >                   from /usr/local/include/io_lib/Read.h:227,
>>  >                   from read.xs:5:
>>  >/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
>>  >/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
>>  >has no type o"
>>  >and lots of similar warnings.
>>  >
>>  >So it seems like there is still a problem with these libraries,
>>  >though I copied them where the compiler seems to be looking for them.
>>  >
>>  >Can someone point me in the right direction?
>>  >
>>  >
>>  >It would be great if there was a way to get rid of the dependency on
>>  >installing bioperl-ext to get bioperl to work. Even if the solution
>>  >for my particular problem is simple, the need to install additional
>>  >layers of dependencies takes a lot of the fun out of it for us lame
>>  >biological types ;-)
>>  >.
>>  >
>>  >Thanks.
>>  >Jim
>>  >--
>>  >---------------------------------------------------------
>>  >Jim Nolan                       email:JNolan@tulane.edu
>>  >Department of Biochemistry SL43
>>  >Tulane University Health Sciences Center
>>  >1430 Tulane Ave.                Phone: (504)-584-2453
>>  >New Orleans, LA 70112-2699      FAX:   (504)-584-2739
>>  >http://www.tulane.edu/~biochem/faculty/nolan.htm
>>  >http://phage.bioc.tulane.edu
>>  >The requirements said: Windows 2000 or better.
>>  >So I got a Macintosh.
>>  >_______________________________________________
>>  >Bioperl-l mailing list
>>  >Bioperl-l@portal.open-bio.org
>>  >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu

From lstein at cshl.edu  Sat Oct  4 14:20:31 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat Oct  4 18:55:52 2003
Subject: [Bioperl-l] GD  problem
In-Reply-To: <871010117.1063954521108.JavaMail.nobody@storage.ni.bg>
References: <871010117.1063954521108.JavaMail.nobody@storage.ni.bg>
Message-ID: <200310041420.31209.lstein@cshl.edu>

When you installed GD, did "make test" pass all its tests?  If so, then 
there's something awry in your script with respect to the @INC path or with 
PERL5LIB environment variable.  If not, then you should send me a copy of the 
GD make test output.

Lincoln

On Friday 19 September 2003 02:55 am, Vesko Baev wrote:
> Hello,
> We have Linux SuSE, Perl(latest ver.),Bioperl(latest ver.).We installed GD
> package and then we started the programm we have this error (but we have
> libgd): Can't locate loadible object for module GD
>
> What's that mean?
> Thanks!
>
>
> -----------------------------------------------------------------
> http://club.abv.bg/jsp/abvCard.jsp - ???? ??? - ??????? ? ?????? ????? ?
> ???? ! _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)

From martin_artist at yahoo.com  Sun Oct  5 09:46:17 2003
From: martin_artist at yahoo.com (ENRON  =  Swarzenegger)
Date: Sun Oct  5 12:45:52 2003
Subject: [Bioperl-l] Stealing CA $9 billions = Recall Election
Message-ID: <200310051645.h95GjSdb025656@portal.open-bio.org>


Bush bible PNAC 

 Swarzeneger got money from ENRON to forgive 9 billions pay back

I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US.  -  Second is here:  1997

http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf

page 48 Clinton economy is good   -   page 51 on document or 63 / on Acrobat viewer.. 

- We have to have major attack on America first, to convince people

OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; 	http://www.alternetnews.com/

Arnold or Adolph, what the different;   D A N K E,    will Terminate US all & California first
Prescott  help Adolph, George him & Enron;  Gasoline $4 per gallon is just the beginning.

Actor = skilled liar, how can we trust them ?  I heard,  his porno job is for sale; & He is ENRON BOY

http://www.tarpley.net/bushb.htm               http://www.bartcop.com/421102.htm

http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml        http://hnn.us/comments/15105.html

 Hitler, Noriega, Hussein, bin Laden, Pinochet   -  did business with the Bush family.
Now we do business with Bush as well;   -  $500 000 000 000 is gone, missing, and make US poor
Perfect Taxpayers Rip Off -  MONEY LAUNDRY    -   true Iraq repair kidding,  - direct to own pocket,



Isn't this a crime ??  + Lie of war reasons, and lie, and lie, and lie.
Please look on this and think by yourself; where we are going ??  
Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. 

http://pnac.tvnewslies.org							http://www.tvnewslies.org
START THINKING AGAIN !!!
www.moveon.org/news/1577.html						www.prisonplanet.com

www.moveon.org	www.votetoimpeach.com

www.kgo810.com		listen       810 AM;    Bernie,   Genie,  Ray only    (night time)

How many Concentration Camps do they need today ?    one for sure is on Cuba.

If,  after that news - you can't sleep too well -;   get Warren book;   " The Governor "   try understand  - how to blackmail Congress   -  Or movie films;       " Enemy of the State"  that most of us  today         " Spy like US "    - abusing power by top managers    " Air America "   - how marihuana come to US

It may happened, Pentagon will have to arrest White House  and his own " Liar in Chief" to save USA  
On the base of George Washington Legacy
War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: 

http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf )

From martin_artist at yahoo.com  Sun Oct  5 09:46:18 2003
From: martin_artist at yahoo.com (ENRON  =  Swarzenegger)
Date: Sun Oct  5 12:45:59 2003
Subject: [Bioperl-l] Stealing CA $9 billions = Recall Election
Message-ID: <200310051645.h95GjSdb025657@portal.open-bio.org>


Bush bible PNAC 

 Swarzeneger got money from ENRON to forgive 9 billions pay back

I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US.  -  Second is here:  1997

http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf

page 48 Clinton economy is good   -   page 51 on document or 63 / on Acrobat viewer.. 

- We have to have major attack on America first, to convince people

OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; 	http://www.alternetnews.com/

Arnold or Adolph, what the different;   D A N K E,    will Terminate US all & California first
Prescott  help Adolph, George him & Enron;  Gasoline $4 per gallon is just the beginning.

Actor = skilled liar, how can we trust them ?  I heard,  his porno job is for sale; & He is ENRON BOY

http://www.tarpley.net/bushb.htm               http://www.bartcop.com/421102.htm

http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml        http://hnn.us/comments/15105.html

 Hitler, Noriega, Hussein, bin Laden, Pinochet   -  did business with the Bush family.
Now we do business with Bush as well;   -  $500 000 000 000 is gone, missing, and make US poor
Perfect Taxpayers Rip Off -  MONEY LAUNDRY    -   true Iraq repair kidding,  - direct to own pocket,



Isn't this a crime ??  + Lie of war reasons, and lie, and lie, and lie.
Please look on this and think by yourself; where we are going ??  
Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. 

http://pnac.tvnewslies.org							http://www.tvnewslies.org
START THINKING AGAIN !!!
www.moveon.org/news/1577.html						www.prisonplanet.com

www.moveon.org	www.votetoimpeach.com

www.kgo810.com		listen       810 AM;    Bernie,   Genie,  Ray only    (night time)

How many Concentration Camps do they need today ?    one for sure is on Cuba.

If,  after that news - you can't sleep too well -;   get Warren book;   " The Governor "   try understand  - how to blackmail Congress   -  Or movie films;       " Enemy of the State"  that most of us  today         " Spy like US "    - abusing power by top managers    " Air America "   - how marihuana come to US

It may happened, Pentagon will have to arrest White House  and his own " Liar in Chief" to save USA  
On the base of George Washington Legacy
War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: 

http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf )

From nel at birc.dk  Sun Oct  5 12:49:57 2003
From: nel at birc.dk (Niels Larsen)
Date: Sun Oct  5 12:52:44 2003
Subject: [Bioperl-l] Bio::Graphics output
In-Reply-To: <200310031227.37523.lstein@cshl.edu>
References: 
	<200309122139.47541.nel@birc.dk>
	<200310031227.37523.lstein@cshl.edu>
Message-ID: <200310051849.57173.nel@birc.dk>

Hmm .. unless one doesnt like temporary files, which someone have 
to come and clean up. The crude piece below does it without, and 
with a separate low-overhead image-serving script and a low number
of images per page it would work reasonably well. 

Niels

On Friday 03 Oct 2003 6:27 pm, Lincoln Stein wrote:
> Then you have to generate a temporary file and point at it.
> 
> Lincoln
> 
> On Friday 12 September 2003 03:39 pm, Niels Larsen wrote:
> > > You have to output the image to a file and make an html img tag pointing
> > > to that file. HTH,
> > > Marc
> >
> > Or have a script make it while the page is loaded,
> >
> > 
> >
> > That works good for few large images; many mall ones would
> > slow the server.
> >
> > Niels L


#!/usr/bin/env perl

# Place script in document root

use strict;
use warnings;

use GD;
use CGI;

my ( $cgi, $img, $black, $red, $script );

$cgi = new CGI;

print qq (Content-type: text/html\n\n);

if ( $cgi->param('make_image') )
{
    $img = new GD::Image(100,100);

    $black = $img->colorAllocate( 0,0,0 );       
    $red = $img->colorAllocate( 255,0,0 );      

    $img->rectangle( 0,0,99,99,$black );
    $img->fill( 50,50,$red );

    binmode STDOUT;

    print $img->png;
}
else
{
    $script = ( split "/", $0 )[-1];
    print qq (\n);
}

From lstein at cshl.edu  Sun Oct  5 12:44:40 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sun Oct  5 14:02:58 2003
Subject: [Bioperl-l] Re: [apollo] Guidance for a newbie
In-Reply-To: 
References: 
Message-ID: <200310051244.40031.lstein@cshl.edu>

On Saturday 04 October 2003 03:28 pm, Andrew Nunberg wrote:
> I am trying to convert genbank records into a format that is readable
> by Appollo.
> I can achieve this with gff format but I would like to do some
> curation/annotation so I am now trying to create game xml.
>

Hi,

This is the same problem that I have.  The approach that I am taking is to 
rewrite the GAME SequenceIO module in Bioperl so that it creates the correct 
version of GAME (the version it currently creates is incompatible with 
Bioperl).  Then what you want to do will be as easy as:

	$in = Bio::SeqIO->new(-file=>'genbank_file',-format=>'genbank');
	$out = Bio::SeqIO->new(-file=>'genbank_file.game',-format=>'GAME');
	while (my $seq = $in->next_seq) {
		$out->write_seq($seq);
	}

Because of many other obligations, this is moving very slowly and don't expect 
much progress until things lighten up for me in November.  If you or anyone 
else on these lists want to work on this, I will gladly share my notes and 
what I've got so far.

Lincoln

On Saturday 04 October 2003 03:28 pm, Andrew Nunberg wrote:
> I am trying to convert genbank records into a format that is readable
> by Appollo.
> I can achieve this with gff format but I would like to do some
> curation/annotation so I am now trying to create game xml.
>
> I see two basic strategies, creating annotation or
> computational_analysis tracks
> In either case, i am lacking data to make the xml
>
> For annotation there is a requirement for one more sequences to go with
> the 'gene'.
> for computational_analysis i am require to give output
> this is according to the dtd i have.
>
> Has anyone tried to do this and what approach did you take?
> Is it possible to fake the sequence requirement for annotations?
> so far the only xml that has worked is one with just the root sequence
> and nothing else..
>
> Thanks
> Andy
> ---------------------------------------------------
> Andrew Nunberg Ph.D
> Bioinfomagician
> Orion Genomics
> 4041 Forest Park
> St Louis, MO
> 314-615-6989
> anunberg@oriongenomics.com
> www.oriongenomics.com
>
> _______________________________________________
> apollo mailing list
> apollo@mail.fruitfly.org
> http://mail.fruitfly.org/mailman/listinfo/apollo

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From e_lyn_goh at yahoo.com  Sun Oct  5 22:09:59 2003
From: e_lyn_goh at yahoo.com (Eileen goh)
Date: Mon Oct  6 00:11:39 2003
Subject: [Bioperl-l] problems running Bio::Graphics
Message-ID: <20031006020959.96255.qmail@web40502.mail.yahoo.com>

hi,
i am trying to use the Bio::Graphics. i kept encountering the following error while running the Bio:: graphics.. wat should i do..
 
GD object version 2.07 does not match $GD::VERSION 1.19 at C:/Perl/lib/DynaLoade
r.pm line 249.
Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Glyph/Factory.pm
line 55.
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics/Glyph/Factory
.pm line 55.
Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Panel.pm line 4.
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics/Panel.pm line
 4.
Compilation failed in require at C:/Perl/site/lib/Bio/Graphics.pm line 3.
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics.pm line 3.
Compilation failed in require at chart.pl line 4.
BEGIN failed--compilation aborted at chart.pl line 4.
 


---------------------------------
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From Richard.Adams at ed.ac.uk  Mon Oct  6 04:44:33 2003
From: Richard.Adams at ed.ac.uk (Richard Adams)
Date: Mon Oct  6 04:42:14 2003
Subject: [Bioperl-l] Bio::Graphics sort_order
Message-ID: <3F812B71.8AB6C28A@ed.ac.uk>

Hello,
    I'm trying to sort the display order  of features based on values
in  one of the features' tags using the syntax
    described in the Bio::Graphics::Panel :doc.
        i.e.,
sort_order =>    sub {(  ($a->each_tag_value('Conserved'))[0]
<=>($b->each_tag_value('Conserved'))[0]  )};
But I get the error message
"Can't call method "each_tag_value" on an undefined value at
Draw_Output.pm". The code doesn't seem to be
recognizing that $a and $b should refer to the features. I've tried
delving into the internal workings of Bio::Graphics::Glyph::Factory
with little enlightenment, would be grateful for any ideas.
Cheers
Richard


--
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams@ed.ac.uk



From lstein at cshl.edu  Mon Oct  6 08:13:14 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Oct  6 08:28:44 2003
Subject: [Bioperl-l] Re: [apollo] Guidance for a newbie
In-Reply-To: <200310051244.40031.lstein@cshl.edu>
References: 
	<200310051244.40031.lstein@cshl.edu>
Message-ID: <200310060813.14881.lstein@cshl.edu>

> This is the same problem that I have.  The approach that I am taking is to
> rewrite the GAME SequenceIO module in Bioperl so that it creates the
> correct version of GAME (the version it currently creates is incompatible
> with Bioperl). 

I meant to say that bioperl currently creates a version of game that is 
incompatible with apollo, and vice-versa.

Lincoln

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From lstein at cshl.edu  Mon Oct  6 10:04:11 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Oct  6 10:02:28 2003
Subject: [Bioperl-l] problems running Bio::Graphics
In-Reply-To: <20031006020959.96255.qmail@web40502.mail.yahoo.com>
References: <20031006020959.96255.qmail@web40502.mail.yahoo.com>
Message-ID: <200310061004.11515.lstein@cshl.edu>

Hi Eileen,

The problem is with the GD library.  You appear to have a newer version of the 
GD .dll code library installed, but an older version of the GD.pm file.  I 
suggest that you go through your Perl library directory and remove everything 
that has a GD in its name.  Then use the ActiveState PPM manager to download 
and install a fresh copy of GD.

Lincoln


On Sunday 05 October 2003 10:09 pm, Eileen goh wrote:
> hi,
> i am trying to use the Bio::Graphics. i kept encountering the following
> error while running the Bio:: graphics.. wat should i do..
>
> GD object version 2.07 does not match $GD::VERSION 1.19 at
> C:/Perl/lib/DynaLoade r.pm line 249.
> Compilation failed in require at
> C:/Perl/site/lib/Bio/Graphics/Glyph/Factory.pm line 55.
> BEGIN failed--compilation aborted at
> C:/Perl/site/lib/Bio/Graphics/Glyph/Factory .pm line 55.
> Compilation failed in require at C:/Perl/site/lib/Bio/Graphics/Panel.pm
> line 4. BEGIN failed--compilation aborted at
> C:/Perl/site/lib/Bio/Graphics/Panel.pm line 4.
> Compilation failed in require at C:/Perl/site/lib/Bio/Graphics.pm line 3.
> BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Graphics.pm line
> 3. Compilation failed in require at chart.pl line 4.
> BEGIN failed--compilation aborted at chart.pl line 4.
>
>
>
> ---------------------------------
> Do you Yahoo!?
> The New Yahoo! Shopping - with improved product search

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From charles at moulinette.dyndns.org  Mon Oct  6 10:05:04 2003
From: charles at moulinette.dyndns.org (Charles Plessy)
Date: Mon Oct  6 10:02:44 2003
Subject: [Bioperl-l] Bio::Biblio
Message-ID: <20031006140504.GA2631@plessy.org>

Hi,

	My goal is to write a quick-and-dirty medline2docbook fliter
for immediate use, using bioperl since it has already a library able
to query medline.

	However, I don't know how to quickly extract basic fields,
like author or journal, to use them in this kind of output system:

print << DOCBOOK
(...)

   
    
     $object->Author_surname
     $object->Author_firstname
    
(...)
DOCBOOK

Can anybody point me to the correct object and its construction method?

-- 
Charles
From jnolan at tulane.edu  Mon Oct  6 10:47:57 2003
From: jnolan at tulane.edu (Jim Nolan)
Date: Mon Oct  6 10:46:32 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
	
	
Message-ID: 

All is right with the world. I rooted around and only found that 
SeqIO/staden/read had been installed, but not the rest of 
bioperl-ext, since I never passed all the tests. I commented the 
lines from SeqIO.pm which required staden/read and ran make test. 
Essentially all passed, with some minor errors.
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/System/Library/Perl/darwin -I/System/Library/Perl -e 'use 
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' 
t/*.t
t/DB.........................ok
         1/78 skipped:
t/SeqIO......................ok
         3/184 skipped:
t/StandAloneBlast............ok 4/10Blast Database swissprot not 
found at t/StandAloneBlast.t line 72.
Blast databases(s) not found, skipping remaining  tests at 
t/StandAloneBlast.t line 76.
t/StandAloneBlast............ok
t/game.......................ok 20/23Use of uninitialized value in 
pattern match (m//) at /Library/Perl/XML/Writer.pm line 307.
Use of uninitialized value in print at 
/System/Library/Perl/darwin/IO/Handle.pm line 379.
t/game.......................ok
All tests successful, 4 subtests skipped.
Files=137, Tests=6319, 460 wallclock secs (93.89 cusr + 16.76 csys = 
110.65 CPU)

Thanks for your help. I would like to reinstate my whine about adding 
new dependencies, though ;-).

I would be happy to provide feedback on errors in installing 
bioperl-ext on OS X if needed.

Thanks again.
Jim

At 8:55 AM -0400 10/4/03, Jason Stajich wrote:
>I would try to get things back to a simple state.
>
>Are you using the system installed perl 5.6.0?
>
>Hopefully you've made your changes on your system by adding things to
>PERL5LIB so you can just reset it to a simple state.   If not, you'll be
>picking out files and dirs from /Library/Perl I guess
>
>Get rid of any of the bioperl-ext stuff from your paths, you don't need
>them.
>
>At a very minimum look at Bio::SeqIO.pm - you can comment out the
>following lines and see if your warnings go away.
>
>#sub BEGIN {
>#    eval { require Bio::SeqIO::staden::read; };
>#}
>
>We've managed to have so many problems with this - I would just suggest
>people comment it out from their local installs if they have problems
>until Aaron or someone can get detailed, reproduceable problem reports
>from folks.
>
>I would really try and whittle things down to a bare minimum and then
>try and run the tests.  You can always run a specific test by saying
>% make test_FootPrinter
>or
>% perl -I. -w t/FootPrinter.t
>
>to see more details and when the error is occuring.
>
>-jason
>
>On Fri, 3 Oct 2003, Jim Nolan wrote:
>
>>  I sent the full list of test errors to Jason, but I got 29 errors
>>  looking for Staden::read when I tested Bioperl 1.2.3.
>>  These were the tests that asked for it:
>>  BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator,
>>  Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO,
>>  Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game,
>>  largefas, multiple, phd, primaryq, qual, scf, splicedseq
>>
>>  I think I get even more for the CVS version.
>>  I guess it must be something specific to my machine, since nobody's
>>  heard of this one. When I saw the Staden::read errors, then I figured
>>  I had to have bioperl-ext.
>>  Sorry I whined, I thought that it was just a new dependency that
>>  wasn't as much of a hassle for most machines as it is for mine.
>>
>>  If anyone has any clues as to what I did wrong, I'd be glad to hear them.
>>
>>  Thanks
>>  Jim
>>
>>  >Jim,
>>  >
>>  >>  It would be great if there was a way to get rid of the dependency on
>>  >installing bioperl-ext to get bioperl to work.
>>  >
>>  >This is odd. I've done 'make install' many, many times but I've never
>>  >installed nor used the bioperl-ext library. Ever. Do you think you could
>>  >have done something unconventional to see the behavior you're seeing?
>  > >
>>  >Brian O.
>  > >
>  > >-----Original Message-----
>  > >From: bioperl-l-bounces@portal.open-bio.org
>  > >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
>  > >Sent: Friday, October 03, 2003 5:06 PM
>  > >To: bioperl-l@portal.open-bio.org
>>  >Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
>>  >
>>  >I have been unable to install bioperl versions later than 1.2.1 on
>>  >Mac OS X. The first error I get is during 'make test':
>>  >"The extension 'Bio::SeqIO::staden::read' is not properly 
>>installed in path:
>>  >    '/Library/Perl'
>>  >If this is a CPAN/distributed module, you may need to reinstall it on your
>>  >system.
>>  >To allow Inline to compile the module in a temporary cache, simply remove
>>  >the
>>  >Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
>>  >   at t/FootPrinter.t line 0"
>>  >and numerous other tests.
>>  >
>>  >So I attempted to install bioperl-ext, which meant instaling the
>>  >Staden io_lib, though I don't use Staden. This had the difficulty of
>>  >errors caused by the locations of os.h and config.h
>>  >(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
>>  >I proceeded with the bioperl-ext install, using the directions at
>>  >http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
>>  >(which worked great until recently) I did the -fPIC edit, I did the
>>  >ranlib, but on make test for bioper-ext, I get:
>>  >/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
>>  >/System/Library/Perl/ExtUtils/xsubpp  -typemap
>>  >/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
>>  >read.xsc read.c
>>  >cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
>>  >-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
>>  >-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
>>  >-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
>>  >-I/System/Library/Perl/darwin/CORE  read.c
>>  >In file included from /usr/local/include/io_lib/os.h:4,
>>  >                   from /usr/local/include/io_lib/Read.h:43,
>>  >                   from read.xs:5:
>>  >/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
>>  >read.c:1:1: warning: this is the location of the previous definition
>>  >In file included from /usr/local/include/io_lib/translate.h:20,
>>  >                   from /usr/local/include/io_lib/Read.h:227,
>>  >                   from read.xs:5:
>>  >/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
>>  >/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
>>  >has no type o"
>>  >and lots of similar warnings.
>>  >
>>  >So it seems like there is still a problem with these libraries,
>>  >though I copied them where the compiler seems to be looking for them.
>>  >
>>  >Can someone point me in the right direction?
>>  >
>>  >
>>  >It would be great if there was a way to get rid of the dependency on
>>  >installing bioperl-ext to get bioperl to work. Even if the solution
>>  >for my particular problem is simple, the need to install additional
>>  >layers of dependencies takes a lot of the fun out of it for us lame
>>  >biological types ;-)
>>  >.
>>  >
>>  >Thanks.
>>  >Jim
>>  >--
>>  >---------------------------------------------------------
>>  >Jim Nolan                       email:JNolan@tulane.edu
>>  >Department of Biochemistry SL43
>>  >Tulane University Health Sciences Center
>>  >1430 Tulane Ave.                Phone: (504)-584-2453
>>  >New Orleans, LA 70112-2699      FAX:   (504)-584-2739
>>  >http://www.tulane.edu/~biochem/faculty/nolan.htm
>>  >http://phage.bioc.tulane.edu
>>  >The requirements said: Windows 2000 or better.
>>  >So I got a Macintosh.
>>  >_______________________________________________
>>  >Bioperl-l mailing list
>>  >Bioperl-l@portal.open-bio.org
>>  >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
From jason at cgt.duhs.duke.edu  Mon Oct  6 10:52:28 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Mon Oct  6 10:50:43 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
	
	
	
Message-ID: 

> Thanks for your help. I would like to reinstate my whine about adding
> new dependencies, though ;-).

Noted - it is always a trade-off, feel free to pipe up when we debate
on-list about whether or not add another dependancy.

>
> I would be happy to provide feedback on errors in installing
> bioperl-ext on OS X if needed.

When I get together with Aaron at the end of the month I will try and go
through it with him so I understand what is supposed to happen and/or how
we might reorg bioperl-ext to be less problematic.


>
> Thanks again.
> Jim
>
> At 8:55 AM -0400 10/4/03, Jason Stajich wrote:
> >I would try to get things back to a simple state.
> >
> >Are you using the system installed perl 5.6.0?
> >
> >Hopefully you've made your changes on your system by adding things to
> >PERL5LIB so you can just reset it to a simple state.   If not, you'll be
> >picking out files and dirs from /Library/Perl I guess
> >
> >Get rid of any of the bioperl-ext stuff from your paths, you don't need
> >them.
> >
> >At a very minimum look at Bio::SeqIO.pm - you can comment out the
> >following lines and see if your warnings go away.
> >
> >#sub BEGIN {
> >#    eval { require Bio::SeqIO::staden::read; };
> >#}
> >
> >We've managed to have so many problems with this - I would just suggest
> >people comment it out from their local installs if they have problems
> >until Aaron or someone can get detailed, reproduceable problem reports
> >from folks.
> >
> >I would really try and whittle things down to a bare minimum and then
> >try and run the tests.  You can always run a specific test by saying
> >% make test_FootPrinter
> >or
> >% perl -I. -w t/FootPrinter.t
> >
> >to see more details and when the error is occuring.
> >
> >-jason
> >
> >On Fri, 3 Oct 2003, Jim Nolan wrote:
> >
> >>  I sent the full list of test errors to Jason, but I got 29 errors
> >>  looking for Staden::read when I tested Bioperl 1.2.3.
> >>  These were the tests that asked for it:
> >>  BioDBGFF, FootPrin, Genewise, Genpred, Index, LocusLin, Mutator,
> >>  Perl, RepeatMa, SeqAnaly, SeqBuild, SeqFeatC, SeqFeatu, SeqIO,
> >>  Sequence, Similari, StandAlo, Swiss, Tools, Variatio, ePCR, game,
> >>  largefas, multiple, phd, primaryq, qual, scf, splicedseq
> >>
> >>  I think I get even more for the CVS version.
> >>  I guess it must be something specific to my machine, since nobody's
> >>  heard of this one. When I saw the Staden::read errors, then I figured
> >>  I had to have bioperl-ext.
> >>  Sorry I whined, I thought that it was just a new dependency that
> >>  wasn't as much of a hassle for most machines as it is for mine.
> >>
> >>  If anyone has any clues as to what I did wrong, I'd be glad to hear them.
> >>
> >>  Thanks
> >>  Jim
> >>
> >>  >Jim,
> >>  >
> >>  >>  It would be great if there was a way to get rid of the dependency on
> >>  >installing bioperl-ext to get bioperl to work.
> >>  >
> >>  >This is odd. I've done 'make install' many, many times but I've never
> >>  >installed nor used the bioperl-ext library. Ever. Do you think you could
> >>  >have done something unconventional to see the behavior you're seeing?
> >  > >
> >>  >Brian O.
> >  > >
> >  > >-----Original Message-----
> >  > >From: bioperl-l-bounces@portal.open-bio.org
> >  > >[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Jim Nolan
> >  > >Sent: Friday, October 03, 2003 5:06 PM
> >  > >To: bioperl-l@portal.open-bio.org
> >>  >Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
> >>  >
> >>  >I have been unable to install bioperl versions later than 1.2.1 on
> >>  >Mac OS X. The first error I get is during 'make test':
> >>  >"The extension 'Bio::SeqIO::staden::read' is not properly
> >>installed in path:
> >>  >    '/Library/Perl'
> >>  >If this is a CPAN/distributed module, you may need to reinstall it on your
> >>  >system.
> >>  >To allow Inline to compile the module in a temporary cache, simply remove
> >>  >the
> >>  >Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.
> >>  >   at t/FootPrinter.t line 0"
> >>  >and numerous other tests.
> >>  >
> >>  >So I attempted to install bioperl-ext, which meant instaling the
> >>  >Staden io_lib, though I don't use Staden. This had the difficulty of
> >>  >errors caused by the locations of os.h and config.h
> >>  >(http://portal.open-bio.org/mailman/htdig/bioperl-l/2003-June/012472.html).
> >>  >I proceeded with the bioperl-ext install, using the directions at
> >>  >http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html#bioperlxs
> >>  >(which worked great until recently) I did the -fPIC edit, I did the
> >>  >ranlib, but on make test for bioper-ext, I get:
> >>  >/usr/bin/perl -I/System/Library/Perl/darwin -I/System/Library/Perl
> >>  >/System/Library/Perl/ExtUtils/xsubpp  -typemap
> >>  >/System/Library/Perl/ExtUtils/typemap  read.xs > read.xsc && mv
> >>  >read.xsc read.c
> >>  >cc -c -I/Users/jnolan/Desktop/download/bioperl-ext/Bio/SeqIO/staden
> >>  >-I/usr/local/include/io_lib -g -pipe -pipe -fno-common
> >>  >-no-cpp-precomp -flat_namespace -DHAS_TELLDIR_PROTOTYPE
> >>  >-fno-strict-aliasing -Os     -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\"
> >>  >-I/System/Library/Perl/darwin/CORE  read.c
> >>  >In file included from /usr/local/include/io_lib/os.h:4,
> >>  >                   from /usr/local/include/io_lib/Read.h:43,
> >>  >                   from read.xs:5:
> >>  >/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
> >>  >read.c:1:1: warning: this is the location of the previous definition
> >>  >In file included from /usr/local/include/io_lib/translate.h:20,
> >>  >                   from /usr/local/include/io_lib/Read.h:227,
> >>  >                   from read.xs:5:
> >>  >/usr/local/include/io_lib/expFileIO.h:42: parse error before "Exp_entries"
> >>  >/usr/local/include/io_lib/expFileIO.h:42: warning: data definition
> >>  >has no type o"
> >>  >and lots of similar warnings.
> >>  >
> >>  >So it seems like there is still a problem with these libraries,
> >>  >though I copied them where the compiler seems to be looking for them.
> >>  >
> >>  >Can someone point me in the right direction?
> >>  >
> >>  >
> >>  >It would be great if there was a way to get rid of the dependency on
> >>  >installing bioperl-ext to get bioperl to work. Even if the solution
> >>  >for my particular problem is simple, the need to install additional
> >>  >layers of dependencies takes a lot of the fun out of it for us lame
> >>  >biological types ;-)
> >>  >.
> >>  >
> >>  >Thanks.
> >>  >Jim
> >>  >--
> >>  >---------------------------------------------------------
> >>  >Jim Nolan                       email:JNolan@tulane.edu
> >>  >Department of Biochemistry SL43
> >>  >Tulane University Health Sciences Center
> >>  >1430 Tulane Ave.                Phone: (504)-584-2453
> >>  >New Orleans, LA 70112-2699      FAX:   (504)-584-2739
> >>  >http://www.tulane.edu/~biochem/faculty/nolan.htm
> >>  >http://phage.bioc.tulane.edu
> >>  >The requirements said: Windows 2000 or better.
> >>  >So I got a Macintosh.
> >>  >_______________________________________________
> >>  >Bioperl-l mailing list
> >>  >Bioperl-l@portal.open-bio.org
> >>  >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >>
> >
> >--
> >Jason Stajich
> >Duke University
> >jason at cgt.mc.duke.edu
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From lstein at cshl.edu  Mon Oct  6 11:19:12 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Oct  6 12:03:24 2003
Subject: [Bioperl-l] Bio::Graphics sort_order
In-Reply-To: <3F812B71.8AB6C28A@ed.ac.uk>
References: <3F812B71.8AB6C28A@ed.ac.uk>
Message-ID: <200310061119.12141.lstein@cshl.edu>

Hi Richard,

This has now been fixed in both the live and 1.2 branches.  You will have to 
get them via CVS.

As it happens, passing an anonymous subroutine to -sort_order could never work 
in the way that was described in the documentation because the automagic 
variables $a and $b are package variables.  To illustrate, consider:

	package main;
	my $sort_sub = sub {warn "comparing $a to $b\n"; $a cmp $b};
	my @a           = sort $sort_sub qw(one two three four five);
	@a                 = Foo::package_sort($sort_sub);

	package Foo;
	sub package_sort {
		my $sort_sub = shift;
		return sort $sort_sub qw(one two three four five);
	}

The first invocation of sort will work because the anonymous sub and the call 
to sort are both in package main.  The second try will not work because the 
anonymous sub will look in package main for $a and $b, but they are defined 
in package Foo.

To work around this in Bio::Graphics, you must create an anonymous subroutine 
that has the $$ prototype:

	-sort_order => sub ($$) {
		my ($a,$b) = @_; 
		$a->feature->display_name cmp $b->feature->display_name; 
	}

When perl sees a sort sub with the $$ prototype, it passes $a and $b on the 
stack rather than as package variables.  Another issue is that the original 
documentation is wrong about what appears in $a and $b.  They are glyph 
objects, not feature objects.  To get at the feature, you must call their 
feature() method as shown above.

The documentation has now been fixed to explain this behavior correctly.

Lincoln


On Monday 06 October 2003 04:44 am, Richard Adams wrote:
> Hello,
>     I'm trying to sort the display order  of features based on values
> in  one of the features' tags using the syntax
>     described in the Bio::Graphics::Panel :doc.
>         i.e.,
> sort_order =>    sub {(  ($a->each_tag_value('Conserved'))[0]
> <=>($b->each_tag_value('Conserved'))[0]  )};
> But I get the error message
> "Can't call method "each_tag_value" on an undefined value at
> Draw_Output.pm". The code doesn't seem to be
> recognizing that $a and $b should refer to the features. I've tried
> delving into the internal workings of Bio::Graphics::Glyph::Factory
> with little enlightenment, would be grateful for any ideas.
> Cheers
> Richard
>
>
> --
> Dr Richard Adams
> Bioinformatician,
> Psychiatric Genetics Group,
> Medical Genetics,
> Molecular Medicine Centre,
> Western General Hospital,
> Crewe Rd West,
> Edinburgh UK
> EH4 2XU
>
> Tel: 44 131 651 1084
> richard.adams@ed.ac.uk
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From senger at ebi.ac.uk  Mon Oct  6 12:21:24 2003
From: senger at ebi.ac.uk (Martin Senger)
Date: Mon Oct  6 12:20:07 2003
Subject: [Bioperl-l] Re: Bio::Biblio
Message-ID: 

Hi Charles,
   I will reply to you (and to the list) with a detailed script that can
do what you asked for (hopefully) in two days when I am back in my office.
Sorry for the delay.

   Martin

-- 
Martin Senger

EMBL Outstation - Hinxton                Senger@EBI.ac.uk     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger


From ypeng at sfu.ca  Mon Oct  6 13:24:30 2003
From: ypeng at sfu.ca (ypeng@sfu.ca)
Date: Mon Oct  6 13:22:15 2003
Subject: [Bioperl-l] Bio::DB::Query::GenBank - how to specify Keyword
Message-ID: <200310061724.h96HOU1n014721@rm-rstar.sfu.ca>

Hi,

I wish to use this module to get the GI number (or accession number) of
somes genes in human, given the species and protein name (or gene name). But
if I use the protein name as the keyword and species as Organism, "phrase
not found" was returned. I was wondering if I can achieve this, and how to
specify the keyword for this module?

Many thanks in advance.


Fred Peng
----------------------------------------------
Department of Molecular Biology & Biochemsitry
Simon Fraser University
8888 University Drive
Burnaby, British Columbia
Canada V5A 1S6
From difazios at ornl.gov  Mon Oct  6 13:50:34 2003
From: difazios at ornl.gov (Stephen DiFazio)
Date: Mon Oct  6 13:48:21 2003
Subject: [Bioperl-l] GD installation problems for Solaris 9
Message-ID: <5.1.1.5.2.20031006134505.01510d38@email.cind.ornl.gov>

Hello,

I'd like to use Bio::Graphics but can't get GD.pm to work under Solaris 9 
on a Sun Blade 2000.  I'm attempting GD 2.07, though I've tried various 
earlier versions as well with no luck.  I've installed the necessary 
prerequisites:

zlib-1.1.3
libgd-2.0.15
libpng-1.2.5
jpeg-6b

Makefile.PL throws the following warnings for GD.pm (only):

WARNING: CAPI is not a known parameter.
Warning: prerequisite Math::Trig 1 not found.

In fact, Math::Trig 1.01 is installed and functioning on my system.

'make install' gives no errors.

Here's the output I get from 'make test':

PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD: 
ld.so.1: /usr/bin/perl: fatal: relocation error: file 
./blib/arch/auto/GD/GD.so: symbol gdImageCreateFromPng: referenced symbol 
not found at /usr/local/lib/perl5/5.8.0/sun4-solaris/DynaLoader.pm line 229.
  at t/GD.t line 13
Compilation failed in require at t/GD.t line 13.
BEGIN failed--compilation aborted at t/GD.t line 13.
t/GD..........dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-10
         Failed 10/10 tests, 0.00% okay
t/Polyline....Can't load '/usr/local/GD-2.07/blib/arch/auto/GD/GD.so' for 
module GD: ld.so.1: /usr/bin/perl: fatal: relocation error: file 
/usr/local/GD-2.07/blib/arch/auto/GD/GD.so: symbol gdImageCreateFromPng: 
referenced symbol not found at 
/usr/local/lib/perl5/5.8.0/sun4-solaris/DynaLoader.pm line 229.
  at /usr/local/GD-2.07/blib/lib/GD/Polyline.pm line 49
Compilation failed in require at /usr/local/GD-2.07/blib/lib/GD/Polyline.pm 
line 49.
BEGIN failed--compilation aborted at 
/usr/local/GD-2.07/blib/lib/GD/Polyline.pm line 49.
Compilation failed in require at t/Polyline.t line 10.
BEGIN failed--compilation aborted at t/Polyline.t line 10.
t/Polyline....dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 1
         Failed 1/1 tests, 0.00% okay
Failed Test  Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/GD.t        255 65280    10   10 100.00%  1-10
t/Polyline.t  255 65280     1    1 100.00%  1
Failed 2/2 test scripts, 0.00% okay. 11/11 subtests failed, 0.00% okay.
make: *** [test_dynamic] Error 2

thanks in advance for any suggestions you may have.

Steve

Stephen P. DiFazio, Ph.D

Staff Scientist
Oak Ridge National Laboratory
Bldg. 1062-206
P.O. Box 2008
Oak Ridge, TN 37831-6422
(865) 574-7844; fax:(865) 576-8143
difazios@ornl.gov
http://www.esd.ornl.gov/PGG/home.html
Stephen P. DiFazio, Ph.D
Staff Scientist
Oak Ridge National Laboratory
Bldg. 1062-206
P.O. Box 2008
Oak Ridge, TN 37831-6422
(865) 574-7844; fax:(865) 576-8143
difazios@ornl.gov
http://www.esd.ornl.gov/PGG/home.html

From fsanchez at cifn.unam.mx  Mon Oct  6 14:30:17 2003
From: fsanchez at cifn.unam.mx (=?ISO-8859-1?Q?Fabiola_S=E1nchez?=)
Date: Mon Oct  6 14:18:17 2003
Subject: [Bioperl-l] How can i get lines without tag, next to organism
Message-ID: <3F81B4B9.3030909@cifn.unam.mx>

Hello!
I'm reading  files in genbank format
i want to parser the lines below  or next to organism, but these don't 
have tag
how can i get this
i can get organism but  i can't get the lines next to organism
for example:

ORGANISM  Pseudospirillum japonicum
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.
I need to get: 
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.

Thank you.

Fabi



LOCUS       AB006766                1459 bp    DNA     linear   BCT 
13-FEB-1999
DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, partial sequence,
            strain:IFO19191.
ACCESSION   AB006766
VERSION     AB006766.1  GI:4049363
KEYWORDS    16S ribosomal RNA.
SOURCE      Pseudospirillum japonicum
  ORGANISM  Pseudospirillum japonicum
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.
REFERENCE   1  (sites)
  AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., Okuzumi,M. and
            Fujii,T.
  TITLE     Marinospirillum gen. nov., with descriptions of Marinospirillum
            megaterium sp. nov., isolated from kusaya gravy, and transfer of
            Oceanospirillum minutulum to Marinospirillum minutulum comb. nov
  JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
  MEDLINE   99045875
   PUBMED   9828435
REFERENCE   2  (bases 1 to 1459)
  AUTHORS   Satomi,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch 
Institute
            of Fisheries Science, Food Processing and Preservation Division;
            Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 236, Japan
            (E-mail:msatomi@nrifs.affrc.go.jp, Tel:81-45-788-7670,
            Fax:81-45-788-7670)
FEATURES             Location/Qualifiers
     source          1..1459
                     /organism="Pseudospirillum japonicum"
                     /mol_type="genomic DNA"
                     /strain="ATCC19191"
                     /db_xref="taxon:64971"
     rRNA            <1..>1459
                     /product="16S ribosomal RNA"
BASE COUNT      368 a    326 c    462 g    302 t      1 others
ORIGIN     
        1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc ggcagcgggg agtagcttgc
       61 tactttgccg gcgagcggcg gacgggtgag taacgcatag gaatctgccc agtagagggg
      121 gatagccagg ggaaactctg attaataccg catacgccct acgggggaaa aggggctttt
      181 agctcctgct attggatgag cctatgtcgg attagctagt tggtagggta aaggcctacc
      241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc acactgggac tgagacacgg
      301 cccagactcc tacgggaggc agcagtgggg aatattgcac aatgggggga accctgatgc
      361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa gcactttcag caaggaggaa
      421 ggccgtatgc ttaataggca tgcggattga cgttacttgc agaagaagca ccggctaact
      481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt aatcggaatt actgggcgta
      541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc ctgggctcaa cctaggacgt
      601 gcacctgata ctgcttatct agagtaaggt agagggtagt agaatttcct gtgtagcggt
      661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc ggctacctgg actattactg
      721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga taccctggta gtccacgctg
      781 taaacgatgt cgactagccg ttgccgacct tgagttggga gtggcgcagc taacgcgata
      841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc aaatgaattg acgggggccc
      901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc gaagaacctt acctactctt
      961 gacatccaga gaactttcca gagatggata ggtgccttcg ggaactctga gacaggtgct
     1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta agtcccgtaa cgagcgcaac
     1081 ccttatcctt atttgccagc gggttatgcc gggaacttta aggaaactgc cggtgacaaa
     1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct tacgagtagg gctacacacg
     1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg tggagctaat ctcagaaaac
     1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg aagtcggaat cgctagtaat
     1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt gtacacaccg cccgtcacac
     1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn aagggggacg attaccacgg
     1441 tggggttcat gactggggt
//

From jason at cgt.duhs.duke.edu  Mon Oct  6 14:42:41 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Mon Oct  6 14:41:13 2003
Subject: [Bioperl-l] How can i get lines without tag, next to organism
In-Reply-To: <3F81B4B9.3030909@cifn.unam.mx>
References: <3F81B4B9.3030909@cifn.unam.mx>
Message-ID: 

See docs for Bio::Species
 my $species = $seq->species;
 my @classification = $species->classification;

-jason
On Mon, 6 Oct 2003, [ISO-8859-1] Fabiola S?nchez wrote:

> Hello!
> I'm reading  files in genbank format
> i want to parser the lines below  or next to organism, but these don't
> have tag
> how can i get this
> i can get organism but  i can't get the lines next to organism
> for example:
>
> ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria;
> Oceanospirillales;
>             Pseudospirillum.
> I need to get:
>             Bacteria; Proteobacteria; Gammaproteobacteria;
> Oceanospirillales;
>             Pseudospirillum.
>
> Thank you.
>
> Fabi
>
>
>
> LOCUS       AB006766                1459 bp    DNA     linear   BCT
> 13-FEB-1999
> DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, partial sequence,
>             strain:IFO19191.
> ACCESSION   AB006766
> VERSION     AB006766.1  GI:4049363
> KEYWORDS    16S ribosomal RNA.
> SOURCE      Pseudospirillum japonicum
>   ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria;
> Oceanospirillales;
>             Pseudospirillum.
> REFERENCE   1  (sites)
>   AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., Okuzumi,M. and
>             Fujii,T.
>   TITLE     Marinospirillum gen. nov., with descriptions of Marinospirillum
>             megaterium sp. nov., isolated from kusaya gravy, and transfer of
>             Oceanospirillum minutulum to Marinospirillum minutulum comb. nov
>   JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
>   MEDLINE   99045875
>    PUBMED   9828435
> REFERENCE   2  (bases 1 to 1459)
>   AUTHORS   Satomi,M.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch
> Institute
>             of Fisheries Science, Food Processing and Preservation Division;
>             Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 236, Japan
>             (E-mail:msatomi@nrifs.affrc.go.jp, Tel:81-45-788-7670,
>             Fax:81-45-788-7670)
> FEATURES             Location/Qualifiers
>      source          1..1459
>                      /organism="Pseudospirillum japonicum"
>                      /mol_type="genomic DNA"
>                      /strain="ATCC19191"
>                      /db_xref="taxon:64971"
>      rRNA            <1..>1459
>                      /product="16S ribosomal RNA"
> BASE COUNT      368 a    326 c    462 g    302 t      1 others
> ORIGIN
>         1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc ggcagcgggg agtagcttgc
>        61 tactttgccg gcgagcggcg gacgggtgag taacgcatag gaatctgccc agtagagggg
>       121 gatagccagg ggaaactctg attaataccg catacgccct acgggggaaa aggggctttt
>       181 agctcctgct attggatgag cctatgtcgg attagctagt tggtagggta aaggcctacc
>       241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc acactgggac tgagacacgg
>       301 cccagactcc tacgggaggc agcagtgggg aatattgcac aatgggggga accctgatgc
>       361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa gcactttcag caaggaggaa
>       421 ggccgtatgc ttaataggca tgcggattga cgttacttgc agaagaagca ccggctaact
>       481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt aatcggaatt actgggcgta
>       541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc ctgggctcaa cctaggacgt
>       601 gcacctgata ctgcttatct agagtaaggt agagggtagt agaatttcct gtgtagcggt
>       661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc ggctacctgg actattactg
>       721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga taccctggta gtccacgctg
>       781 taaacgatgt cgactagccg ttgccgacct tgagttggga gtggcgcagc taacgcgata
>       841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc aaatgaattg acgggggccc
>       901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc gaagaacctt acctactctt
>       961 gacatccaga gaactttcca gagatggata ggtgccttcg ggaactctga gacaggtgct
>      1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta agtcccgtaa cgagcgcaac
>      1081 ccttatcctt atttgccagc gggttatgcc gggaacttta aggaaactgc cggtgacaaa
>      1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct tacgagtagg gctacacacg
>      1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg tggagctaat ctcagaaaac
>      1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg aagtcggaat cgctagtaat
>      1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt gtacacaccg cccgtcacac
>      1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn aagggggacg attaccacgg
>      1441 tggggttcat gactggggt
> //
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From heikki at nildram.co.uk  Mon Oct  6 14:47:57 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Mon Oct  6 14:49:03 2003
Subject: [Bioperl-l] How can i get lines without tag, next to organism
In-Reply-To: <3F81B4B9.3030909@cifn.unam.mx>
References: <3F81B4B9.3030909@cifn.unam.mx>
Message-ID: <1065466076.2475.8.camel@localhost>

Fabiola,

Organism information is put into a Bio::Species object which can be
accessed by $seq->species().

$seq->species->classification() gives you the whole parsed taxomomy
hierarchy from species upwards in an array.

	-Heikki


On Mon, 2003-10-06 at 19:30, Fabiola S?nchez wrote:
> Hello!
> I'm reading  files in genbank format
> i want to parser the lines below  or next to organism, but these don't 
> have tag
> how can i get this
> i can get organism but  i can't get the lines next to organism
> for example:
> 
> ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> I need to get: 
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> 
> Thank you.
> 
> Fabi
> 
> 
> 
> LOCUS       AB006766                1459 bp    DNA     linear   BCT 
> 13-FEB-1999
> DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, partial sequence,
>             strain:IFO19191.
> ACCESSION   AB006766
> VERSION     AB006766.1  GI:4049363
> KEYWORDS    16S ribosomal RNA.
> SOURCE      Pseudospirillum japonicum
>   ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> REFERENCE   1  (sites)
>   AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., Okuzumi,M. and
>             Fujii,T.
>   TITLE     Marinospirillum gen. nov., with descriptions of Marinospirillum
>             megaterium sp. nov., isolated from kusaya gravy, and transfer of
>             Oceanospirillum minutulum to Marinospirillum minutulum comb. nov
>   JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
>   MEDLINE   99045875
>    PUBMED   9828435
> REFERENCE   2  (bases 1 to 1459)
>   AUTHORS   Satomi,M.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch 
> Institute
>             of Fisheries Science, Food Processing and Preservation Division;
>             Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 236, Japan
>             (E-mail:msatomi@nrifs.affrc.go.jp, Tel:81-45-788-7670,
>             Fax:81-45-788-7670)
> FEATURES             Location/Qualifiers
>      source          1..1459
>                      /organism="Pseudospirillum japonicum"
>                      /mol_type="genomic DNA"
>                      /strain="ATCC19191"
>                      /db_xref="taxon:64971"
>      rRNA            <1..>1459
>                      /product="16S ribosomal RNA"
> BASE COUNT      368 a    326 c    462 g    302 t      1 others
> ORIGIN     
>         1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc ggcagcgggg agtagcttgc
>        61 tactttgccg gcgagcggcg gacgggtgag taacgcatag gaatctgccc agtagagggg
>       121 gatagccagg ggaaactctg attaataccg catacgccct acgggggaaa aggggctttt
>       181 agctcctgct attggatgag cctatgtcgg attagctagt tggtagggta aaggcctacc
>       241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc acactgggac tgagacacgg
>       301 cccagactcc tacgggaggc agcagtgggg aatattgcac aatgggggga accctgatgc
>       361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa gcactttcag caaggaggaa
>       421 ggccgtatgc ttaataggca tgcggattga cgttacttgc agaagaagca ccggctaact
>       481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt aatcggaatt actgggcgta
>       541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc ctgggctcaa cctaggacgt
>       601 gcacctgata ctgcttatct agagtaaggt agagggtagt agaatttcct gtgtagcggt
>       661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc ggctacctgg actattactg
>       721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga taccctggta gtccacgctg
>       781 taaacgatgt cgactagccg ttgccgacct tgagttggga gtggcgcagc taacgcgata
>       841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc aaatgaattg acgggggccc
>       901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc gaagaacctt acctactctt
>       961 gacatccaga gaactttcca gagatggata ggtgccttcg ggaactctga gacaggtgct
>      1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta agtcccgtaa cgagcgcaac
>      1081 ccttatcctt atttgccagc gggttatgcc gggaacttta aggaaactgc cggtgacaaa
>      1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct tacgagtagg gctacacacg
>      1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg tggagctaat ctcagaaaac
>      1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg aagtcggaat cgctagtaat
>      1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt gtacacaccg cccgtcacac
>      1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn aagggggacg attaccacgg
>      1441 tggggttcat gactggggt
> //
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From cain at cshl.edu  Mon Oct  6 16:06:40 2003
From: cain at cshl.edu (Scott Cain)
Date: Mon Oct  6 16:04:18 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
Message-ID: 

Hello all,

First, thanks to the kind soul who provided the 1.2.3 version of bioperl
as a ppm.  Unfortunately, I can't seem to get it installed due to a failed
dependency.  While using AS Perl 5.8, it seems that none of the
repositories know what 'libxml-perl' is, and since it is listed as a
prerequisite in the ppd file, installation cannot continue.  Is there
somewhere special to get that from?  At the moment, I am only searching
the ActiveState and bioperl repositories.

As a side note, it seems like a bad idea to force the installation of
every prereq module for bioperl.  In my case, I have no need of
libxml-perl, but can't install bioperl for a lack of it.

Thanks,
Scott

----------------------------------------------------------------------
Scott Cain, Ph. D.				 	 cain@cshl.org
GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
----------------------------------------------------------------------


From vesko_baev at abv.bg  Mon Oct  6 19:23:50 2003
From: vesko_baev at abv.bg (Vesko Baev)
Date: Mon Oct  6 19:21:32 2003
Subject: [Bioperl-l] protein localiz. & signal peptide
Message-ID: <699462842.1065482630568.JavaMail.nobody@app1.ni.bg>

Hi,
Are there any modules for prediction of protein localization and signal peptides (excluding SigCleave)?

Thanks!
Vesko

-----------------------------------------------------------------
http://club.abv.bg/jsp/abvCard.jsp - ???? ??? - ??????? ? ?????? ????? ? ???? !
From lstein at cshl.edu  Mon Oct  6 18:58:26 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Oct  6 19:48:17 2003
Subject: [Bioperl-l] GD installation problems for Solaris 9
In-Reply-To: <5.1.1.5.2.20031006134505.01510d38@email.cind.ornl.gov>
References: <5.1.1.5.2.20031006134505.01510d38@email.cind.ornl.gov>
Message-ID: <200310061858.26935.lstein@cshl.edu>

Hi,

The CAPI warning comes from using a newer version of perl.  I will issue a new 
version of GD that avoids this warning.  The Math::Trig errors warning 
because Jarkko forgot to return a 1; at the bottom of Math::Trig in the 
latest version, and hence Perl things it didn't load properly.  You will have 
to wait for version 1.02 of Math::Trig or add a 1; to the Trig.pm file 
yourself.

To track down the runtime errors, make sure that libgd passed its regression 
tests when you installed it (there are a number of example applications that 
it compiles; make sure they run).  Then make sure that it is installed in a 
library that is included in your standard library path.  Finally, make sure 
that there is not an older version of libgd lurking somewhere.

Lincoln



On Monday 06 October 2003 01:50 pm, Stephen DiFazio wrote:
> Hello,
>
> I'd like to use Bio::Graphics but can't get GD.pm to work under Solaris 9
> on a Sun Blade 2000.  I'm attempting GD 2.07, though I've tried various
> earlier versions as well with no luck.  I've installed the necessary
> prerequisites:
>
> zlib-1.1.3
> libgd-2.0.15
> libpng-1.2.5
> jpeg-6b
>
> Makefile.PL throws the following warnings for GD.pm (only):
>
> WARNING: CAPI is not a known parameter.
> Warning: prerequisite Math::Trig 1 not found.
>
> In fact, Math::Trig 1.01 is installed and functioning on my system.
>
> 'make install' gives no errors.
>
> Here's the output I get from 'make test':
>
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD:
> ld.so.1: /usr/bin/perl: fatal: relocation error: file
> ./blib/arch/auto/GD/GD.so: symbol gdImageCreateFromPng: referenced symbol
> not found at /usr/local/lib/perl5/5.8.0/sun4-solaris/DynaLoader.pm line
> 229. at t/GD.t line 13
> Compilation failed in require at t/GD.t line 13.
> BEGIN failed--compilation aborted at t/GD.t line 13.
> t/GD..........dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-10
>          Failed 10/10 tests, 0.00% okay
> t/Polyline....Can't load '/usr/local/GD-2.07/blib/arch/auto/GD/GD.so' for
> module GD: ld.so.1: /usr/bin/perl: fatal: relocation error: file
> /usr/local/GD-2.07/blib/arch/auto/GD/GD.so: symbol gdImageCreateFromPng:
> referenced symbol not found at
> /usr/local/lib/perl5/5.8.0/sun4-solaris/DynaLoader.pm line 229.
>   at /usr/local/GD-2.07/blib/lib/GD/Polyline.pm line 49
> Compilation failed in require at /usr/local/GD-2.07/blib/lib/GD/Polyline.pm
> line 49.
> BEGIN failed--compilation aborted at
> /usr/local/GD-2.07/blib/lib/GD/Polyline.pm line 49.
> Compilation failed in require at t/Polyline.t line 10.
> BEGIN failed--compilation aborted at t/Polyline.t line 10.
> t/Polyline....dubious
>          Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED test 1
>          Failed 1/1 tests, 0.00% okay
> Failed Test  Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------------
>---- t/GD.t        255 65280    10   10 100.00%  1-10
> t/Polyline.t  255 65280     1    1 100.00%  1
> Failed 2/2 test scripts, 0.00% okay. 11/11 subtests failed, 0.00% okay.
> make: *** [test_dynamic] Error 2
>
> thanks in advance for any suggestions you may have.
>
> Steve
>
> Stephen P. DiFazio, Ph.D
>
> Staff Scientist
> Oak Ridge National Laboratory
> Bldg. 1062-206
> P.O. Box 2008
> Oak Ridge, TN 37831-6422
> (865) 574-7844; fax:(865) 576-8143
> difazios@ornl.gov
> http://www.esd.ornl.gov/PGG/home.html
> Stephen P. DiFazio, Ph.D
> Staff Scientist
> Oak Ridge National Laboratory
> Bldg. 1062-206
> P.O. Box 2008
> Oak Ridge, TN 37831-6422
> (865) 574-7844; fax:(865) 576-8143
> difazios@ornl.gov
> http://www.esd.ornl.gov/PGG/home.html
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From Richard.Holland at agresearch.co.nz  Mon Oct  6 20:58:11 2003
From: Richard.Holland at agresearch.co.nz (Holland, Richard)
Date: Mon Oct  6 20:56:00 2003
Subject: [Bioperl-l] RE: [Pubmednew] Problem with esearch.fcgi
Message-ID: 

Hi,

Thanks for your answer regarding non-accessible accessions via
esearch.fcgi, but it doesn't quite solve my problem.

I am accessing GenBank programmatically via a set of modules called
BioPerl (http://www.bioperl.org/), specifically Bio::DB::GenBank. These
access the database on my behalf via the esearch.fcgi script. They
depend on the script returning the plain GenBank file without any HTML
markup.

The URL you sent me in response to my original question marks up the
response in HTML, and doesn't return just the plain GenBank file on its
own. 

My question was why are the two scripts unable to agree on the existence
of a particular accession (XM_055766)? Surely they are accessing the
same database under the hood? Are there any plans to make esearch.fcgi
recognise these more recent accessions?

I am copying this email to the BioPerl mailing list in case somebody
there can help out too.

BioPerl people - what are the alternatives? I am having the same
problems with the EBI servers, dbfetch, and Bio::DB::EMBL, which also
does not believe that the accession XM_055766 exists (although I can see
it quite clearly using Entrez at the NCBI).

cheers,
Richard

---
Richard Holland
Bioinformatics Database Developer
ITS, Agresearch Invermay x3279



-----Original Message-----
From: Monica Romiti [mailto:romiti@ncbi.nlm.nih.gov] 
Sent: Tuesday, 7 October 2003 1:42 p.m.
To: Holland, Richard
Cc: romiti@ncbi.nlm.nih.gov
Subject: FW: [Pubmednew] Problem with esearch.fcgi


Dear Colleague,

Use:


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&t
erm=XM_0
55766[accn]&doptcmdl=GenBank


Best regards,

Monica at NCBI
-----Original Message-----

From:  custhelp@mail.nlm.nih.gov
Sent:  10/4/2003 04:24:45 PM
To:  Richard.Holland@agresearch.co.nz
Subject:  [Pubmednew] Problem with esearch.fcgi

Richard Holland:

Your email has been forwarded to the National Center for Biotechnology 
Information (info@ncbi.nlm.nih.gov)

Ellen M. Layman
National Library of Medicine


-----Original Message-----

From:  Richard.Holland@agresearch.co.nz
Sent:  10/1/2003 05:03:16 PM
To:  
Subject:  [Pubmednew] Problem with esearch.fcgi

Hi,

I can successfully search Entrez using the web-based forms for the
following term:

XM_055766

However, the same search via the eutils tool esearch.fcgi
(?db=nucleotide&term=XM_055766) returns no results. What's going on?

cheers,
Richard



=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities to
which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================

------------- End Forwarded Message -------------


------------- End Forwarded Message -------------


Best regards,

Monica L. Romiti
NCBI User Services

=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================

From btclimd at nus.edu.sg  Mon Oct  6 22:43:05 2003
From: btclimd at nus.edu.sg (Desmond Lim)
Date: Mon Oct  6 22:40:47 2003
Subject: [Bioperl-l] seqIO
Message-ID: <653C572D8746D341AAA25C494CDFB9E338001C@MBXSRV05.stf.nus.edu.sg>

Hi,

I'm trying to make an array into a SeqIO object

my $seq_in = Bio::SeqIO->new('-ph' => @arr, '-format' => 'fasta');

but it doesn't work. I have gone through the documentation for the SeqIO module but have no idea how to 'read' the sequences directly from an array.

I need to do this because there is a sequence manipulation that happens to the file that is opened in the beginning.

I have a work around of creating a file with the array and then opening it using -file but I think reading from an array should be possible.

Thanks.

From btclimd at nus.edu.sg  Mon Oct  6 22:43:48 2003
From: btclimd at nus.edu.sg (Desmond Lim)
Date: Mon Oct  6 22:41:29 2003
Subject: [Bioperl-l] seqIO
Message-ID: <653C572D8746D341AAA25C494CDFB9E338001D@MBXSRV05.stf.nus.edu.sg>

Hi,

I'm trying to make an array into a SeqIO object

my $seq_in = Bio::SeqIO->new('-ph' => @arr, '-format' => 'fasta');

but it doesn't work. I have gone through the documentation for the SeqIO module but have no idea how to 'read' the sequences directly from an array.

I need to do this because there is a sequence manipulation that happens to the file that is opened in the beginning.

I have a work around of creating a file with the array and then opening it using -file but I think reading from an array should be possible.

Thanks.

From hlapp at gnf.org  Tue Oct  7 00:31:06 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Oct  7 00:28:46 2003
Subject: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E338001C@MBXSRV05.stf.nus.edu.sg>
Message-ID: 

On 10/6/03 7:43 PM, "Desmond Lim"  wrote:

> Hi,
> 
> I'm trying to make an array into a SeqIO object
> 
> my $seq_in = Bio::SeqIO->new('-ph' => @arr, '-format' => 'fasta');
> 

What made you think it would accept a -ph parameter? Besides, if there was
one you'd have to provide an array reference.

> but it doesn't work. I have gone through the documentation for the SeqIO
> module but have no idea how to 'read' the sequences directly from an array.
> 
> I need to do this because there is a sequence manipulation that happens to the
> file that is opened in the beginning.
> 

I'm not sure I understand your use case. Could you try to elaborate a bit.

If what you're attempting to do is apply post-processing to the sequences
coming off of a sequence file through a SeqIO module and have the result
appear as a SeqIO-compatible stream to pass on, Bio::Seq::BaseSeqProcessor
may be for you (that's what it was designed for).

    -hilmar


> I have a work around of creating a file with the array and then opening it
> using -file but I think reading from an array should be possible.
> 
> Thanks.
> 
> _______________________________________________
> 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 btclimd at nus.edu.sg  Tue Oct  7 00:45:18 2003
From: btclimd at nus.edu.sg (Desmond Lim)
Date: Tue Oct  7 00:42:59 2003
Subject: [Bioperl-l] seqIO
Message-ID: <653C572D8746D341AAA25C494CDFB9E338001E@MBXSRV05.stf.nus.edu.sg>

> What made you think it would accept a -ph parameter? Besides, if
> there was
> one you'd have to provide an array reference.

I didn't think it would work but I wanted to try it out.

What I'm trying to do is get SeqIO to accept an array of sequences and not a file.

Desmond

From laurichj at bioinfo.ucr.edu  Tue Oct  7 01:25:01 2003
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Tue Oct  7 01:22:39 2003
Subject: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E338001E@MBXSRV05.stf.nus.edu.sg>
References: <653C572D8746D341AAA25C494CDFB9E338001E@MBXSRV05.stf.nus.edu.sg>
Message-ID: <20031007052501.GA26215@bioinfo.ucr.edu>

On Tue 10/07/03 12:45, Desmond Lim wrote:
> I didn't think it would work but I wanted to try it out.
> 
> What I'm trying to do is get SeqIO to accept an array of sequences and
> not a file.

At the risk of sounding stupid, why? If you already have the sequences
in memory why do you want to read them in twice?

If the array is something like:
@a = ;

then join them and use IO::String (or IO::Scalar).

-- 

----------------------------
| Josh Lauricha            |
| laurichj@bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|
From heikki at ebi.ac.uk  Tue Oct  7 05:23:15 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Tue Oct  7 05:21:07 2003
Subject: [Bioperl-l] RE: [Pubmednew] Problem with esearch.fcgi
In-Reply-To: 
References: 
Message-ID: <1065518595.7939.14.camel@localhost>

Richard,

If you look carefully at the entry XM_055766 in the Entrez server, you
notice this:

COMMENT     MODEL REFSEQ:  This record is predicted by automated  
            computational analysis. This record is derived from an 
            annotated genomic sequence (NT_024812) using gene 
            prediction method: BLAST, supported by mRNA and EST 
            evidence.

It is not a GenBank entry although it looks like one and NCBI Entrez
claims it is one but in fact it is from the RefSeq database. 

The XP_* entries can not be retrieved using Bio::DB::RefSeq, either,
because it fetches entries from EBI copy of the datebase which doeas not
contain all the latest sequence subclasses (only NC_*, NT_*, NM_*,
NP_*). I'll try to get that updated.

	-Heikki



On Tue, 2003-10-07 at 14:58, Holland, Richard wrote:
> Hi,
> 
> Thanks for your answer regarding non-accessible accessions via
> esearch.fcgi, but it doesn't quite solve my problem.
> 
> I am accessing GenBank programmatically via a set of modules called
> BioPerl (http://www.bioperl.org/), specifically Bio::DB::GenBank. These
> access the database on my behalf via the esearch.fcgi script. They
> depend on the script returning the plain GenBank file without any HTML
> markup.
> 
> The URL you sent me in response to my original question marks up the
> response in HTML, and doesn't return just the plain GenBank file on its
> own. 
> 
> My question was why are the two scripts unable to agree on the existence
> of a particular accession (XM_055766)? Surely they are accessing the
> same database under the hood? Are there any plans to make esearch.fcgi
> recognise these more recent accessions?
> 
> I am copying this email to the BioPerl mailing list in case somebody
> there can help out too.
> 
> BioPerl people - what are the alternatives? I am having the same
> problems with the EBI servers, dbfetch, and Bio::DB::EMBL, which also
> does not believe that the accession XM_055766 exists (although I can see
> it quite clearly using Entrez at the NCBI).
> 
> cheers,
> Richard
> 
> ---
> Richard Holland
> Bioinformatics Database Developer
> ITS, Agresearch Invermay x3279
> 
> 
> 
> -----Original Message-----
> From: Monica Romiti [mailto:romiti@ncbi.nlm.nih.gov] 
> Sent: Tuesday, 7 October 2003 1:42 p.m.
> To: Holland, Richard
> Cc: romiti@ncbi.nlm.nih.gov
> Subject: FW: [Pubmednew] Problem with esearch.fcgi
> 
> 
> Dear Colleague,
> 
> Use:
> 
> 
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&t
> erm=XM_0
> 55766[accn]&doptcmdl=GenBank
> 
> 
> Best regards,
> 
> Monica at NCBI
> -----Original Message-----
> 
> From:  custhelp@mail.nlm.nih.gov
> Sent:  10/4/2003 04:24:45 PM
> To:  Richard.Holland@agresearch.co.nz
> Subject:  [Pubmednew] Problem with esearch.fcgi
> 
> Richard Holland:
> 
> Your email has been forwarded to the National Center for Biotechnology 
> Information (info@ncbi.nlm.nih.gov)
> 
> Ellen M. Layman
> National Library of Medicine
> 
> 
> -----Original Message-----
> 
> From:  Richard.Holland@agresearch.co.nz
> Sent:  10/1/2003 05:03:16 PM
> To:  
> Subject:  [Pubmednew] Problem with esearch.fcgi
> 
> Hi,
> 
> I can successfully search Entrez using the web-based forms for the
> following term:
> 
> XM_055766
> 
> However, the same search via the eutils tool esearch.fcgi
> (?db=nucleotide&term=XM_055766) returns no results. What's going on?
> 
> cheers,
> Richard
> 
> 
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities to
> which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> ------------- End Forwarded Message -------------
> 
> 
> ------------- End Forwarded Message -------------
> 
> 
> Best regards,
> 
> Monica L. Romiti
> NCBI User Services
> 
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From Richard.Adams at ed.ac.uk  Tue Oct  7 07:19:33 2003
From: Richard.Adams at ed.ac.uk (Richard Adams)
Date: Tue Oct  7 07:17:11 2003
Subject: [Bioperl-l] Homologene parsing
Message-ID: <3F82A145.E9782924@ed.ac.uk>

Hello,
    I'm writing some code to access data from NCBI's homologene dataset
of reciprocal best blast matches
 (see http://www.ncbi.nlm.nih.gov/HomoloGene/details.shtml) and am
thinking of Bioperlifying it.
At the moment I just have code for trawling through the file,  parsing
individual entries and accessing their attributes
     e.g.,

            my @orthologueget_orthologous_accessions ()
             my @locus_ids     =get_orthologous_locusIds()
             my $cluster_size = orthologue_count()
           my $boolean =  has_orthologue('mouse') etc

    but to be useful for accessing clusters quickly I guess it needs
some sort of indexing - there are about 21 000 entries. I don't know
much about databases /indexing etc but would inheriting from
Bio::Index::Abstract be the way to go,, in a similar way to swissPfam?
Ideally one would get a db handle and use that to retrieve a particular
entry indexed by any of the identifiers in the cluster

    e.g., my $db= new Bio::DB::Homologene
                    $db->fetch_cluster_by_name('UBE2B'); access by gene
name
                    $db->fetch_cluster_by_id('NM_005197');

    of by taxon id
                  my @human_clusters =   $db->fetch_all_by_taxon(9606);

Any broad pointers in the right direction concerning indexing would be
greatly appreciated, I am quite happy to do all the coding
but want to make sure it's useful at the end of the day.

Cheers

Richard





--
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams@ed.ac.uk



From brian_osborne at cognia.com  Tue Oct  7 07:57:07 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Tue Oct  7 07:59:35 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
In-Reply-To: 
Message-ID: 

Scott,

> As a side note, it seems like a bad idea to force the installation of
every prereq module for bioperl

Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
shell, for example, you can do "force install". There is also a "force
install" option in ActiveState, something like setting force-install to 1?
Please check the ActiveState documentation and tell me if I'm wrong.

A few months ago I took a look at the "required modules" list in Bioperl and
found that many of them were not supplied by ActiveState, just as you're
finding.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Scott Cain
Sent: Monday, October 06, 2003 4:07 PM
To: bioperl-l@bioperl.org
Cc: cain@cshl.org
Subject: [Bioperl-l] bp 1.2.3 ppm install fails

Hello all,

First, thanks to the kind soul who provided the 1.2.3 version of bioperl
as a ppm.  Unfortunately, I can't seem to get it installed due to a failed
dependency.  While using AS Perl 5.8, it seems that none of the
repositories know what 'libxml-perl' is, and since it is listed as a
prerequisite in the ppd file, installation cannot continue.  Is there
somewhere special to get that from?  At the moment, I am only searching
the ActiveState and bioperl repositories.

As a side note, it seems like a bad idea to force the installation of
every prereq module for bioperl.  In my case, I have no need of
libxml-perl, but can't install bioperl for a lack of it.

Thanks,
Scott

----------------------------------------------------------------------
Scott Cain, Ph. D.                                       cain@cshl.org
GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
----------------------------------------------------------------------


_______________________________________________
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  Tue Oct  7 08:19:13 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Tue Oct  7 08:21:11 2003
Subject: [Bioperl-l] Bio::Biblio
In-Reply-To: <20031006140504.GA2631@plessy.org>
Message-ID: 

Charles,

Take a look at examples/biblio/biblio_examples.pl, there are some
one-liner's there that you might find useful.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Charles Plessy
Sent: Monday, October 06, 2003 10:05 AM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Bio::Biblio

Hi,

        My goal is to write a quick-and-dirty medline2docbook fliter
for immediate use, using bioperl since it has already a library able
to query medline.

        However, I don't know how to quickly extract basic fields,
like author or journal, to use them in this kind of output system:

print << DOCBOOK
(...)

   
    
     $object->Author_surname
     $object->Author_firstname
    
(...)
DOCBOOK

Can anybody point me to the correct object and its construction method?

--
Charles
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Bioperl-l@portal.open-bio.org
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From fsanchez at cifn.unam.mx  Mon Oct  6 14:25:26 2003
From: fsanchez at cifn.unam.mx (=?ISO-8859-1?Q?Fabiola_S=E1nchez?=)
Date: Tue Oct  7 08:32:12 2003
Subject: [Bioperl-l] How can i get ...
Message-ID: <3F81B396.3010804@cifn.unam.mx>

Hello!
I'm reading  files in genbank format
i want to parser the lines below  or next to organism, but these don't 
have tag
how can i get this
i can get organism but  i can't get the lines next to organism
for example:

ORGANISM  Pseudospirillum japonicum
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.
I need to get: 
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.
but i can't

Thank you.

Fabi



LOCUS       AB006766                1459 bp    DNA     linear   BCT 
13-FEB-1999
DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, partial sequence,
            strain:IFO19191.
ACCESSION   AB006766
VERSION     AB006766.1  GI:4049363
KEYWORDS    16S ribosomal RNA.
SOURCE      Pseudospirillum japonicum
  ORGANISM  Pseudospirillum japonicum
            Bacteria; Proteobacteria; Gammaproteobacteria; 
Oceanospirillales;
            Pseudospirillum.
REFERENCE   1  (sites)
  AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., Okuzumi,M. and
            Fujii,T.
  TITLE     Marinospirillum gen. nov., with descriptions of Marinospirillum
            megaterium sp. nov., isolated from kusaya gravy, and transfer of
            Oceanospirillum minutulum to Marinospirillum minutulum comb. nov
  JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
  MEDLINE   99045875
   PUBMED   9828435
REFERENCE   2  (bases 1 to 1459)
  AUTHORS   Satomi,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch 
Institute
            of Fisheries Science, Food Processing and Preservation Division;
            Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 236, Japan
            (E-mail:msatomi@nrifs.affrc.go.jp, Tel:81-45-788-7670,
            Fax:81-45-788-7670)
FEATURES             Location/Qualifiers
     source          1..1459
                     /organism="Pseudospirillum japonicum"
                     /mol_type="genomic DNA"
                     /strain="ATCC19191"
                     /db_xref="taxon:64971"
     rRNA            <1..>1459
                     /product="16S ribosomal RNA"
BASE COUNT      368 a    326 c    462 g    302 t      1 others
ORIGIN     
        1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc ggcagcgggg agtagcttgc
       61 tactttgccg gcgagcggcg gacgggtgag taacgcatag gaatctgccc agtagagggg
      121 gatagccagg ggaaactctg attaataccg catacgccct acgggggaaa aggggctttt
      181 agctcctgct attggatgag cctatgtcgg attagctagt tggtagggta aaggcctacc
      241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc acactgggac tgagacacgg
      301 cccagactcc tacgggaggc agcagtgggg aatattgcac aatgggggga accctgatgc
      361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa gcactttcag caaggaggaa
      421 ggccgtatgc ttaataggca tgcggattga cgttacttgc agaagaagca ccggctaact
      481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt aatcggaatt actgggcgta
      541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc ctgggctcaa cctaggacgt
      601 gcacctgata ctgcttatct agagtaaggt agagggtagt agaatttcct gtgtagcggt
      661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc ggctacctgg actattactg
      721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga taccctggta gtccacgctg
      781 taaacgatgt cgactagccg ttgccgacct tgagttggga gtggcgcagc taacgcgata
      841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc aaatgaattg acgggggccc
      901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc gaagaacctt acctactctt
      961 gacatccaga gaactttcca gagatggata ggtgccttcg ggaactctga gacaggtgct
     1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta agtcccgtaa cgagcgcaac
     1081 ccttatcctt atttgccagc gggttatgcc gggaacttta aggaaactgc cggtgacaaa
     1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct tacgagtagg gctacacacg
     1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg tggagctaat ctcagaaaac
     1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg aagtcggaat cgctagtaat
     1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt gtacacaccg cccgtcacac
     1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn aagggggacg attaccacgg
     1441 tggggttcat gactggggt
//
From walsh at cenix-bioscience.com  Tue Oct  7 07:33:59 2003
From: walsh at cenix-bioscience.com (Andrew Walsh)
Date: Tue Oct  7 08:32:36 2003
Subject: [Bioperl-l] RE: [Pubmednew] Problem with esearch.fcgi
In-Reply-To: <1065518595.7939.14.camel@localhost>
References: 
	<1065518595.7939.14.camel@localhost>
Message-ID: <3F82A4A7.8070205@cenix-bioscience.com>

I seem to be able to retrieve X[MP] sequences using Bioperl version 1.2.2.

Depending on the type of accession I'm dealing with, I use either 
Bio::DB::GenBank or Bio::DB::RefSeq.

The following code retrieves both XM_055766 and XP_055766 (the 
corresponding peptide) from the web:

As a side note (maybe someone with more knowledge of the SeqIO parser 
knows why). The 'KEYWORD' part of the Genbank file does not seem to be 
retrieved properly.
I get this line in the sequence file: 'KEYWORDS    ARRAY(0x8ba8f30).'

# the code...

# $fmt has been set to 'genbank' or 'fasta'
# get $accs, ref to array of accessions

for my $acc (@$accs) {
     my %ext_map = (genbank => 'gbff',
                    fasta   => 'fasta');
     my $file = "$acc.$ext_map{$fmt}";
     my $io   = Bio::SeqIO->new(-file => ">$file", -format => $fmt);
     my $seq;
     eval {
         $seq = get_seq_obj_from_web($acc);
     };
     if ($@) {
         warn "Could not get $acc: $@\n";
     }
     else {
         $io->write_seq($seq);
     }
}

sub get_seq_obj_from_web {
     my ($acc_num) = @_;
     warn "Getting $acc_num from web\n";
     my $ncbi_db = get_web_database_obj($acc_num);
     my $seq;
     eval {
	$seq = $ncbi_db->get_Seq_by_id($acc_num);
     };
     if ($@ || !$seq) {
	cluck "Could not retrieve $acc_num from NCBI: $@";
	return undef;
     }
     else {
         return $seq;
     }
}

sub get_web_database_obj {
     my $acc = shift;
     my $ncbi_db;
     # appears that XM #'s only retrievable from GenBank, not RefSeq.
     if ($acc =~ /^[N]M_/) {
	$ncbi_db = new Bio::DB::RefSeq()

     elsif ($acc =~ /^[NX]P_/) {
	$ncbi_db = new Bio::DB::GenPept()
     }
     else {
	$ncbi_db = new Bio::DB::GenBank()
     }
     my $proxy = 'http://my.proxy.com:3128/';
     $ncbi_db->proxy(['http','ftp'], $proxy);
     return $ncbi_db;
}

Heikki Lehvaslaiho wrote:
> Richard,
> 
> If you look carefully at the entry XM_055766 in the Entrez server, you
> notice this:
> 
> COMMENT     MODEL REFSEQ:  This record is predicted by automated  
>             computational analysis. This record is derived from an 
>             annotated genomic sequence (NT_024812) using gene 
>             prediction method: BLAST, supported by mRNA and EST 
>             evidence.
> 
> It is not a GenBank entry although it looks like one and NCBI Entrez
> claims it is one but in fact it is from the RefSeq database. 
> 
> The XP_* entries can not be retrieved using Bio::DB::RefSeq, either,
> because it fetches entries from EBI copy of the datebase which doeas not
> contain all the latest sequence subclasses (only NC_*, NT_*, NM_*,
> NP_*). I'll try to get that updated.
> 
> 	-Heikki
> 
> 
> 
> On Tue, 2003-10-07 at 14:58, Holland, Richard wrote:
> 
>>Hi,
>>
>>Thanks for your answer regarding non-accessible accessions via
>>esearch.fcgi, but it doesn't quite solve my problem.
>>
>>I am accessing GenBank programmatically via a set of modules called
>>BioPerl (http://www.bioperl.org/), specifically Bio::DB::GenBank. These
>>access the database on my behalf via the esearch.fcgi script. They
>>depend on the script returning the plain GenBank file without any HTML
>>markup.
>>
>>The URL you sent me in response to my original question marks up the
>>response in HTML, and doesn't return just the plain GenBank file on its
>>own. 
>>
>>My question was why are the two scripts unable to agree on the existence
>>of a particular accession (XM_055766)? Surely they are accessing the
>>same database under the hood? Are there any plans to make esearch.fcgi
>>recognise these more recent accessions?
>>
>>I am copying this email to the BioPerl mailing list in case somebody
>>there can help out too.
>>
>>BioPerl people - what are the alternatives? I am having the same
>>problems with the EBI servers, dbfetch, and Bio::DB::EMBL, which also
>>does not believe that the accession XM_055766 exists (although I can see
>>it quite clearly using Entrez at the NCBI).
>>
>>cheers,
>>Richard
>>
>>---
>>Richard Holland
>>Bioinformatics Database Developer
>>ITS, Agresearch Invermay x3279
>>
>>
>>
>>-----Original Message-----
>>From: Monica Romiti [mailto:romiti@ncbi.nlm.nih.gov] 
>>Sent: Tuesday, 7 October 2003 1:42 p.m.
>>To: Holland, Richard
>>Cc: romiti@ncbi.nlm.nih.gov
>>Subject: FW: [Pubmednew] Problem with esearch.fcgi
>>
>>
>>Dear Colleague,
>>
>>Use:
>>
>>
>>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&t
>>erm=XM_0
>>55766[accn]&doptcmdl=GenBank
>>
>>
>>Best regards,
>>
>>Monica at NCBI
>>-----Original Message-----
>>
>>From:  custhelp@mail.nlm.nih.gov
>>Sent:  10/4/2003 04:24:45 PM
>>To:  Richard.Holland@agresearch.co.nz
>>Subject:  [Pubmednew] Problem with esearch.fcgi
>>
>>Richard Holland:
>>
>>Your email has been forwarded to the National Center for Biotechnology 
>>Information (info@ncbi.nlm.nih.gov)
>>
>>Ellen M. Layman
>>National Library of Medicine
>>
>>
>>-----Original Message-----
>>
>>From:  Richard.Holland@agresearch.co.nz
>>Sent:  10/1/2003 05:03:16 PM
>>To:  
>>Subject:  [Pubmednew] Problem with esearch.fcgi
>>
>>Hi,
>>
>>I can successfully search Entrez using the web-based forms for the
>>following term:
>>
>>XM_055766
>>
>>However, the same search via the eutils tool esearch.fcgi
>>(?db=nucleotide&term=XM_055766) returns no results. What's going on?
>>
>>cheers,
>>Richard
>>
>>
>>
>>=======================================================================
>>Attention: The information contained in this message and/or attachments
>>from AgResearch Limited is intended only for the persons or entities to
>>which it is addressed and may contain confidential and/or privileged
>>material. Any review, retransmission, dissemination or other use of, or
>>taking of any action in reliance upon, this information by persons or
>>entities other than the intended recipients is prohibited by AgResearch
>>Limited. If you have received this message in error, please notify the
>>sender immediately.
>>=======================================================================
>>
>>------------- End Forwarded Message -------------
>>
>>
>>------------- End Forwarded Message -------------
>>
>>
>>Best regards,
>>
>>Monica L. Romiti
>>NCBI User Services
>>
>>=======================================================================
>>Attention: The information contained in this message and/or attachments
>>from AgResearch Limited is intended only for the persons or entities
>>to which it is addressed and may contain confidential and/or privileged
>>material. Any review, retransmission, dissemination or other use of, or
>>taking of any action in reliance upon, this information by persons or
>>entities other than the intended recipients is prohibited by AgResearch
>>Limited. If you have received this message in error, please notify the
>>sender immediately.
>>=======================================================================
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l@portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l


-- 
------------------------------------------------------------------
Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Pfotenhauerstr. 108
01307 Dresden, Germany
Tel. +49(351)210-2699
Fax  +49(351)210-1309

public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg
------------------------------------------------------------------


From Marc.Logghe at devgen.com  Tue Oct  7 08:58:42 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Tue Oct  7 08:56:38 2003
Subject: [Bioperl-l] How can i get ...
Message-ID: 

Hi,
it is like Heikki already mentioned, you need the classification() method of Bio::Species.
You get the output 
"Bacteria; Proteobacteria; Gammaproteobacteria; Oceanospirillales; Pseudospirillum"
when you run the code:
my $species = $seq->species;
my @classification = reverse $species->classification;
pop @classification;
print join( '; ', @classification), "\n";

ML
> -----Original Message-----
> From: Fabiola S?nchez [mailto:fsanchez@cifn.unam.mx]
> Sent: Monday, October 06, 2003 8:25 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] How can i get ...
> 
> 
> Hello!
> I'm reading  files in genbank format
> i want to parser the lines below  or next to organism, but 
> these don't 
> have tag
> how can i get this
> i can get organism but  i can't get the lines next to organism
> for example:
> 
> ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> I need to get: 
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> but i can't
> 
> Thank you.
> 
> Fabi
> 
> 
> 
> LOCUS       AB006766                1459 bp    DNA     linear   BCT 
> 13-FEB-1999
> DEFINITION  Oceanospirillum japonicum gene for 16S rRNA, 
> partial sequence,
>             strain:IFO19191.
> ACCESSION   AB006766
> VERSION     AB006766.1  GI:4049363
> KEYWORDS    16S ribosomal RNA.
> SOURCE      Pseudospirillum japonicum
>   ORGANISM  Pseudospirillum japonicum
>             Bacteria; Proteobacteria; Gammaproteobacteria; 
> Oceanospirillales;
>             Pseudospirillum.
> REFERENCE   1  (sites)
>   AUTHORS   Satomi,M., Kimura,B., Hayashi,M., Shouzen,Y., 
> Okuzumi,M. and
>             Fujii,T.
>   TITLE     Marinospirillum gen. nov., with descriptions of 
> Marinospirillum
>             megaterium sp. nov., isolated from kusaya gravy, 
> and transfer of
>             Oceanospirillum minutulum to Marinospirillum 
> minutulum comb. nov
>   JOURNAL   Int. J. Syst. Bacteriol. 48 Pt 4, 1341-1348 (1998)
>   MEDLINE   99045875
>    PUBMED   9828435
> REFERENCE   2  (bases 1 to 1459)
>   AUTHORS   Satomi,M.
>   TITLE     Direct Submission
>   JOURNAL   Submitted (20-AUG-1997) Masataka Satomi, National Reserch 
> Institute
>             of Fisheries Science, Food Processing and 
> Preservation Division;
>             Fukuura 2-12-4, Kanazawa-ku,, Yokohama, Kanagawa 
> 236, Japan
>             (E-mail:msatomi@nrifs.affrc.go.jp, Tel:81-45-788-7670,
>             Fax:81-45-788-7670)
> FEATURES             Location/Qualifiers
>      source          1..1459
>                      /organism="Pseudospirillum japonicum"
>                      /mol_type="genomic DNA"
>                      /strain="ATCC19191"
>                      /db_xref="taxon:64971"
>      rRNA            <1..>1459
>                      /product="16S ribosomal RNA"
> BASE COUNT      368 a    326 c    462 g    302 t      1 others
> ORIGIN     
>         1 attgaacgct ggcggcaggc ctaacacatg caagtcgagc 
> ggcagcgggg agtagcttgc
>        61 tactttgccg gcgagcggcg gacgggtgag taacgcatag 
> gaatctgccc agtagagggg
>       121 gatagccagg ggaaactctg attaataccg catacgccct 
> acgggggaaa aggggctttt
>       181 agctcctgct attggatgag cctatgtcgg attagctagt 
> tggtagggta aaggcctacc
>       241 aaggcgacga tccgtagctg ttctgagagg atgatcagcc 
> acactgggac tgagacacgg
>       301 cccagactcc tacgggaggc agcagtgggg aatattgcac 
> aatgggggga accctgatgc
>       361 acccatcccg cgtgtgtgaa gaaggccttc gggttgtaaa 
> gcactttcag caaggaggaa
>       421 ggccgtatgc ttaataggca tgcggattga cgttacttgc 
> agaagaagca ccggctaact
>       481 ccgtgccagc agccgcggta atacggaggg tgcgagcgtt 
> aatcggaatt actgggcgta
>       541 aagcgcgcgt aggcggatag gtcagtcaga tgtgaaagcc 
> ctgggctcaa cctaggacgt
>       601 gcacctgata ctgcttatct agagtaaggt agagggtagt 
> agaatttcct gtgtagcggt
>       661 gaaatgcgta gatataggaa ggaataccgg tggcgaaggc 
> ggctacctgg actattactg
>       721 acgctgaggt gcgaaagcgt ggggatcaaa caggattaga 
> taccctggta gtccacgctg
>       781 taaacgatgt cgactagccg ttgccgacct tgagttggga 
> gtggcgcagc taacgcgata
>       841 agtcgaccgc ctggggagta cggccgcaag gttaaaactc 
> aaatgaattg acgggggccc
>       901 gcacaagcgg tggagcatgt ggtttaattc gatgcaacgc 
> gaagaacctt acctactctt
>       961 gacatccaga gaactttcca gagatggata ggtgccttcg 
> ggaactctga gacaggtgct
>      1021 gcatggctgt cgtcagctcg tgttgtgaaa tgttgggtta 
> agtcccgtaa cgagcgcaac
>      1081 ccttatcctt atttgccagc gggttatgcc gggaacttta 
> aggaaactgc cggtgacaaa
>      1141 ccggaggaag gtggggacga cgtcaagtca tcatggccct 
> tacgagtagg gctacacacg
>      1201 tgctacaatg gtaagtacag agggttgcaa gaccgcgagg 
> tggagctaat ctcagaaaac
>      1261 ttatcgtagt ccggattgga gtctgcaact cgactccatg 
> aagtcggaat cgctagtaat
>      1321 cgcgaatcag aatgtcgcgg tgaatacgtt cccgggcctt 
> gtacacaccg cccgtcacac
>      1381 catgggagtg gacttcacca gaagtagtta gtctaaccgn 
> aagggggacg attaccacgg
>      1441 tggggttcat gactggggt
> //
> 

From cain at cshl.org  Tue Oct  7 09:32:19 2003
From: cain at cshl.org (Scott Cain)
Date: Tue Oct  7 09:29:56 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
In-Reply-To: 
References: 
Message-ID: <1065533538.1757.5.camel@localhost.localdomain>

Brian,

As far as I can tell, the '-force' option in ppm (for perl 5.8) is only
useful for reinstalling modules that it thinks are already installed
(and even then, it doesn't always do that).  I'm not sure what a good
solution is, since I don't think the ActiveState framework allows
"optional" modules.   :-/

As a side note, I did find a libxml that I could install via ppm
elsewhere with google, but this mess means that I have to give
directions to users who want to install GBrowse via ppm how to get
libxml even though they don't need it for GBrowse.

Thanks,
Scott

On Tue, 2003-10-07 at 07:57, Brian Osborne wrote:
> Scott,
> 
> > As a side note, it seems like a bad idea to force the installation of
> every prereq module for bioperl
> 
> Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
> shell, for example, you can do "force install". There is also a "force
> install" option in ActiveState, something like setting force-install to 1?
> Please check the ActiveState documentation and tell me if I'm wrong.
> 
> A few months ago I took a look at the "required modules" list in Bioperl and
> found that many of them were not supplied by ActiveState, just as you're
> finding.
> 
> Brian O.
> 
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Scott Cain
> Sent: Monday, October 06, 2003 4:07 PM
> To: bioperl-l@bioperl.org
> Cc: cain@cshl.org
> Subject: [Bioperl-l] bp 1.2.3 ppm install fails
> 
> Hello all,
> 
> First, thanks to the kind soul who provided the 1.2.3 version of bioperl
> as a ppm.  Unfortunately, I can't seem to get it installed due to a failed
> dependency.  While using AS Perl 5.8, it seems that none of the
> repositories know what 'libxml-perl' is, and since it is listed as a
> prerequisite in the ppd file, installation cannot continue.  Is there
> somewhere special to get that from?  At the moment, I am only searching
> the ActiveState and bioperl repositories.
> 
> As a side note, it seems like a bad idea to force the installation of
> every prereq module for bioperl.  In my case, I have no need of
> libxml-perl, but can't install bioperl for a lack of it.
> 
> Thanks,
> Scott
> 
> ----------------------------------------------------------------------
> Scott Cain, Ph. D.                                       cain@cshl.org
> GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
> ----------------------------------------------------------------------
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain@cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

From cjfields at uiuc.edu  Tue Oct  7 10:49:02 2003
From: cjfields at uiuc.edu (Chris Fields)
Date: Tue Oct  7 10:46:53 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
In-Reply-To: <1065533538.1757.5.camel@localhost.localdomain>
References: 
	<1065533538.1757.5.camel@localhost.localdomain>
Message-ID: <6.0.0.22.2.20031007092544.01cd2c70@staff.uiuc.edu>

Scott,

Randy Kobes has a number of PPM's for Windows that ActiveState doesn't 
provide, for both Perl 5.6 and 5.8.  I believe ActiveState has an automated 
build engine that will not post PPM's to the PPM depositories unless they 
successfully build (no failed tests).  The only other way to get them to 
post is to specifically ask for it on ASPN, and that may take them a 
while.  I think I picked up most of the required external modules from 
there, including GD (v 2.07).

If using ppm3:

rep add Kobes http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer

I think ppm2 is similar, but I haven't used it in a while.

Chris Fields

At 08:32 AM 10/7/2003, you wrote:
>Brian,
>
>As far as I can tell, the '-force' option in ppm (for perl 5.8) is only
>useful for reinstalling modules that it thinks are already installed
>(and even then, it doesn't always do that).  I'm not sure what a good
>solution is, since I don't think the ActiveState framework allows
>"optional" modules.   :-/
>
>As a side note, I did find a libxml that I could install via ppm
>elsewhere with google, but this mess means that I have to give
>directions to users who want to install GBrowse via ppm how to get
>libxml even though they don't need it for GBrowse.
>
>Thanks,
>Scott
>
>On Tue, 2003-10-07 at 07:57, Brian Osborne wrote:
> > Scott,
> >
> > > As a side note, it seems like a bad idea to force the installation of
> > every prereq module for bioperl
> >
> > Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
> > shell, for example, you can do "force install". There is also a "force
> > install" option in ActiveState, something like setting force-install to 1?
> > Please check the ActiveState documentation and tell me if I'm wrong.
> >
> > A few months ago I took a look at the "required modules" list in 
> Bioperl and
> > found that many of them were not supplied by ActiveState, just as you're
> > finding.
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: bioperl-l-bounces@portal.open-bio.org
> > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Scott Cain
> > Sent: Monday, October 06, 2003 4:07 PM
> > To: bioperl-l@bioperl.org
> > Cc: cain@cshl.org
> > Subject: [Bioperl-l] bp 1.2.3 ppm install fails
> >
> > Hello all,
> >
> > First, thanks to the kind soul who provided the 1.2.3 version of bioperl
> > as a ppm.  Unfortunately, I can't seem to get it installed due to a failed
> > dependency.  While using AS Perl 5.8, it seems that none of the
> > repositories know what 'libxml-perl' is, and since it is listed as a
> > prerequisite in the ppd file, installation cannot continue.  Is there
> > somewhere special to get that from?  At the moment, I am only searching
> > the ActiveState and bioperl repositories.
> >
> > As a side note, it seems like a bad idea to force the installation of
> > every prereq module for bioperl.  In my case, I have no need of
> > libxml-perl, but can't install bioperl for a lack of it.
> >
> > Thanks,
> > Scott
> >
> > ----------------------------------------------------------------------
> > Scott Cain, Ph. D.                                       cain@cshl.org
> > GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
> > ----------------------------------------------------------------------
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>--
>------------------------------------------------------------------------
>Scott Cain, Ph. D.                                         cain@cshl.org
>GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
>Cold Spring Harbor Laboratory
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l

__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
Dept. of Biochemistry - 323 RAL
600 S. Mathews Ave.
Urbana, IL 61801

Phone : (217) 333-7098
Fax : (217) 244-5858 

From lstein at cshl.edu  Tue Oct  7 11:09:01 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Oct  7 11:06:45 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
In-Reply-To: 
References: 
Message-ID: <200310071109.01780.lstein@cshl.edu>

It sounds like the modules that aren't supported by ActiveState should be 
removed from the PPM dependencies list.  The CPAN version of BioPerl doesn't 
have ANY dependencies right now.  I think this is an issue because one almost 
immediately wants IO::String to work with the seqio modules and it wouldn't 
hurt to add it as a dependency.

Lincoln

On Tuesday 07 October 2003 07:57 am, Brian Osborne wrote:
> Scott,
>
> > As a side note, it seems like a bad idea to force the installation of
>
> every prereq module for bioperl
>
> Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
> shell, for example, you can do "force install". There is also a "force
> install" option in ActiveState, something like setting force-install to 1?
> Please check the ActiveState documentation and tell me if I'm wrong.
>
> A few months ago I took a look at the "required modules" list in Bioperl
> and found that many of them were not supplied by ActiveState, just as
> you're finding.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Scott Cain
> Sent: Monday, October 06, 2003 4:07 PM
> To: bioperl-l@bioperl.org
> Cc: cain@cshl.org
> Subject: [Bioperl-l] bp 1.2.3 ppm install fails
>
> Hello all,
>
> First, thanks to the kind soul who provided the 1.2.3 version of bioperl
> as a ppm.  Unfortunately, I can't seem to get it installed due to a failed
> dependency.  While using AS Perl 5.8, it seems that none of the
> repositories know what 'libxml-perl' is, and since it is listed as a
> prerequisite in the ppd file, installation cannot continue.  Is there
> somewhere special to get that from?  At the moment, I am only searching
> the ActiveState and bioperl repositories.
>
> As a side note, it seems like a bad idea to force the installation of
> every prereq module for bioperl.  In my case, I have no need of
> libxml-perl, but can't install bioperl for a lack of it.
>
> Thanks,
> Scott
>
> ----------------------------------------------------------------------
> Scott Cain, Ph. D.                                       cain@cshl.org
> GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
> ----------------------------------------------------------------------
>
>
> _______________________________________________
> 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

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From jason at cgt.duhs.duke.edu  Tue Oct  7 11:33:34 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Oct  7 11:31:11 2003
Subject: [Bioperl-l] RE: [Pubmednew] Problem with esearch.fcgi
In-Reply-To: <3F82A4A7.8070205@cenix-bioscience.com>
References: 
	<1065518595.7939.14.camel@localhost>
	<3F82A4A7.8070205@cenix-bioscience.com>
Message-ID: 

On Tue, 7 Oct 2003, Andrew Walsh wrote:

> As a side note (maybe someone with more knowledge of the SeqIO parser
> knows why). The 'KEYWORD' part of the Genbank file does not seem to be
> retrieved properly.
> I get this line in the sequence file: 'KEYWORDS    ARRAY(0x8ba8f30).'

This was fixed in bioperl 1.2.3.

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From nigam at psu.edu  Tue Oct  7 12:05:06 2003
From: nigam at psu.edu (Nigam Shah)
Date: Tue Oct  7 12:02:44 2003
Subject: [Bioperl-l] PPM Install for libxml-perl
Message-ID: <000501c38cec$c65f7120$34167680@Vivek>

Hi! Scott,

add the following repository:
repository add "Winnipeg_server" http://theoryx5.uwinnipeg.ca/ppms

(the repository name _has_ to be in double quotes and no trailing '/' after
the URL other wise ppm will die with: Missing base argument at
C:/Perl8/site/lib/PPM/Repository.pm line 174)

You will find most of the dependencies there. Look at
http://www.personal.psu.edu/faculty/n/h/nhs109/Bioperl/ for more details
about installation on perl 5.8.

Regards,
Nigam.


Nigam Shah
Graduate Fellow, 
Huck Institute for Life Sciences,
Penn State University.
Ph:(814)863-5720
Web: www.personal.psu.edu/nhs109/

From raphael.bauer at informatik.hu-berlin.de  Tue Oct  7 12:24:44 2003
From: raphael.bauer at informatik.hu-berlin.de (Raphael A. Bauer)
Date: Tue Oct  7 12:22:24 2003
Subject: [Bioperl-l] bioperl-db: Updating existing Databases with
 load_seqdatabase.pl and load_ontology
Message-ID: <3F82E8CC.3050703@informatik.hu-berlin.de>

Hello bioperl-l members,

i wonder how to perform a "safe" (incremental) update on a
working biosql schema.

My setup is the following: BioSQL schema on Postgres equipped with 
Swissprot (via load_seqdatabase.pl and GeneOntology (via load_ontology.pl).

Now i simply want to feed the existing BioSQL schema with
new versions of both databases.
The question ist how to do it in a safe way - especially so that no 
links in tables are dead and all information in the relevant tables and
dbxrefs is upadated too.

There is of course the --lookup flag for both scripts (and the 
update-on-new-date.pl for SProt) - but does it take care of everything?
Or would it be better to build up the database from scratch in order
to remain in a consistent state...

Many thanks in advance,

Raphael




From lstein at cshl.edu  Tue Oct  7 12:52:26 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Oct  7 12:50:14 2003
Subject: [Bioperl-l] bp 1.2.3 ppm install fails
In-Reply-To: <6.0.0.22.2.20031007092544.01cd2c70@staff.uiuc.edu>
References: 
	<1065533538.1757.5.camel@localhost.localdomain>
	<6.0.0.22.2.20031007092544.01cd2c70@staff.uiuc.edu>
Message-ID: <200310071252.26364.lstein@cshl.edu>

More fundamentally, however, the BioPerl PPM should have no more and no less 
dependencies than the BioPerl CPAN.  We need to do it this way so that we 
have a common platform on which to evaluate bug reports, &c.

Lincoln

On Tuesday 07 October 2003 10:49 am, Chris Fields wrote:
> Scott,
>
> Randy Kobes has a number of PPM's for Windows that ActiveState doesn't
> provide, for both Perl 5.6 and 5.8.  I believe ActiveState has an automated
> build engine that will not post PPM's to the PPM depositories unless they
> successfully build (no failed tests).  The only other way to get them to
> post is to specifically ask for it on ASPN, and that may take them a
> while.  I think I picked up most of the required external modules from
> there, including GD (v 2.07).
>
> If using ppm3:
>
> rep add Kobes http://theoryx5.uwinnipeg.ca/cgi-bin/ppmserver?urn:/PPMServer
>
> I think ppm2 is similar, but I haven't used it in a while.
>
> Chris Fields
>
> At 08:32 AM 10/7/2003, you wrote:
> >Brian,
> >
> >As far as I can tell, the '-force' option in ppm (for perl 5.8) is only
> >useful for reinstalling modules that it thinks are already installed
> >(and even then, it doesn't always do that).  I'm not sure what a good
> >solution is, since I don't think the ActiveState framework allows
> >"optional" modules.   :-/
> >
> >As a side note, I did find a libxml that I could install via ppm
> >elsewhere with google, but this mess means that I have to give
> >directions to users who want to install GBrowse via ppm how to get
> >libxml even though they don't need it for GBrowse.
> >
> >Thanks,
> >Scott
> >
> >On Tue, 2003-10-07 at 07:57, Brian Osborne wrote:
> > > Scott,
> > >
> > > > As a side note, it seems like a bad idea to force the installation of
> > >
> > > every prereq module for bioperl
> > >
> > > Definitely a bad idea, that's why Bioperl doesn't do this. In the CPAN
> > > shell, for example, you can do "force install". There is also a "force
> > > install" option in ActiveState, something like setting force-install to
> > > 1? Please check the ActiveState documentation and tell me if I'm wrong.
> > >
> > > A few months ago I took a look at the "required modules" list in
> >
> > Bioperl and
> >
> > > found that many of them were not supplied by ActiveState, just as
> > > you're finding.
> > >
> > > Brian O.
> > >
> > > -----Original Message-----
> > > From: bioperl-l-bounces@portal.open-bio.org
> > > [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Scott Cain
> > > Sent: Monday, October 06, 2003 4:07 PM
> > > To: bioperl-l@bioperl.org
> > > Cc: cain@cshl.org
> > > Subject: [Bioperl-l] bp 1.2.3 ppm install fails
> > >
> > > Hello all,
> > >
> > > First, thanks to the kind soul who provided the 1.2.3 version of
> > > bioperl as a ppm.  Unfortunately, I can't seem to get it installed due
> > > to a failed dependency.  While using AS Perl 5.8, it seems that none of
> > > the repositories know what 'libxml-perl' is, and since it is listed as
> > > a prerequisite in the ppd file, installation cannot continue.  Is there
> > > somewhere special to get that from?  At the moment, I am only searching
> > > the ActiveState and bioperl repositories.
> > >
> > > As a side note, it seems like a bad idea to force the installation of
> > > every prereq module for bioperl.  In my case, I have no need of
> > > libxml-perl, but can't install bioperl for a lack of it.
> > >
> > > Thanks,
> > > Scott
> > >
> > > ----------------------------------------------------------------------
> > > Scott Cain, Ph. D.                                       cain@cshl.org
> > > GMOD Coordinator, http://www.gmod.org/                   (216)392-3087
> > > ----------------------------------------------------------------------
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >--
> >------------------------------------------------------------------------
> >Scott Cain, Ph. D.                                         cain@cshl.org
> >GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
> >Cold Spring Harbor Laboratory
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l@portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> __________________________________
>
> Chris Fields - Postdoctoral Researcher
> Lab of Dr. Robert Switzer
>
> Address:
>
> University of Illinois at Urbana-Champaign
> Dept. of Biochemistry - 323 RAL
> 600 S. Mathews Ave.
> Urbana, IL 61801
>
> Phone : (217) 333-7098
> Fax : (217) 244-5858
>
> _______________________________________________
> 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From amackey at pcbi.upenn.edu  Tue Oct  7 14:26:58 2003
From: amackey at pcbi.upenn.edu (Aaron J. Mackey)
Date: Tue Oct  7 14:24:36 2003
Subject: [Bioperl-l] Fwd: having problems with abi.pm
Message-ID: 


I'm stumped on this one ...


> From: "Pinar Kondu" 
> Date: Tue Oct 7, 2003  12:03:02 PM US/Eastern
> To: "Aaron J. Mackey" 
> Subject: Re: having problems with abi.pm
>
> Hi again Aaron,
>
> It looks like it is working now, but I received an error message in 
> read.pm
> Since I assume I am not supposed to make any modifications in the 
> modules, I
> wanted to ask you what this message means:
>
> Here is how I ran my program:
> [root@iontek pinarperl]# perl test2.pl -a
> /home/ORTAKSKY/SEQUENCES/myfile.abi -p 
> /home/ORTAKSKY/SEQUENCES/myfileout
>
> Here is the message I got:
> Can't use an undefined value as filehandle reference at
> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/staden/read.pm line 115.
>
> The script is below.
>
> many thanks! -pinar
>
>
>>>>>>>
>>>>>>> #!/usr/bin/perl -w
>>>>>>>
>>>>>>> use strict;
>>>>>>> use Bio::SeqIO;
>>>>>>> use Getopt::Std;
>>>>>>>
>>>>>>> my %args;
>>>>>>> getopt("ap", \%args);
>>>>>>> if (!$args{a}) {
>>>>>>>   die "Please specify the input ABI file name!";
>>>>>>> }
>>>>>>> if (!$args{p}) {
>>>>>>>   die "Please specify the output PHD file name!";
>>>>>>> }
>>>>>>>
>>>>>>> my $ABIin = new Bio::SeqIO( -format => "ABI", -file => "$args{a}"
>>>>>>> );
>>>>>>>
>>>>>>> my $PHDout = new Bio::SeqIO( -format => "phd", -file =>
>>>>>>> ">$args{p}" );
>>>>>>>
>>>>>>> while (my $seq = $ABIin->next_seq) {
>>>>>>>     $PHDout->write_seq($seq);
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>

From hlapp at gnf.org  Tue Oct  7 14:55:49 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Oct  7 14:53:27 2003
Subject: [Bioperl-l] bioperl-db: Updating existing Databases with
	load_seqdatabase.pl and load_ontology
In-Reply-To: <3F82E8CC.3050703@informatik.hu-berlin.de>
Message-ID: 

I don't know what you mean by 'everything'. Update is a known and known to
be completely non-trivial problem.

The load_XXX scripts themselves just issue an update to the persistent
objects (if they have been found by prior lookup). The update call as
implemented in the bioperl-db adaptors translate to SQL UPDATE statements
*only* (where undefined attributes are prevented from overriding database
column values). By 'only' I mean that there won't be any magically performed
DELETEs on entity associations as far as the adaptors are concerned.

'Updating' the associations is the main issue that makes a database update
non-trivial, because there is no SQL UPDATE equivalent: the association is
either present or absent. If this is confusing, take sequences and their
associated seqfeatures as a very simple example. If the number of features
changes for a sequence, you can't reflect that by issuing a SQL UPDATE
against some table, because seqfeature and bioentry are two tables connected
by a foreign key. You either a) figure out which features are modified,
added, and deleted, and correspondingly update, insert, and delete those, or
b) you delete all existing features and insert all from the updated sequence
entry from scratch.

There are arguments for and against both a) and b). The approach of the
load_XXX scripts is to leave this decision to the user. It is the script
supplied via --mergeobjs that does the magic if any. A couple of (working)
example scripts for this purpose come with the package in the scripts/biosql
directory, and if you check them out you'll see exactly what's going on (as
there is no magic anywhere else other than cascading plain UPDATEs):

    freshen-annot.pl    # replace all old annotations with the new
annotations regardless
    merge-unique-ann.pl # leave old annotation untouched, add on new that
are different from any of the old annotations
    update-on-new-version.pl # like freshen, but only for bioentries that
changed version
    update-on-new-date.pl    # like freshen, but only for bioentries that
have a more recent date

Note that databanks not only update and add entries, they also obsolete
entries. This is not at all handled by load_seqdatabase.pl.

So, returning to your question, it depends on your situation. If you are
never going to add your own annotations, purging and re-populating is
guaranteed to leave you in a state consistent with the datasource, but is
likely to be slower than a smart update (smart meaning update only if the
entry indeed changed). If you add your own annotations, purging the content
is not an option, and you need to decide how to merge an existing entry with
its updated counterpart using either one of the aforementioned scriptlets,
or one you write yourself. Similarly for ontology update: if you want to
update ontologies w/o updating everything else too, purging is not an
option, and you'll need to decide how you want to merge.

Merging entries currently leaves you with possibly obsoleted bioentries
hanging around in your biosql instance. I have this very problem myself and
can't present a good solution yet as I'll just start to address it within
the next few weeks.

Hth.

    -hilmar

On 10/7/03 9:24 AM, "Raphael A. Bauer"
 wrote:

> Hello bioperl-l members,
> 
> i wonder how to perform a "safe" (incremental) update on a
> working biosql schema.
> 
> My setup is the following: BioSQL schema on Postgres equipped with
> Swissprot (via load_seqdatabase.pl and GeneOntology (via load_ontology.pl).
> 
> Now i simply want to feed the existing BioSQL schema with
> new versions of both databases.
> The question ist how to do it in a safe way - especially so that no
> links in tables are dead and all information in the relevant tables and
> dbxrefs is upadated too.
> 
> There is of course the --lookup flag for both scripts (and the
> update-on-new-date.pl for SProt) - but does it take care of everything?
> Or would it be better to build up the database from scratch in order
> to remain in a consistent state...
> 
> Many thanks in advance,
> 
> Raphael
> 
> 
> 
> 
> _______________________________________________
> 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 lstein at cshl.edu  Tue Oct  7 19:18:16 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Tue Oct  7 19:18:47 2003
Subject: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E338001E@MBXSRV05.stf.nus.edu.sg>
References: <653C572D8746D341AAA25C494CDFB9E338001E@MBXSRV05.stf.nus.edu.sg>
Message-ID: <200310071918.16412.lstein@cshl.edu>

If you have an array of sequences then you can just create them using 
Bio::Seq:

	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;

Lincoln


On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > What made you think it would accept a -ph parameter? Besides, if
> > there was
> > one you'd have to provide an array reference.
>
> I didn't think it would work but I wanted to try it out.
>
> What I'm trying to do is get SeqIO to accept an array of sequences and not
> a file.
>
> Desmond
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From btclimd at nus.edu.sg  Tue Oct  7 21:16:22 2003
From: btclimd at nus.edu.sg (Desmond Lim)
Date: Tue Oct  7 21:14:05 2003
Subject: [Bioperl-l] seqIO
Message-ID: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>

Hi Lincoln,

Thanks but what am I to do after this?

I have a file that contains EMBL sequences. And I'm reading it into an array, manipulating it and then print it a file in fasta format.

I know how to use the:

my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 'fasta'); 

while ( my $inseq = $seq_in->next_seq ) {
  $seq_out->write_seq($inseq);
}

But I don't have a file for filename1 but an array. Is there a way for reading the array (the manipulated embl one) and then write it as a fasta file?

Thanks.

-----Original Message-----
From: Lincoln Stein [mailto:lstein@cshl.edu]
Sent: Wednesday, October 08, 2003 7:18 AM
To: Desmond Lim; Hilmar Lapp; BioPerl
Subject: Re: [Bioperl-l] seqIO


If you have an array of sequences then you can just create them using 
Bio::Seq:

	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;

Lincoln


On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > What made you think it would accept a -ph parameter? Besides, if
> > there was
> > one you'd have to provide an array reference.
>
> I didn't think it would work but I wanted to try it out.
>
> What I'm trying to do is get SeqIO to accept an array of sequences and not
> a file.
>
> Desmond
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)

From shawnh at stanford.edu  Tue Oct  7 21:46:41 2003
From: shawnh at stanford.edu (Shawn Hoon)
Date: Tue Oct  7 21:40:33 2003
Subject: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
References: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
Message-ID: <436625B0-F931-11D7-A809-000A95783436@stanford.edu>


> Hi Lincoln,
>
> Thanks but what am I to do after this?
>
> I have a file that contains EMBL sequences. And I'm reading it into an 
> array, manipulating it and then print it a file in fasta format.
>
> I know how to use the:
>
> my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 
> 'embl');
> my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 
> 'fasta');
>
> while ( my $inseq = $seq_in->next_seq ) {
>   $seq_out->write_seq($inseq);
> }
>
> But I don't have a file for filename1 but an array. Is there a way for 
> reading the array (the manipulated embl one) and then write it as a 
> fasta file?
>

Uhm I don't get it. Once you have read the sequences into memory (i.e. 
into the array) you have Seq objects which SeqIO objects
can take regardless of the source format, embl/genbank etc so you can 
pass it to SeqIO in a loop like so:

my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
my @array;

while ( my $inseq = $seq_in->next_seq ) {
  push @array, $inseq;
}

#do some manipulation here...


my $sout = Bio::SeqIO->new(-file=>">output.fa",-format=>'fasta');
foreach my $s(@array){
	$sout->write_seq($s);
}






> Thanks.
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.edu]
> Sent: Wednesday, October 08, 2003 7:18 AM
> To: Desmond Lim; Hilmar Lapp; BioPerl
> Subject: Re: [Bioperl-l] seqIO
>
>
> If you have an array of sequences then you can just create them using
> Bio::Seq:
>
> 	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;
>
> Lincoln
>
>
> On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
>>> What made you think it would accept a -ph parameter? Besides, if
>>> there was
>>> one you'd have to provide an array reference.
>>
>> I didn't think it would work but I wanted to try it out.
>>
>> What I'm trying to do is get SeqIO to accept an array of sequences 
>> and not
>> a file.
>>
>> Desmond
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> Lincoln Stein
> lstein@cshl.edu
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
-shawn

From jason at cgt.duhs.duke.edu  Tue Oct  7 21:43:55 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Oct  7 21:41:22 2003
Subject: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
References: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
Message-ID: 

As has already been suggest on the list - use IO::String.

You don't have Bioperl Bio::Seq sequences yet, but an array of
strings which are EMBL format sequence data.

See the FAQ -
  http://www.bioperl.org/Core/Latest/faq.html#Q2.4
(hint - turn the array back into a single string with join )

-jason
On Wed, 8 Oct 2003, Desmond Lim wrote:

> Hi Lincoln,
>
> Thanks but what am I to do after this?
>
> I have a file that contains EMBL sequences. And I'm reading it into an
> array, manipulating it and then print it a file in fasta format.
>
> I know how to use the:
>
> my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
> my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 'fasta');
>
> while ( my $inseq = $seq_in->next_seq ) {
>   $seq_out->write_seq($inseq);
> }
>
> But I don't have a file for filename1 but an array. Is there a way for reading the array (the manipulated embl one) and then write it as a fasta file?
>
> Thanks.
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.edu]
> Sent: Wednesday, October 08, 2003 7:18 AM
> To: Desmond Lim; Hilmar Lapp; BioPerl
> Subject: Re: [Bioperl-l] seqIO
>
>
> If you have an array of sequences then you can just create them using
> Bio::Seq:
>
> 	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;
>
> Lincoln
>
>
> On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > > What made you think it would accept a -ph parameter? Besides, if
> > > there was
> > > one you'd have to provide an array reference.
> >
> > I didn't think it would work but I wanted to try it out.
> >
> > What I'm trying to do is get SeqIO to accept an array of sequences and not
> > a file.
> >
> > Desmond
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From lstein at cshl.edu  Wed Oct  8 10:18:38 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Wed Oct  8 10:16:31 2003
Subject: Asking for help on the bioperl mailing list.  WAS: [Bioperl-l] seqIO
In-Reply-To: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
References: <653C572D8746D341AAA25C494CDFB9E3380020@MBXSRV05.stf.nus.edu.sg>
Message-ID: <200310081018.38994.lstein@cshl.edu>

Hi Desmond and Others who Write to this Mailing List for Help,

The bioperl mailing list welcomes requests for help from programmers of all 
levels of experience.  However, as the recent thread indicates, a great deal 
of unhelpful and redundant traffic can be generated when the question is 
vague.

It would really help us all if next time you state the problem explicitly and 
concisely, as in "I have a file that contains EMBL sequences, I've read them 
into an array and want to print the results out as FASTA format."  Note that 
this is still underspecified because some people will understand this to mean 
that you've created an array in which each element is a line from the EMBL 
file, while others will think you've created one element per EMBL entry.  But 
it's much better than showing us a fragment of nonfunctional code taken out 
of context and then asking us "why doesn't bioperl work the way I think it 
should."

Also your problem raises another question.  Why did you read the EMBL file 
into a string array rather than using Bio::SeqIO from the beginning to do it?

Lincoln

On Tuesday 07 October 2003 09:16 pm, Desmond Lim wrote:
> Hi Lincoln,
>
> Thanks but what am I to do after this?
>
> I have a file that contains EMBL sequences. And I'm reading it into an
> array, manipulating it and then print it a file in fasta format.
>
> I know how to use the:
>
> my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' => 'embl');
> my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' => 'fasta');
>
> while ( my $inseq = $seq_in->next_seq ) {
>   $seq_out->write_seq($inseq);
> }
>
> But I don't have a file for filename1 but an array. Is there a way for
> reading the array (the manipulated embl one) and then write it as a fasta
> file?
>
> Thanks.
>
> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.edu]
> Sent: Wednesday, October 08, 2003 7:18 AM
> To: Desmond Lim; Hilmar Lapp; BioPerl
> Subject: Re: [Bioperl-l] seqIO
>
>
> If you have an array of sequences then you can just create them using
> Bio::Seq:
>
> 	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;
>
> Lincoln
>
> On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
> > > What made you think it would accept a -ph parameter? Besides, if
> > > there was
> > > one you'd have to provide an array reference.
> >
> > I didn't think it would work but I wanted to try it out.
> >
> > What I'm trying to do is get SeqIO to accept an array of sequences and
> > not a file.
> >
> > Desmond
> >
> > _______________________________________________
> > 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From hlapp at gmx.net  Wed Oct  8 12:40:15 2003
From: hlapp at gmx.net (Hilmar Lapp)
Date: Wed Oct  8 12:37:57 2003
Subject: Asking for help on the bioperl mailing list. WAS: [Bioperl-l]
	seqIO
In-Reply-To: <200310081018.38994.lstein@cshl.edu>
Message-ID: <1861501A-F9AE-11D7-A595-000A959EB4C4@gmx.net>

I agree wholeheartedly. The better the question is formulated the  
better your answer is going to be. It's not productive to waste  
people's time on figuring out what you wanted to ask in the first place.

There is such a thing as doing your homework first. Good and quick  
answers don't come for free even though it may seem so sometimes.

	-hilmar

On Wednesday, October 8, 2003, at 07:18  AM, Lincoln Stein wrote:

> Hi Desmond and Others who Write to this Mailing List for Help,
>
> The bioperl mailing list welcomes requests for help from programmers  
> of all
> levels of experience.  However, as the recent thread indicates, a  
> great deal
> of unhelpful and redundant traffic can be generated when the question  
> is
> vague.
>
> It would really help us all if next time you state the problem  
> explicitly and
> concisely, as in "I have a file that contains EMBL sequences, I've  
> read them
> into an array and want to print the results out as FASTA format."   
> Note that
> this is still underspecified because some people will understand this  
> to mean
> that you've created an array in which each element is a line from the  
> EMBL
> file, while others will think you've created one element per EMBL  
> entry.  But
> it's much better than showing us a fragment of nonfunctional code  
> taken out
> of context and then asking us "why doesn't bioperl work the way I  
> think it
> should."
>
> Also your problem raises another question.  Why did you read the EMBL  
> file
> into a string array rather than using Bio::SeqIO from the beginning to  
> do it?
>
> Lincoln
>
> On Tuesday 07 October 2003 09:16 pm, Desmond Lim wrote:
>> Hi Lincoln,
>>
>> Thanks but what am I to do after this?
>>
>> I have a file that contains EMBL sequences. And I'm reading it into an
>> array, manipulating it and then print it a file in fasta format.
>>
>> I know how to use the:
>>
>> my $seq_in = Bio::SeqIO->new('-file' => filename1, '-format' =>  
>> 'embl');
>> my $seq_out = Bio::SeqIO->new('-file' => filename2, '-format' =>  
>> 'fasta');
>>
>> while ( my $inseq = $seq_in->next_seq ) {
>>   $seq_out->write_seq($inseq);
>> }
>>
>> But I don't have a file for filename1 but an array. Is there a way for
>> reading the array (the manipulated embl one) and then write it as a  
>> fasta
>> file?
>>
>> Thanks.
>>
>> -----Original Message-----
>> From: Lincoln Stein [mailto:lstein@cshl.edu]
>> Sent: Wednesday, October 08, 2003 7:18 AM
>> To: Desmond Lim; Hilmar Lapp; BioPerl
>> Subject: Re: [Bioperl-l] seqIO
>>
>>
>> If you have an array of sequences then you can just create them using
>> Bio::Seq:
>>
>> 	@bioperl_sequences = map {Bio::Seq->new(-seq=>$_)} @raw_seq;
>>
>> Lincoln
>>
>> On Tuesday 07 October 2003 12:45 am, Desmond Lim wrote:
>>>> What made you think it would accept a -ph parameter? Besides, if
>>>> there was
>>>> one you'd have to provide an array reference.
>>>
>>> I didn't think it would work but I wanted to try it out.
>>>
>>> What I'm trying to do is get SeqIO to accept an array of sequences  
>>> and
>>> not a file.
>>>
>>> Desmond
>>>
>>> _______________________________________________
>>> 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
> lstein@cshl.org			                  Cold Spring Harbor, NY
> ======================================================================= 
> =
>
>
> _______________________________________________
> 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 Daniel.Lang at biologie.uni-freiburg.de  Wed Oct  8 14:05:04 2003
From: Daniel.Lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Wed Oct  8 14:02:40 2003
Subject: [Bioperl-l] HTMLResultWriter questions
Message-ID: <3F8451D0.70707@biologie.uni-freiburg.de>

Hi,

I have quite some problems with generating BLAST HTML reports with local
database links and own layout...

All the examples I found about HTMLResultWriter cover filtering of
results, but I haven?t found anything about the usage of the
"hit_link_desc" method etc.
Does anyone have some example code for me?
Thanx

-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

From hlapp at gnf.org  Wed Oct  8 14:54:04 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct  8 14:51:41 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 

This has nothing to do with the input file but everything with run-time
loading of modules in perl on Windows. The error you get is generated by the
following line of code:

    $self->debug("attempting to load driver for adaptor class $class\n");

The class Bio::DB::BioSQL::BasePersistenceAdaptor.pm has a 'use
Bio::Root::Root' statement, it inherits directly from Bio::Root::Root, and
Bio::Root::Root does have a debug() method as you can (and should) easily
convince yourself of.

Have you run the bioperl-db test suite? If so, what was the result? If not,
run it.

So, I'm copying the bioperl list here in case somebody has more clues as to
why you might be seeing this error on WinXP. We've had a case before on the
list where it turned out eventually that there had been a version mix-up on
the machine and everything worked fine after re-installing from scratch.

    -hilmar

On 10/8/03 4:24 AM, "Robert Roth"  wrote:

> 
> Hello,
> 
> I'm using Mysql 4.0.15, Bioperl 1.2.3, bioperl-db from the cvs and perl
> 5.6.1 on WinXP.
> After installation I pre-loaded the the biosql database with the NCBI taxon
> database using
> load_ncbi_taxonomy.pl. Now when I try to load sequence data with
> load_seqdatabase.pl I get
> the following error,
> 
> perl load_seqdatabase.pl --host localhost --dbname biosql --dbus
> er root --namespace bioperl --debug --safe --testonly --format
> genbank test.genbank
> Loading test.genbank ...
> attempting to load adaptor class for Bio::Seq::RichSeq
>       attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
> attempting to load adaptor class for Bio::Seq
>       attempting to load module Bio::DB::BioSQL::SeqAdaptor
> instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
> attempting to load adaptor class for Bio::SeqFeature::Generic
>       attempting to load module Bio::DB::BioSQL::GenericAdaptor
> attempting to load adaptor class for Bio::Root::Root
>       attempting to load module Bio::DB::BioSQL::RootAdaptor
> Undefined subroutine &Bio::Root::Root::debug called at
> E:/Perl/site/lib/Bio/DB/B
> ioSQL/BasePersistenceAdaptor.pm line 1502,  line 41.
> 
> I've tried different formats (swiss and genbank) and different files with
> the same
> result. The line number given in the error always correspond to the end of
> the first
> record (and it doesn't matter if the file contains one or more records).
> Any ideas?
> 
> Many thanks in advance,
> 
> Robert
> 
> 
> _______________________________________________
> 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 ajm6q at virginia.edu  Wed Oct  8 15:59:30 2003
From: ajm6q at virginia.edu (Aaron J Mackey)
Date: Wed Oct  8 15:57:08 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
Message-ID: 


On Mon, 6 Oct 2003, Jason Stajich wrote:

> When I get together with Aaron at the end of the month I will try and go
> through it with him so I understand what is supposed to happen and/or how
> we might reorg bioperl-ext to be less problematic.

The problem (over-and-over-again) has been that while people think they
have the staden io-lib successfully installed, they don't (because they
have to manually do a few things that the io-lib install doesn't do for
them).  It's a royal pain, of course.  And then they try to install
bioperl-ext, which doesn't successfully complete (you can, btw, install
only parts of bioperl-ext, so the whole staden read lib stuff shouldn't
prevent someone from installing the other alignment code).

Then, if they ignore that and try to run the normal bioperl test suite,
they get various odd cryptic errors about read not being successfully
installed.

-Aaron

From hlapp at gnf.org  Wed Oct  8 20:00:41 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct  8 19:58:19 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 

This is definitely related to the perl setup I'd claim. Have you been able
to run the bioperl test suite without similar trouble?

Again, I'm cc'ing the bioperl list in case anybody has seen this also and
has clues as to what the cause is and how to remedy it.
 
    -hilmar
 
On 10/8/03 3:18 PM, "Robert Roth"  wrote:

> Hi,
> 
> I've tried to run the test suite and most tests failed with outputs like the
> one below. Only the
> test_dbadaptor was succesful and but also there a lot of comments about
> redefined subroutines like the ones below were generated.
> I will reinstall everything tomorrow to see if that helps.
> 
> /Robert
> 
> E:\temp\bioperl-db>e:\Perl\bin\perl.exe -Iblib\arch -Ilib\lib -IE:\perl\lib
> -IE:
> Perl\lib -e "use Test::Harness qw(&runtests $verbose); $verbose=0; runtests
> @ARG
> V;" t/comment.t
> t/comment...........ok 2/11Subroutine new redefined at
> e:/Perl/site/lib/Bio\Seq\
> RichSeq.pm line 112,  line 72.
> Subroutine division redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 172, <
> GEN0> line 72.
> Subroutine molecule redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 193, <
> GEN0> line 72.
> Subroutine add_date redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 215, <
> GEN0> line 72.
> Subroutine get_dates redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 234,
>  line 72.
> Subroutine pid redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line 253,
> 
> line 72.
> Subroutine accession redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 279,
>  line 72.
> Subroutine add_secondary_accession redefined at
> e:/Perl/site/lib/Bio\Seq\RichSeq
> .pm line 296,  line 72.
> Subroutine get_secondary_accessions redefined at
> e:/Perl/site/lib/Bio\Seq\RichSe
> q.pm line 315,  line 72.
> Subroutine seq_version redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 332
> ,  line 72.
> Subroutine keywords redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 353, <
> GEN0> line 72.
> Subroutine each_date redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line
> 369,
>  line 72.
> Subroutine each_secondary_accession redefined at
> e:/Perl/site/lib/Bio\Seq\RichSe
> q.pm line 376,  line 72.
> Subroutine sv redefined at e:/Perl/site/lib/Bio\Seq\RichSeq.pm line 383,
> 
> line 72.
> Subroutine new redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 146,
>  line 72.
> Subroutine set_attributes redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 188,  line 72.
> Subroutine direct_new redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 253,  line 72.
> Subroutine location redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 274,  line 72.
> Subroutine start redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 30
> 4,  line 72.
> Subroutine end redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 321,
>  line 72.
> Subroutine length redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 3
> 38,  line 72.
> Subroutine strand redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 3
> 55,  line 72.
> Subroutine score redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 37
> 2,  line 72.
> Subroutine frame redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 39
> 7,  line 72.
> Subroutine primary_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm l
> ine 423,  line 72.
> Subroutine source_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 444,  line 72.
> Subroutine has_tag redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 465,  line 72.
> Subroutine add_tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 480,  line 72.
> Subroutine get_tag_values redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 499,  line 72.
> Subroutine get_all_tags redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 521,  line 72.
> Subroutine remove_tag redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 537,  line 72.
> Subroutine attach_seq redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 562,  line 72.
> Subroutine seq redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm line
> 592,
>  line 72.
> Subroutine entire_seq redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 633,  line 72.
> Subroutine seq_id redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 6
> 58,  line 72.
> Subroutine display_name redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 677,  line 72.
> Subroutine annotation redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 702,  line 72.
> Subroutine get_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.
> pm line 733,  line 72.
> Subroutine add_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 763,  line 72.
> Subroutine remove_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gener
> ic.pm line 800,  line 72.
> Subroutine gff_format redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 832,  line 72.
> Subroutine gff_string redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 862,  line 72.
> Subroutine slurp_gff_file redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 885,  line 72.
> Subroutine _from_gff_string redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic
> .pm line 921,  line 72.
> Subroutine _expand_region redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 943,  line 72.
> Subroutine _parse redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line 9
> 73,  line 72.
> Subroutine _tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 991,  line 72.
> Subroutine seqname redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 1006,  line 72.
> Subroutine display_id redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.pm li
> ne 1012,  line 72.
> Subroutine each_tag_value redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 1019,  line 72.
> Subroutine all_tags redefined at e:/Perl/site/lib/Bio\SeqFeature\Generic.pm
> line
> 1020,  line 72.
> Subroutine sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Generic.p
> m line 1024,  line 72.
> Subroutine add_sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gener
> ic.pm line 1025,  line 72.
> Subroutine flush_sub_SeqFeatures redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Ge
> neric.pm line 1026,  line 72.
> Subroutine flush_sub_SeqFeature redefined at
> e:/Perl/site/lib/Bio\SeqFeature\Gen
> eric.pm line 1028,  line 72.
> Subroutine new redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 195,
>  l
> ine 72.
> Subroutine verbose redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 228,
>  0> line 72.
> Subroutine _register_for_cleanup redefined at
> e:/Perl/site/lib/Bio\Root\Root.pm
> line 240,  line 72.
> Subroutine _unregister_for_cleanup redefined at
> e:/Perl/site/lib/Bio\Root\Root.p
> m line 250,  line 72.
> Subroutine _cleanup_methods redefined at e:/Perl/site/lib/Bio\Root\Root.pm
> line
> 257,  line 72.
> Subroutine throw redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 307,
> 
> line 72.
> Subroutine debug redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 370,
> 
> line 72.
> Subroutine _load_module redefined at e:/Perl/site/lib/Bio\Root\Root.pm line
> 390,
>  line 72.
> Subroutine DESTROY redefined at e:/Perl/site/lib/Bio\Root\Root.pm line 416,
>  0> line 72.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio\DB\BioSQL\DBAdaptor.pm line 173,  line 72.
> Undefined subroutine &Bio::Root::Root::debug called at
> e:/Perl/site/lib/Bio/DB/B
> ioSQL/BasePersistenceAdaptor.pm line 689,  line 72.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 1756 during
> global d
> estruction.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at e:
> /Perl/site/lib/Bio/DB/DBI/base.pm line 411 during global destruction.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
>       (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> durin
> g global destruction.
> t/comment...........dubious
>       Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-11
>       Failed 9/11 tests, 18.18% okay
> Failed Test Status Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------------
> ----
> 
> t/comment.t      255 65280    11    9  81.82%  3-11
> Failed 1/1 test scripts, 0.00% okay. 9/11 subtests failed, 18.18% okay.
> 
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp@gnf.org]
> Sent: 08 October 2003 20:54
> To: Robert Roth; OBDA BioSQL
> Cc: BioPerl
> Subject: Re: [BioSQL-l] Error using load_seqdatabase.pl
> 
> 
> This has nothing to do with the input file but everything with run-time
> loading of modules in perl on Windows. The error you get is generated by the
> following line of code:
> 
>   $self->debug("attempting to load driver for adaptor class $class\n");
> 
> The class Bio::DB::BioSQL::BasePersistenceAdaptor.pm has a 'use
> Bio::Root::Root' statement, it inherits directly from Bio::Root::Root, and
> Bio::Root::Root does have a debug() method as you can (and should) easily
> convince yourself of.
> 
> Have you run the bioperl-db test suite? If so, what was the result? If not,
> run it.
> 
> So, I'm copying the bioperl list here in case somebody has more clues as to
> why you might be seeing this error on WinXP. We've had a case before on the
> list where it turned out eventually that there had been a version mix-up on
> the machine and everything worked fine after re-installing from scratch.
> 
>   -hilmar
> 
> On 10/8/03 4:24 AM, "Robert Roth"  wrote:
> 
>> 
>> Hello,
>> 
>> I'm using Mysql 4.0.15, Bioperl 1.2.3, bioperl-db from the cvs and perl
>> 5.6.1 on WinXP.
>> After installation I pre-loaded the the biosql database with the NCBI
> taxon
>> database using
>> load_ncbi_taxonomy.pl. Now when I try to load sequence data with
>> load_seqdatabase.pl I get
>> the following error,
>> 
>> perl load_seqdatabase.pl --host localhost --dbname biosql --dbus
>> er root --namespace bioperl --debug --safe --testonly --format
>> genbank test.genbank
>> Loading test.genbank ...
>> attempting to load adaptor class for Bio::Seq::RichSeq
>>       attempting to load module Bio::DB::BioSQL::RichSeqAdaptor
>> attempting to load adaptor class for Bio::Seq
>>       attempting to load module Bio::DB::BioSQL::SeqAdaptor
>> instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
>> attempting to load adaptor class for Bio::SeqFeature::Generic
>>       attempting to load module Bio::DB::BioSQL::GenericAdaptor
>> attempting to load adaptor class for Bio::Root::Root
>>       attempting to load module Bio::DB::BioSQL::RootAdaptor
>> Undefined subroutine &Bio::Root::Root::debug called at
>> E:/Perl/site/lib/Bio/DB/B
>> ioSQL/BasePersistenceAdaptor.pm line 1502,  line 41.
>> 
>> I've tried different formats (swiss and genbank) and different files with
>> the same
>> result. The line number given in the error always correspond to the end of
>> the first
>> record (and it doesn't matter if the file contains one or more records).
>> Any ideas?
>> 
>> Many thanks in advance,
>> 
>> Robert
>> 
>> 
>> _______________________________________________
>> 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
> -------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> 

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From wafzig at axaron.com  Thu Oct  9 04:21:10 2003
From: wafzig at axaron.com (Oliver Wafzig)
Date: Thu Oct  9 04:18:42 2003
Subject: [Bioperl-l] HTMLResultWriter questions
In-Reply-To: <3F8451D0.70707@biologie.uni-freiburg.de>
References: <3F8451D0.70707@biologie.uni-freiburg.de>
Message-ID: <200310091021.10195.wafzig@axaron.com>

On Wednesday 08 October 2003 20:05, Daniel Lang wrote:
Hi Daniel,

Generating local database links:
Method 1: call your HTMLResultWriter like this

		 my $htmlwriter =  
			new Bio::SearchIO::Writer::HTMLResultWriter('foo1%s','foo2%s' );
		where 'foo1' points to your protein-db source and 'foo2' points to your
		nucleotide db.

Methode 2: write your own 'hit_link' method and pass it as a coderef to 
"hit_link_desc" like  
 	 my $htmlwriter =
		new Bio::SearchIO::Writer::HTMLResultWriter('bla1%s','bla2%s' );
 	 $htmlwriter->hit_link_desc(\&my_hit_link);

You can use Bio::SearchIO::Writer::HTMLResultWriter::default_hit_link_desc as 
a starting piont for your own method.

Here is some code, linking all 'Hits' starting with '>gnl|database|Acc' to one 
URL, while all others ('>emb|....' or '>sw|....') will be fetched with our 
local BioRS system.   

Oliver
 
######################################################

#!/usr/bin/perl -w
use strict; 
use Bio::SearchIO; 
use Bio::SearchIO::Writer::HTMLResultWriter;

my %dbsource = ();
my $biors = 
"http://pink:4700/searchtool/searchtool.cgi?start_guest_session=1&request=query_adv&file=results&out_format=fasta&query=%s";
my $fastacmd = "http://pink/blast2ncbi/dispfastaseq?%s:%s:%s:%s";
$dbsource{"emb"} = "{embl_nest,embl_est}:[([AccNumber+EQ+text:%s;])]";
$dbsource{"sw"}  = "{swissprot,swissnew}:[([AccNumber+EQ+text:%s;])]";

die "no infile" unless defined ($ARGV[0]) && (-f $ARGV[0]);
my $infile = $ARGV[0];

my $in = new Bio::SearchIO(-format => 'blast',
			   -file => $infile); 

my $result = $in->next_result;
my $htmlwriter = new Bio::SearchIO::Writer::HTMLResultWriter();
$htmlwriter->hit_link_desc(\&my_hit_link);
$htmlwriter->hit_link_align(\&my_hit_link);
my $outhtml = new Bio::SearchIO(-writer => $htmlwriter,
				-file => ">searchio.html");
$outhtml->write_result($result);


#bereitet den html-link vor#
#dient als codereferenz in $writer->hit_link_desc (\&CODE)
#                   und in $writer->hit_link_align(\&CODE)
sub my_hit_link {
  my($self, $hit, $result) = @_;
  my $urlpattern = undef;
  my $source = undef; #biors oder fastacmd
  my $database = undef;
  my @spl = split( /[|]/, $hit->name);
  if ($spl[0] eq "gnl"){
    my ($beg, $end) = $hit->hsp('best')->range('sbjct');
    $urlpattern = sprintf ($fastacmd, $spl[1] ,"%s", $beg, $end);
  }else{
    $urlpattern = sprintf ($biors, $dbsource{$spl[0]});
  }
  #print STDERR "URLPATTERN:\t$urlpattern\n";
  
  my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE';
  my ($gi,$acc) = &{$self->id_parser}($hit->name);
  
  
  my $url = length($self->remote_database_url($type,)) > 0 ? 
    sprintf('%s',
	    sprintf($self->remote_database_url($type, $urlpattern),$gi || $acc), 
	    $hit->name()) :  $hit->name();
  
  return $url;
} 


From robert.roth at home.se  Thu Oct  9 07:51:13 2003
From: robert.roth at home.se (Robert Roth)
Date: Thu Oct  9 07:48:52 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 



I started over again and also upgraded to perl 5.8 (from ActiveState). The
claim in INSTALL.WIN that not all external modules are available from the
ppm repositories is no longer true.
Since the the installation of Bioperl with ppm does not give the possiblity
to run the test suite I skipped it and installed Bioperl-1.2.3 with nmake
instead. The test suite for bioperl ran without any major problems. With all
test that just returned "ok" removed for brevity the output was,

************************************************************************
t\Assembly...................DB_File not installed. This means the Assembly
modules are not available.  Skipping tests.
t\Assembly...................ok
t\DB.........................ok
        1/78 skipped:
t\flat.......................DB_File not loaded. This means flat.t test
cannot
be executed. Skipping
t\flat.......................ok
t\Index......................ok 11/32Can't call method "accession" on an
undefined value at E:\temp\bioperl-1.2.3\blib\lib/Bio/DB/InMemoryCache.pm
line 220,  line 54.
t\Index......................dubious
        Test returned status 22 (wstat 5632, 0x1600)
        after all the subtests completed successfully
t\SeqFeatCollection..........DB_File not installed. This means the
SeqFeatCollection wont work
t\SeqFeatCollection..........ok
Failed Test Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t\Index.t     22  5632    32    0   0.00%  ??
4 subtests skipped.
Failed 1/123 test scripts, 99.19% okay. 0/5977 subtests failed, 100.00%
okay.
************************************************************************



After this I moved on and installed bioperl-db. Running the test suite gives
the lengthy (sorry...) output below. They all (except dbadaptor.t and
query.t) fail with the same output. Attempting to run load_seqdatabase.pl
fails with the same output as before.
The complains about redefined subroutines that I showed in an earlier
message that I get when running load_seqdatabase.pl is something that is
known and attributed to a more "sensitive" perl on windows.
If the problem still seems to be related to the perl setup I guess I have to
build perl also and abandon activestate. Is there someone else who have a
working installation of Bioperl/bioperl-db/biosql under windows?
Your help is very much appreciated.

/Robert


*************************************************************************
 C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
ib\lib', 'blib\arch')" t\cluster.t t\comment.t t\dbadaptor.t t\dblink.t
t\ensemb
l.t t\fuzzy2.t t\genbank.t t\locuslink.t t\ontology.t t\query.t t\remove.t
t\seq
feature.t t\simpleseq.t t\species.t t\swiss.t
t\cluster.......ok 2/160Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 205,  line
1.
t\cluster.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-160
        Failed 158/160 tests, 1.25% okay
t\comment.......ok 2/11Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\comment.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-11
        Failed 9/11 tests, 18.18% okay
t\dbadaptor.....ok
t\dblink........ok 2/18Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\dblink........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t\ensembl.......ok 2/15Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 1420.
t\ensembl.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-15
        Failed 13/15 tests, 13.33% okay
t\fuzzy2........ok 2/21Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 64.
t\fuzzy2........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-21
        Failed 19/21 tests, 9.52% okay
t\genbank.......ok 2/18Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\genbank.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t\locuslink.....ok 3/110Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
 line 1.
t\locuslink.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-110
        Failed 107/110 tests, 2.73% okay
t\ontology......ok 4/291Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
 line 98.
t\ontology......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-291
        Failed 287/291 tests, 1.37% okay
t\query.........ok
t\remove........ok 1/59Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 41.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
remove.t line 32,  line 41.
Undefined subroutine &Bio::Root::Root::throw called at
E:\temp\bioperl-db\blib\l
ib/Bio\DB\BioSQL\DBAdaptor.pm line 174,  line 41.
t\remove........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-59
        Failed 58/59 tests, 1.69% okay
t\seqfeature....ok 2/48Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\seqfeature....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-48
        Failed 46/48 tests, 4.17% okay
t\simpleseq.....ok 8/27Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 1.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
simpleseq.t line 45,  line 1.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
simpleseq.t line 73,  line 1.
Undefined subroutine &Bio::Root::Root::debug called at
E:\temp\bioperl-db\blib\l
ib/Bio/DB/BioSQL/BaseDriver.pm line 410,  line 1.
t\simpleseq.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 9-27
        Failed 19/27 tests, 29.63% okay
t\species.......ok 2/65Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198.
t\species.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-65
        Failed 63/65 tests, 3.08% okay
t\swiss.........ok 2/52Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 78.
t\swiss.........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-52
        Failed 50/52 tests, 3.85% okay
Failed Test    Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t\cluster.t     255 65280   160  158  98.75%  3-160
t\comment.t     255 65280    11    9  81.82%  3-11
t\dblink.t      255 65280    18   16  88.89%  3-18
t\ensembl.t     255 65280    15   13  86.67%  3-15
t\fuzzy2.t      255 65280    21   19  90.48%  3-21
t\genbank.t     255 65280    18   16  88.89%  3-18
t\locuslink.t   255 65280   110  107  97.27%  4-110
t\ontology.t    255 65280   291  287  98.63%  5-291
t\remove.t      255 65280    59   58  98.31%  2-59
t\seqfeature.t  255 65280    48   46  95.83%  3-48
t\simpleseq.t   255 65280    27   19  70.37%  9-27
t\species.t     255 65280    65   63  96.92%  3-65
t\swiss.t       255 65280    52   50  96.15%  3-52
Failed 13/15 test scripts, 13.33% okay. 861/919 subtests failed, 6.31% okay.
****************************************************************************
****




-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Hilmar Lapp
Sent: 09 October 2003 02:01
To: Robert Roth
Cc: BioPerl
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl


This is definitely related to the perl setup I'd claim. Have you been able
to run the bioperl test suite without similar trouble?

Again, I'm cc'ing the bioperl list in case anybody has seen this also and
has clues as to what the cause is and how to remedy it.

    -hilmar


From brian_osborne at cognia.com  Thu Oct  9 08:44:26 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Thu Oct  9 08:46:31 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 

Robert,

> Is there someone else who have a working installation of
Bioperl/bioperl-db/biosql under windows?

I've not done extensive use or testing of my Mysql database but I've set up
a small one using load_taxonomy.pl followed by load_seqdatabase.pl. This was
a month or so ago. I used Cygwin, the latest bioperl from CVS, latest
biosql-schema, and the latest bioperl-db, installed in that order. Mysql
4.0.13. The only tricky part is getting DBD::Mysql running under Cygwin. I
was getting a bit frustrated but then I stumbled on this:

http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#windows/cygwi
n


Brian O.




-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robert Roth
Sent: Thursday, October 09, 2003 7:51 AM
To: bioperl-l@bioperl.org
Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl


I started over again and also upgraded to perl 5.8 (from ActiveState). The
claim in INSTALL.WIN that not all external modules are available from the
ppm repositories is no longer true.
Since the the installation of Bioperl with ppm does not give the possiblity
to run the test suite I skipped it and installed Bioperl-1.2.3 with nmake
instead. The test suite for bioperl ran without any major problems. With all
test that just returned "ok" removed for brevity the output was,

************************************************************************
t\Assembly...................DB_File not installed. This means the Assembly
modules are not available.  Skipping tests.
t\Assembly...................ok
t\DB.........................ok
        1/78 skipped:
t\flat.......................DB_File not loaded. This means flat.t test
cannot
be executed. Skipping
t\flat.......................ok
t\Index......................ok 11/32Can't call method "accession" on an
undefined value at E:\temp\bioperl-1.2.3\blib\lib/Bio/DB/InMemoryCache.pm
line 220,  line 54.
t\Index......................dubious
        Test returned status 22 (wstat 5632, 0x1600)
        after all the subtests completed successfully
t\SeqFeatCollection..........DB_File not installed. This means the
SeqFeatCollection wont work
t\SeqFeatCollection..........ok
Failed Test Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t\Index.t     22  5632    32    0   0.00%  ??
4 subtests skipped.
Failed 1/123 test scripts, 99.19% okay. 0/5977 subtests failed, 100.00%
okay.
************************************************************************



After this I moved on and installed bioperl-db. Running the test suite gives
the lengthy (sorry...) output below. They all (except dbadaptor.t and
query.t) fail with the same output. Attempting to run load_seqdatabase.pl
fails with the same output as before.
The complains about redefined subroutines that I showed in an earlier
message that I get when running load_seqdatabase.pl is something that is
known and attributed to a more "sensitive" perl on windows.
If the problem still seems to be related to the perl setup I guess I have to
build perl also and abandon activestate. Is there someone else who have a
working installation of Bioperl/bioperl-db/biosql under windows?
Your help is very much appreciated.

/Robert


*************************************************************************
 C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
ib\lib', 'blib\arch')" t\cluster.t t\comment.t t\dbadaptor.t t\dblink.t
t\ensemb
l.t t\fuzzy2.t t\genbank.t t\locuslink.t t\ontology.t t\query.t t\remove.t
t\seq
feature.t t\simpleseq.t t\species.t t\swiss.t
t\cluster.......ok 2/160Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 205,  line
1.
t\cluster.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-160
        Failed 158/160 tests, 1.25% okay
t\comment.......ok 2/11Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\comment.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-11
        Failed 9/11 tests, 18.18% okay
t\dbadaptor.....ok
t\dblink........ok 2/18Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\dblink........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t\ensembl.......ok 2/15Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 1420.
t\ensembl.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-15
        Failed 13/15 tests, 13.33% okay
t\fuzzy2........ok 2/21Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 64.
t\fuzzy2........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-21
        Failed 19/21 tests, 9.52% okay
t\genbank.......ok 2/18Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\genbank.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-18
        Failed 16/18 tests, 11.11% okay
t\locuslink.....ok 3/110Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
 line 1.
t\locuslink.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 4-110
        Failed 107/110 tests, 2.73% okay
t\ontology......ok 4/291Undefined subroutine &Bio::Root::Root::throw called
at E
:\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
 line 98.
t\ontology......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 5-291
        Failed 287/291 tests, 1.37% okay
t\query.........ok
t\remove........ok 1/59Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 41.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
remove.t line 32,  line 41.
Undefined subroutine &Bio::Root::Root::throw called at
E:\temp\bioperl-db\blib\l
ib/Bio\DB\BioSQL\DBAdaptor.pm line 174,  line 41.
t\remove........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 2-59
        Failed 58/59 tests, 1.69% okay
t\seqfeature....ok 2/48Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 72.
t\seqfeature....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-48
        Failed 46/48 tests, 4.17% okay
t\simpleseq.....ok 8/27Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 1.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
simpleseq.t line 45,  line 1.
        (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
at t\
simpleseq.t line 73,  line 1.
Undefined subroutine &Bio::Root::Root::debug called at
E:\temp\bioperl-db\blib\l
ib/Bio/DB/BioSQL/BaseDriver.pm line 410,  line 1.
t\simpleseq.....dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 9-27
        Failed 19/27 tests, 29.63% okay
t\species.......ok 2/65Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198.
t\species.......dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-65
        Failed 63/65 tests, 3.08% okay
t\swiss.........ok 2/52Undefined subroutine &Bio::Root::Root::throw called
at E:
\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,

 line 78.
t\swiss.........dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 3-52
        Failed 50/52 tests, 3.85% okay
Failed Test    Stat Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
---
t\cluster.t     255 65280   160  158  98.75%  3-160
t\comment.t     255 65280    11    9  81.82%  3-11
t\dblink.t      255 65280    18   16  88.89%  3-18
t\ensembl.t     255 65280    15   13  86.67%  3-15
t\fuzzy2.t      255 65280    21   19  90.48%  3-21
t\genbank.t     255 65280    18   16  88.89%  3-18
t\locuslink.t   255 65280   110  107  97.27%  4-110
t\ontology.t    255 65280   291  287  98.63%  5-291
t\remove.t      255 65280    59   58  98.31%  2-59
t\seqfeature.t  255 65280    48   46  95.83%  3-48
t\simpleseq.t   255 65280    27   19  70.37%  9-27
t\species.t     255 65280    65   63  96.92%  3-65
t\swiss.t       255 65280    52   50  96.15%  3-52
Failed 13/15 test scripts, 13.33% okay. 861/919 subtests failed, 6.31% okay.
****************************************************************************
****




-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Hilmar Lapp
Sent: 09 October 2003 02:01
To: Robert Roth
Cc: BioPerl
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl


This is definitely related to the perl setup I'd claim. Have you been able
to run the bioperl test suite without similar trouble?

Again, I'm cc'ing the bioperl list in case anybody has seen this also and
has clues as to what the cause is and how to remedy it.

    -hilmar


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


From Steven.Roels at mpi.com  Thu Oct  9 14:26:23 2003
From: Steven.Roels at mpi.com (Roels, Steven)
Date: Thu Oct  9 14:25:14 2003
Subject: [Bioperl-l] cvs access problems?
Message-ID: 


Is the open-bio cvs server up and running?

I'm trying to login as I've done before, but today I'm timing out.  As
near as we can tell its not a firewall issue and I can (for example)
access ensembl.

I'm doing the following:

% cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login

when prompted, the password is 'cvs'


Thanks,

-Steve

*****************************************************************
Steve Roels, Ph.D.                       
Senior Scientist I - Computational Biology     Phone: (617) 761-6820
Millennium Pharmaceuticals, Inc.         FAX:   (617) 577-3555
640 Memorial Drive                       Email: roels@mpi.com
Cambridge, MA 02139-4853
*****************************************************************




This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged.  This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else.  If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender.  Thank you.


From Steven.Roels at mpi.com  Thu Oct  9 15:04:13 2003
From: Steven.Roels at mpi.com (Roels, Steven)
Date: Thu Oct  9 15:02:59 2003
Subject: [Bioperl-l] cvs access problems?
Message-ID: 


Before anyone else troubles themselves...

It was just a firewall problem (the permissions were tied to IP address,
which had apparently changed since I last connected).

Thanks Jason for checking,

-Steve

*****************************************************************
Steve Roels, Ph.D.                       
Senior Scientist I - Computational Biology     Phone: (617) 761-6820
Millennium Pharmaceuticals, Inc.         FAX:   (617) 577-3555
640 Memorial Drive                       Email: roels@mpi.com
Cambridge, MA 02139-4853
*****************************************************************

>-----Original Message-----
>From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
>Sent: Thursday, October 09, 2003 2:36 PM
>To: Roels, Steven
>Subject: Re: [Bioperl-l] cvs access problems?
>
>works for me....
>
>-j
>
>On Thu, 9 Oct 2003, Roels, Steven wrote:
>
>>
>> Is the open-bio cvs server up and running?
>>
>> I'm trying to login as I've done before, but today I'm timing out.
As
>> near as we can tell its not a firewall issue and I can (for example)
>> access ensembl.
>>
>> I'm doing the following:
>>
>> % cvs -d :pserver:cvs@cvs.open-bio.org:/home/repository/bioperl login
>>
>> when prompted, the password is 'cvs'
>>
>>
>> Thanks,
>>
>> -Steve
>>
>> *****************************************************************
>> Steve Roels, Ph.D.
>> Senior Scientist I - Computational Biology     Phone: (617) 761-6820
>> Millennium Pharmaceuticals, Inc.         FAX:   (617) 577-3555
>> 640 Memorial Drive                       Email: roels@mpi.com
>> Cambridge, MA 02139-4853
>> *****************************************************************
>>
>>
>>
>>
>> This e-mail, including any attachments, is a confidential business
>communication, and may contain information that is confidential,
>proprietary and/or privileged.  This e-mail is intended only for the
>individual(s) to whom it is addressed, and may not be saved, copied,
>printed, disclosed or used by anyone else.  If you are not the(an)
intended
>recipient, please immediately delete this e-mail from your computer
system
>and notify the sender.  Thank you.
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu



This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged.  This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else.  If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender.  Thank you.


From vamsi at warta.bio.psu.edu  Thu Oct  9 15:23:03 2003
From: vamsi at warta.bio.psu.edu (Vamsi)
Date: Thu Oct  9 15:20:36 2003
Subject: [Bioperl-l] load_gff.pl error
Message-ID: <200310091923.h99JN3k23009@warta.bio.psu.edu>

Hi,

I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts directory
of the bioperl-1.2.3 distribution. 

When I try
"perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"

I get the error

Can't use string ("ARGV") as a symbol ref while "strict refs" in use at 
/usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.

When I modify sub do_load_gff in GFF.pm by having as the first line
"no strict 'refs';"
the error disappears.

Is this something anyone else has faced?

Thanks,
Vamsi

From jnolan at tulane.edu  Thu Oct  9 16:20:10 2003
From: jnolan at tulane.edu (Jim Nolan)
Date: Thu Oct  9 16:20:28 2003
Subject: [Bioperl-l] OS X bioperl, staden/read, install problems
In-Reply-To: 
References: 
Message-ID: 

I tried installing bioperl-1.2.3 again on a relatively naive machine 
(has bioperl 1.1.1, but no -ext). Installation went off without a 
hitch. I think I must have gotten the idea of installing bioper-ext 
from the www.bioperl.org/Core/external.shtml, after having looked 
there for some other dependency like SOAP::Lite. Modules that are 
this tricky to install (I did try to do the manual installation of 
the missing io_lib files) should have a big skull and crossbones on 
them to keep guys like me out. Or better yet, instructions in the 
readme to tell us how to do it right.

At any rate, I ask that the evaluation for modules outside the core 
release be minimized and that they not cause failure of make test.

Whining aside, thanks to everyone for making such a great resource 
free to all of us, and Thanks for getting me going again after the 
little detour.

Jim

At 3:59 PM -0400 10/8/03, Aaron J Mackey wrote:
>On Mon, 6 Oct 2003, Jason Stajich wrote:
>
>>  When I get together with Aaron at the end of the month I will try and go
>>  through it with him so I understand what is supposed to happen and/or how
>>  we might reorg bioperl-ext to be less problematic.
>
>The problem (over-and-over-again) has been that while people think they
>have the staden io-lib successfully installed, they don't (because they
>have to manually do a few things that the io-lib install doesn't do for
>them).  It's a royal pain, of course.  And then they try to install
>bioperl-ext, which doesn't successfully complete (you can, btw, install
>only parts of bioperl-ext, so the whole staden read lib stuff shouldn't
>prevent someone from installing the other alignment code).
>
>Then, if they ignore that and try to run the normal bioperl test suite,
>they get various odd cryptic errors about read not being successfully
>installed.
>
>-Aaron


-- 
---------------------------------------------------------
Jim Nolan			email:JNolan@tulane.edu
Department of Biochemistry SL43
Tulane University Health Sciences Center
1430 Tulane Ave.		Phone: (504)-584-2453
New Orleans, LA 70112-2699	FAX:   (504)-584-2739
http://www.tulane.edu/~biochem/faculty/nolan.htm
http://phage.bioc.tulane.edu
The requirements said: Windows 2000 or better.
So I got a Macintosh.
From lstein at cshl.edu  Thu Oct  9 16:26:59 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Oct  9 16:24:41 2003
Subject: [Bioperl-l] load_gff.pl error
In-Reply-To: <200310091923.h99JN3k23009@warta.bio.psu.edu>
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
Message-ID: <200310091626.59317.lstein@cshl.edu>

The issue is fixed in bioperl live.

Lincoln

PS: Mark, remember when I told you that your soul would be consigned to 
purgatory if you broke anything when you changed the ARGV handling?  Well, it 
happened.

On Thursday 09 October 2003 03:23 pm, Vamsi wrote:
> Hi,
>
> I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts
> directory of the bioperl-1.2.3 distribution.
>
> When I try
> "perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"
>
> I get the error
>
> Can't use string ("ARGV") as a symbol ref while "strict refs" in use at
> /usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.
>
> When I modify sub do_load_gff in GFF.pm by having as the first line
> "no strict 'refs';"
> the error disappears.
>
> Is this something anyone else has faced?
>
> Thanks,
> Vamsi
>
> _______________________________________________
> 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From markw at illuminae.com  Thu Oct  9 16:57:03 2003
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu Oct  9 16:57:04 2003
Subject: [BioPerl] Re: [Bioperl-l] load_gff.pl error
In-Reply-To: <200310091626.59317.lstein@cshl.edu>
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
	<200310091626.59317.lstein@cshl.edu>
Message-ID: <1065732852.2767.29.camel@localhost.localdomain>

Uh... no, you threatened me with purgatory if I broke the way data
loading from filehandles worked - you said nothing about messing with
ARGV ;-)

..besides, it doesn't look like this error is my fault??  I don't see
any code in there that came from my fingers.  do you know what bit of
code I wrote that is causing that error?

M

On Thu, 2003-10-09 at 14:26, Lincoln Stein wrote:
> The issue is fixed in bioperl live.
> 
> Lincoln
> 
> PS: Mark, remember when I told you that your soul would be consigned to 
> purgatory if you broke anything when you changed the ARGV handling?  Well, it 
> happened.
> 
> On Thursday 09 October 2003 03:23 pm, Vamsi wrote:
> > Hi,
> >
> > I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts
> > directory of the bioperl-1.2.3 distribution.
> >
> > When I try
> > "perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"
> >
> > I get the error
> >
> > Can't use string ("ARGV") as a symbol ref while "strict refs" in use at
> > /usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.
> >
> > When I modify sub do_load_gff in GFF.pm by having as the first line
> > "no strict 'refs';"
> > the error disappears.
> >
> > Is this something anyone else has faced?
> >
> > Thanks,
> > Vamsi
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
Mark Wilkinson 
Illuminae

From lcarey at odd.bio.sunysb.edu  Thu Oct  9 18:48:13 2003
From: lcarey at odd.bio.sunysb.edu (Lucas Carey)
Date: Thu Oct  9 18:45:45 2003
Subject: [Bioperl-l] search for only C-terminal degenerate motifs
Message-ID: <20031009224813.GA11656@odd.bio.sunysb.edu>

Hi,
I'm not sure if this is the correct list, but I figured someone here would be able to help me.
I'd like to use blast to search for a protein motif within a certain number of residues of the C-terminus. What is the best way to go about doing this?
It seems like someone would have already had to do this, and written software to do it. That's what made me think of bioperl.
-Lucas
From palle at birc.dk  Fri Oct 10 05:09:59 2003
From: palle at birc.dk (Palle Villesen)
Date: Fri Oct 10 05:07:49 2003
Subject: [Bioperl-l] Problem retrieving peptides using GenPept
Message-ID: <3F867767.3090609@birc.dk>

Hi,

I have the following code (below), but I get the following error and I'm 
stuck. I have tried various queries and I always get <300 seqs back 
before the exception occurs. I'm not sure if it a speed problem, i.e. 
retrieving the datastream quickjly enough, but I have tried the 
-retrievaltype=>'tempfile' as well - which didn't help.

I couldn't find anything in the docs, hence this mail. Sorry to disturb.

Greetings,
P.
--

   Palle Villesen, Ph.D. 
   BiRC, Build. 090, University of Aarhus
   DK - 8000 Aarhus C, Denmark

   Http://www.daimi.au.dk/~biopv - +45 61708600
---------------------------------------------------------------------



OUTPUT:

Getting accession number for the following query:
BSE

Hits: 118
1 Seq length 176
2 Seq length 253
3 Seq length 176
4 Seq length 178
5 Seq length 96
6 Seq length 179
7 Seq length 179
8 Seq length 253
9 Seq length 360

-------------------- WARNING ---------------------
MSG: exception while parsing location line [bond(179,214)] in reading 
EMBL/GenBank/SwissProt, ignoring feature Bond (seqid=Q60506):
------------- EXCEPTION  -------------
MSG: operator "bond" unrecognized by parser
STACK Bio::Factory::FTLocationFactory::from_string 
/home/serine/palle/bioperl-live/Bio/Factory/FTLocationFactory.pm:160
STACK (eval) /home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:124
STACK Bio::SeqIO::FTHelper::_generic_seqfeature 
/home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:123
STACK Bio::SeqIO::genbank::next_seq 
/home/serine/palle/bioperl-live/Bio/SeqIO/genbank.pm:396
STACK main::get_query get_RVproteins_from_GB.pl:30
STACK (eval) get_RVproteins_from_GB.pl:8
STACK toplevel get_RVproteins_from_GB.pl:7

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

---------------------------------------------------
Caught exception
Done


Program:

#!/usr/local/bin/perl
my $query_string = "BSE";

print "Getting the following query:$query_string\n";

eval {
  get_query($query_string);
};

if ($@) {
  print "Caught exception\n";
}
print "Done\n\n";
exit();

sub get_query {
  use Bio::DB::GenPept;
  use Bio::DB::Query::GenBank;
  my ($query_string) = @_;
  my $query = Bio::DB::Query::GenBank->new(-db=>'protein',
					   -query=>$query_string
					  );
  my $gb = Bio::DB::GenPept->new ();
  print "Hits: ".$query->count."\n";
  my @ids = $query->ids;
  my $current =1;
  my $seqio = $gb->get_Stream_by_query($query);
  my $current =1;
  while (my $seq = $seqio->next_seq()) {
    print $current++." Seq length ".$seq->length()."\n";
  }
return 1;
}




From senger at ebi.ac.uk  Fri Oct 10 07:16:50 2003
From: senger at ebi.ac.uk (Martin Senger)
Date: Fri Oct 10 07:15:04 2003
Subject: [Bioperl-l] Re: Bio::Biblio
Message-ID: 

Hi again,

>        My goal is to write a quick-and-dirty medline2docbook fliter for
> immediate use, using bioperl since it has already a library able to
> query medline.
> ...
> Can anybody point me to the correct object and its construction method?>
>

   As mentioned already, the good source for that is the script provided 
within bioperl. The script is: examples/biblio/biblio.PLS.
   Here I am ataching an example doing hopefully what you wish (and few 
explanations labelled by '(digit)' pattern:

#!/usr/bin/perl -w

use Bio::Biblio;       # to read data via SOAP
use Bio::Biblio::IO;   # to convert resulting XML to Biblio objects

# (1)
# --- taking citations from MEDLINE at EBI using SOAP
my $biblio = new Bio::Biblio;
my $citation = $biblio->get_by_id ('11112222');

# (2)
# --- make an instance of a converter
my $io = new Bio::Biblio::IO ('-data' => $citation);

# (3)
# --- and make the conversion (use the citation)
print << 'DOCBOOK_START';

   
DOCBOOK_START

while (my $bibref = $io->next_bibref) {
    foreach (@ {$$bibref{'_authors'}} ) {
	print << "DOCBOOK";
	 
	    $$_{_lastname}
	    $$_{_forename}
	 
DOCBOOK
    }
}
print << 'DOCBOOK_END';
   

DOCBOOK_END

__END__

Notes:

(1) First you need to get a citation (or a collection of citations. You
may get it from MEDLINEW at EBI (as shown in the script above), but you
can also get it from the PubMed web page, or you have it already in your
local file. The script shows how to get a citation by its ID, but you can 
slo get them by using a query, e.g. using:
   my $citation = $biblio->find ('brazma')->get_all;
   Anyway, the citation (or citations) is now in your possesion in an XML
format.

(2) You may specify various arguments in the constructor. By default it 
expects that you wish result as perl biblio objects. If you rather wish a 
raw hashtable use ('-result' => 'raw') in the constructor.
   Also you say where is your citation to be converted. If you have it in 
a file use ('-file' => $citation).
   If you got your citatioin from PubMed which is slightly different XML 
from Medline) use ('-format' => 'pubmedxml').

(3) The created biblio objects do not have any methods, you just use their 
attributes. It is not ideal I know but there is no object representing all 
attributes as get methods.
   The best way hiw to find what attributes are available is to print the 
whole citation:
   print $bibref->print_me;

   I hope this helps you. Please let me know if you need more.
   Regards, Martin

PS. BTW, this is what you should get when running the script above:

   
         
            Oyer
            C E
         
         
            Ongcapin
            E H
         
         
            Ni
            J
         
         
            Bowles
            N E
         
         
            Towbin
            J A
         
   


-- 
Martin Senger

EMBL Outstation - Hinxton                Senger@EBI.ac.uk     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger

From brian_osborne at cognia.com  Fri Oct 10 08:54:36 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Fri Oct 10 08:56:42 2003
Subject: [Bioperl-l] Problem retrieving peptides using GenPept
In-Reply-To: <3F867767.3090609@birc.dk>
Message-ID: 

Palle,

This is not a problem with your code or your connection, it's the "bond"
operator in the entry you're trying to retrieve. The Genbank and GenPept
parsers were written to respect the formal specifications for the
Genbank/EMBL/DDBJ feature tables (see
http://www.ncbi.nlm.nih.gov/projects/collab/FT/ for the details). The bond
operator is not in the standard, yet Genbank, for some reason, has allowed
it to appear so Bioperl is complaining. One possible work-around is to use
eval{} around the appropriate lines in your get_query().

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Palle Villesen
Sent: Friday, October 10, 2003 5:10 AM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Problem retrieving peptides using GenPept

Hi,

I have the following code (below), but I get the following error and I'm
stuck. I have tried various queries and I always get <300 seqs back
before the exception occurs. I'm not sure if it a speed problem, i.e.
retrieving the datastream quickjly enough, but I have tried the
-retrievaltype=>'tempfile' as well - which didn't help.

I couldn't find anything in the docs, hence this mail. Sorry to disturb.

Greetings,
P.
--

   Palle Villesen, Ph.D.
   BiRC, Build. 090, University of Aarhus
   DK - 8000 Aarhus C, Denmark

   Http://www.daimi.au.dk/~biopv - +45 61708600
---------------------------------------------------------------------



OUTPUT:

Getting accession number for the following query:
BSE

Hits: 118
1 Seq length 176
2 Seq length 253
3 Seq length 176
4 Seq length 178
5 Seq length 96
6 Seq length 179
7 Seq length 179
8 Seq length 253
9 Seq length 360

-------------------- WARNING ---------------------
MSG: exception while parsing location line [bond(179,214)] in reading
EMBL/GenBank/SwissProt, ignoring feature Bond (seqid=Q60506):
------------- EXCEPTION  -------------
MSG: operator "bond" unrecognized by parser
STACK Bio::Factory::FTLocationFactory::from_string
/home/serine/palle/bioperl-live/Bio/Factory/FTLocationFactory.pm:160
STACK (eval) /home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:124
STACK Bio::SeqIO::FTHelper::_generic_seqfeature
/home/serine/palle/bioperl-live/Bio/SeqIO/FTHelper.pm:123
STACK Bio::SeqIO::genbank::next_seq
/home/serine/palle/bioperl-live/Bio/SeqIO/genbank.pm:396
STACK main::get_query get_RVproteins_from_GB.pl:30
STACK (eval) get_RVproteins_from_GB.pl:8
STACK toplevel get_RVproteins_from_GB.pl:7

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

---------------------------------------------------
Caught exception
Done


Program:

#!/usr/local/bin/perl
my $query_string = "BSE";

print "Getting the following query:$query_string\n";

eval {
  get_query($query_string);
};

if ($@) {
  print "Caught exception\n";
}
print "Done\n\n";
exit();

sub get_query {
  use Bio::DB::GenPept;
  use Bio::DB::Query::GenBank;
  my ($query_string) = @_;
  my $query = Bio::DB::Query::GenBank->new(-db=>'protein',
                                           -query=>$query_string
                                          );
  my $gb = Bio::DB::GenPept->new ();
  print "Hits: ".$query->count."\n";
  my @ids = $query->ids;
  my $current =1;
  my $seqio = $gb->get_Stream_by_query($query);
  my $current =1;
  while (my $seq = $seqio->next_seq()) {
    print $current++." Seq length ".$seq->length()."\n";
  }
return 1;
}




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


From robert.roth at home.se  Fri Oct 10 09:21:22 2003
From: robert.roth at home.se (Robert Roth)
Date: Fri Oct 10 09:18:54 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 


Brian,

Thank you for your advice. I got the database set up under cygwin now
and everything seems to work so far. The only thing that caused some trouble
was that I am not able to use 'localhost' as host when running the test for
bioperl-db. Using 127.0.0.1 as described at the link below for the
installation of DBD-mysql also solved these problems. Now
load_seqdatabase.pl seem to work so I guess I'll load the data under cygwin.

/Robert


>
>
> Robert,
>
> > Is there someone else who have a working installation of
> Bioperl/bioperl-db/biosql under windows?
>
> I've not done extensive use or testing of my Mysql database but
> I've set up
> a small one using load_taxonomy.pl followed by
> load_seqdatabase.pl. This was
> a month or so ago. I used Cygwin, the latest bioperl from CVS, latest
> biosql-schema, and the latest bioperl-db, installed in that order. Mysql
> 4.0.13. The only tricky part is getting DBD::Mysql running under Cygwin. I
> was getting a bit frustrated but then I stumbled on this:
>
> http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#win
> dows/cygwi
> n
>
>
> Brian O.
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robert Roth
> Sent: Thursday, October 09, 2003 7:51 AM
> To: bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> I started over again and also upgraded to perl 5.8 (from ActiveState). The
> claim in INSTALL.WIN that not all external modules are available from the
> ppm repositories is no longer true.
> Since the the installation of Bioperl with ppm does not give the
> possiblity
> to run the test suite I skipped it and installed Bioperl-1.2.3 with nmake
> instead. The test suite for bioperl ran without any major
> problems. With all
> test that just returned "ok" removed for brevity the output was,
>
> ************************************************************************
> t\Assembly...................DB_File not installed. This means
> the Assembly
> modules are not available.  Skipping tests.
> t\Assembly...................ok
> t\DB.........................ok
>         1/78 skipped:
> t\flat.......................DB_File not loaded. This means flat.t test
> cannot
> be executed. Skipping
> t\flat.......................ok
> t\Index......................ok 11/32Can't call method "accession" on an
> undefined value at E:\temp\bioperl-1.2.3\blib\lib/Bio/DB/InMemoryCache.pm
> line 220,  line 54.
> t\Index......................dubious
>         Test returned status 22 (wstat 5632, 0x1600)
>         after all the subtests completed successfully
> t\SeqFeatCollection..........DB_File not installed. This means the
> SeqFeatCollection wont work
> t\SeqFeatCollection..........ok
> Failed Test Stat Wstat Total Fail  Failed  List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\Index.t     22  5632    32    0   0.00%  ??
> 4 subtests skipped.
> Failed 1/123 test scripts, 99.19% okay. 0/5977 subtests failed, 100.00%
> okay.
> ************************************************************************
>
>
>
> After this I moved on and installed bioperl-db. Running the test
> suite gives
> the lengthy (sorry...) output below. They all (except dbadaptor.t and
> query.t) fail with the same output. Attempting to run load_seqdatabase.pl
> fails with the same output as before.
> The complains about redefined subroutines that I showed in an earlier
> message that I get when running load_seqdatabase.pl is something that is
> known and attributed to a more "sensitive" perl on windows.
> If the problem still seems to be related to the perl setup I
> guess I have to
> build perl also and abandon activestate. Is there someone else who have a
> working installation of Bioperl/bioperl-db/biosql under windows?
> Your help is very much appreciated.
>
> /Robert
>
>
> *************************************************************************
>  C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
> ib\lib', 'blib\arch')" t\cluster.t t\comment.t t\dbadaptor.t t\dblink.t
> t\ensemb
> l.t t\fuzzy2.t t\genbank.t t\locuslink.t t\ontology.t t\query.t t\remove.t
> t\seq
> feature.t t\simpleseq.t t\species.t t\swiss.t
> t\cluster.......ok 2/160Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 205,
>  line
> 1.
> t\cluster.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-160
>         Failed 158/160 tests, 1.25% okay
> t\comment.......ok 2/11Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\comment.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-11
>         Failed 9/11 tests, 18.18% okay
> t\dbadaptor.....ok
> t\dblink........ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\dblink........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
>         Failed 16/18 tests, 11.11% okay
> t\ensembl.......ok 2/15Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 1420.
> t\ensembl.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-15
>         Failed 13/15 tests, 13.33% okay
> t\fuzzy2........ok 2/21Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 64.
> t\fuzzy2........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-21
>         Failed 19/21 tests, 9.52% okay
> t\genbank.......ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\genbank.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
>         Failed 16/18 tests, 11.11% okay
> t\locuslink.....ok 3/110Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
>  > line 1.
> t\locuslink.....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 4-110
>         Failed 107/110 tests, 2.73% okay
> t\ontology......ok 4/291Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
>  > line 98.
> t\ontology......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-291
>         Failed 287/291 tests, 1.37% okay
> t\query.........ok
> t\remove........ok 1/59Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 41.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> remove.t line 32,  line 41.
> Undefined subroutine &Bio::Root::Root::throw called at
> E:\temp\bioperl-db\blib\l
> ib/Bio\DB\BioSQL\DBAdaptor.pm line 174,  line 41.
> t\remove........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-59
>         Failed 58/59 tests, 1.69% okay
> t\seqfeature....ok 2/48Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\seqfeature....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-48
>         Failed 46/48 tests, 4.17% okay
> t\simpleseq.....ok 8/27Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 1.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 45,  line 1.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 73,  line 1.
> Undefined subroutine &Bio::Root::Root::debug called at
> E:\temp\bioperl-db\blib\l
> ib/Bio/DB/BioSQL/BaseDriver.pm line 410,  line 1.
> t\simpleseq.....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 9-27
>         Failed 19/27 tests, 29.63% okay
> t\species.......ok 2/65Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198.
> t\species.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-65
>         Failed 63/65 tests, 3.08% okay
> t\swiss.........ok 2/52Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 78.
> t\swiss.........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-52
>         Failed 50/52 tests, 3.85% okay
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\cluster.t     255 65280   160  158  98.75%  3-160
> t\comment.t     255 65280    11    9  81.82%  3-11
> t\dblink.t      255 65280    18   16  88.89%  3-18
> t\ensembl.t     255 65280    15   13  86.67%  3-15
> t\fuzzy2.t      255 65280    21   19  90.48%  3-21
> t\genbank.t     255 65280    18   16  88.89%  3-18
> t\locuslink.t   255 65280   110  107  97.27%  4-110
> t\ontology.t    255 65280   291  287  98.63%  5-291
> t\remove.t      255 65280    59   58  98.31%  2-59
> t\seqfeature.t  255 65280    48   46  95.83%  3-48
> t\simpleseq.t   255 65280    27   19  70.37%  9-27
> t\species.t     255 65280    65   63  96.92%  3-65
> t\swiss.t       255 65280    52   50  96.15%  3-52
> Failed 13/15 test scripts, 13.33% okay. 861/919 subtests failed,
> 6.31% okay.
> ******************************************************************
> **********
> ****
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: 09 October 2003 02:01
> To: Robert Roth
> Cc: BioPerl
> Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> This is definitely related to the perl setup I'd claim. Have you been able
> to run the bioperl test suite without similar trouble?
>
> Again, I'm cc'ing the bioperl list in case anybody has seen this also and
> has clues as to what the cause is and how to remedy it.
>
>     -hilmar
>
>
> _______________________________________________
> 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  Fri Oct 10 09:27:36 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Fri Oct 10 09:29:35 2003
Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
In-Reply-To: 
Message-ID: 

Cool.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robert Roth
Sent: Friday, October 10, 2003 9:21 AM
To: Brian Osborne; bioperl-l@bioperl.org
Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl


Brian,

Thank you for your advice. I got the database set up under cygwin now
and everything seems to work so far. The only thing that caused some trouble
was that I am not able to use 'localhost' as host when running the test for
bioperl-db. Using 127.0.0.1 as described at the link below for the
installation of DBD-mysql also solved these problems. Now
load_seqdatabase.pl seem to work so I guess I'll load the data under cygwin.

/Robert


>
>
> Robert,
>
> > Is there someone else who have a working installation of
> Bioperl/bioperl-db/biosql under windows?
>
> I've not done extensive use or testing of my Mysql database but
> I've set up
> a small one using load_taxonomy.pl followed by
> load_seqdatabase.pl. This was
> a month or so ago. I used Cygwin, the latest bioperl from CVS, latest
> biosql-schema, and the latest bioperl-db, installed in that order. Mysql
> 4.0.13. The only tricky part is getting DBD::Mysql running under Cygwin. I
> was getting a bit frustrated but then I stumbled on this:
>
> http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#win
> dows/cygwi
> n
>
>
> Brian O.
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Robert Roth
> Sent: Thursday, October 09, 2003 7:51 AM
> To: bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> I started over again and also upgraded to perl 5.8 (from ActiveState). The
> claim in INSTALL.WIN that not all external modules are available from the
> ppm repositories is no longer true.
> Since the the installation of Bioperl with ppm does not give the
> possiblity
> to run the test suite I skipped it and installed Bioperl-1.2.3 with nmake
> instead. The test suite for bioperl ran without any major
> problems. With all
> test that just returned "ok" removed for brevity the output was,
>
> ************************************************************************
> t\Assembly...................DB_File not installed. This means
> the Assembly
> modules are not available.  Skipping tests.
> t\Assembly...................ok
> t\DB.........................ok
>         1/78 skipped:
> t\flat.......................DB_File not loaded. This means flat.t test
> cannot
> be executed. Skipping
> t\flat.......................ok
> t\Index......................ok 11/32Can't call method "accession" on an
> undefined value at E:\temp\bioperl-1.2.3\blib\lib/Bio/DB/InMemoryCache.pm
> line 220,  line 54.
> t\Index......................dubious
>         Test returned status 22 (wstat 5632, 0x1600)
>         after all the subtests completed successfully
> t\SeqFeatCollection..........DB_File not installed. This means the
> SeqFeatCollection wont work
> t\SeqFeatCollection..........ok
> Failed Test Stat Wstat Total Fail  Failed  List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\Index.t     22  5632    32    0   0.00%  ??
> 4 subtests skipped.
> Failed 1/123 test scripts, 99.19% okay. 0/5977 subtests failed, 100.00%
> okay.
> ************************************************************************
>
>
>
> After this I moved on and installed bioperl-db. Running the test
> suite gives
> the lengthy (sorry...) output below. They all (except dbadaptor.t and
> query.t) fail with the same output. Attempting to run load_seqdatabase.pl
> fails with the same output as before.
> The complains about redefined subroutines that I showed in an earlier
> message that I get when running load_seqdatabase.pl is something that is
> known and attributed to a more "sensitive" perl on windows.
> If the problem still seems to be related to the perl setup I
> guess I have to
> build perl also and abandon activestate. Is there someone else who have a
> working installation of Bioperl/bioperl-db/biosql under windows?
> Your help is very much appreciated.
>
> /Robert
>
>
> *************************************************************************
>  C:\Perl\bin\perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'bl
> ib\lib', 'blib\arch')" t\cluster.t t\comment.t t\dbadaptor.t t\dblink.t
> t\ensemb
> l.t t\fuzzy2.t t\genbank.t t\locuslink.t t\ontology.t t\query.t t\remove.t
> t\seq
> feature.t t\simpleseq.t t\species.t t\swiss.t
> t\cluster.......ok 2/160Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio\DB\BioSQL\DBAdaptor.pm line 205,
>  line
> 1.
> t\cluster.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-160
>         Failed 158/160 tests, 1.25% okay
> t\comment.......ok 2/11Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\comment.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-11
>         Failed 9/11 tests, 18.18% okay
> t\dbadaptor.....ok
> t\dblink........ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\dblink........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
>         Failed 16/18 tests, 11.11% okay
> t\ensembl.......ok 2/15Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 1420.
> t\ensembl.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-15
>         Failed 13/15 tests, 13.33% okay
> t\fuzzy2........ok 2/21Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 64.
> t\fuzzy2........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-21
>         Failed 19/21 tests, 9.52% okay
> t\genbank.......ok 2/18Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\genbank.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-18
>         Failed 16/18 tests, 11.11% okay
> t\locuslink.....ok 3/110Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
>  > line 1.
> t\locuslink.....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 4-110
>         Failed 107/110 tests, 2.73% okay
> t\ontology......ok 4/291Undefined subroutine
> &Bio::Root::Root::throw called
> at E
> :\temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
>  > line 98.
> t\ontology......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 5-291
>         Failed 287/291 tests, 1.37% okay
> t\query.........ok
> t\remove........ok 1/59Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 41.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> remove.t line 32,  line 41.
> Undefined subroutine &Bio::Root::Root::throw called at
> E:\temp\bioperl-db\blib\l
> ib/Bio\DB\BioSQL\DBAdaptor.pm line 174,  line 41.
> t\remove........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 2-59
>         Failed 58/59 tests, 1.69% okay
> t\seqfeature....ok 2/48Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 72.
> t\seqfeature....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-48
>         Failed 46/48 tests, 4.17% okay
> t\simpleseq.....ok 8/27Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 1.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 45,  line 1.
>         (in cleanup) Undefined subroutine &Bio::Root::Root::DESTROY called
> at t\
> simpleseq.t line 73,  line 1.
> Undefined subroutine &Bio::Root::Root::debug called at
> E:\temp\bioperl-db\blib\l
> ib/Bio/DB/BioSQL/BaseDriver.pm line 410,  line 1.
> t\simpleseq.....dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 9-27
>         Failed 19/27 tests, 29.63% okay
> t\species.......ok 2/65Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198.
> t\species.......dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-65
>         Failed 63/65 tests, 3.08% okay
> t\swiss.........ok 2/52Undefined subroutine &Bio::Root::Root::throw called
> at E:
> \temp\bioperl-db\blib\lib/Bio/DB/Persistent/PersistentObject.pm line 198,
> 
>  line 78.
> t\swiss.........dubious
>         Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 3-52
>         Failed 50/52 tests, 3.85% okay
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> ------------------------------------------------------------------
> ----------
> ---
> t\cluster.t     255 65280   160  158  98.75%  3-160
> t\comment.t     255 65280    11    9  81.82%  3-11
> t\dblink.t      255 65280    18   16  88.89%  3-18
> t\ensembl.t     255 65280    15   13  86.67%  3-15
> t\fuzzy2.t      255 65280    21   19  90.48%  3-21
> t\genbank.t     255 65280    18   16  88.89%  3-18
> t\locuslink.t   255 65280   110  107  97.27%  4-110
> t\ontology.t    255 65280   291  287  98.63%  5-291
> t\remove.t      255 65280    59   58  98.31%  2-59
> t\seqfeature.t  255 65280    48   46  95.83%  3-48
> t\simpleseq.t   255 65280    27   19  70.37%  9-27
> t\species.t     255 65280    65   63  96.92%  3-65
> t\swiss.t       255 65280    52   50  96.15%  3-52
> Failed 13/15 test scripts, 13.33% okay. 861/919 subtests failed,
> 6.31% okay.
> ******************************************************************
> **********
> ****
>
>
>
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: 09 October 2003 02:01
> To: Robert Roth
> Cc: BioPerl
> Subject: [Bioperl-l] Re: [BioSQL-l] Error using load_seqdatabase.pl
>
>
> This is definitely related to the perl setup I'd claim. Have you been able
> to run the bioperl test suite without similar trouble?
>
> Again, I'm cc'ing the bioperl list in case anybody has seen this also and
> has clues as to what the cause is and how to remedy it.
>
>     -hilmar
>
>
> _______________________________________________
> 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 lstein at cshl.edu  Fri Oct 10 12:26:37 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri Oct 10 12:24:21 2003
Subject: [Bioperl-l] Problem retrieving peptides using GenPept
In-Reply-To: <3F867767.3090609@birc.dk>
References: <3F867767.3090609@birc.dk>
Message-ID: <200310101226.37841.lstein@cshl.edu>

Hi,

This looks like a problem in the parser when it hits an entry that is not 
prepared for.  My prediction would be that you will always get the exception 
at the same accession number, but it sounds like you get sometimes more and 
sometimes less?  Please see whether you can isolate the issue to a particular 
entry.  This will help debug the problem.

Lincoln

On Friday 10 October 2003 05:09 am, Palle Villesen wrote:
> Hi,
>
> I have the following code (below), but I get the following error and I'm
> stuck. I have tried various queries and I always get <300 seqs back
> before the exception occurs. I'm not sure if it a speed problem, i.e.
> retrieving the datastream quickjly enough, but I have tried the
> -retrievaltype=>'tempfile' as well - which didn't help.
>
> I couldn't find anything in the docs, hence this mail. Sorry to disturb.
>
> Greetings,
> P.

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From brian_osborne at cognia.com  Fri Oct 10 15:31:44 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Fri Oct 10 15:34:14 2003
Subject: [Bioperl-l] search for only C-terminal degenerate motifs
In-Reply-To: <20031009224813.GA11656@odd.bio.sunysb.edu>
Message-ID: 

Lucas,

I don't think a script exactly like this exists in Bioperl but certainly the
means to write this script does. A good start might be the SearchIO HOWTO
(bioperl.org/HOWTOs). The combination of SearchIO and StandAloneBlast
(section III.4.5 of the bptutorial) enables you to run BLAST and parse the
results. The details of the C-terminal match should be straightforward, I
think, but it depends on your familiarity with Perl.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Lucas Carey
Sent: Thursday, October 09, 2003 6:48 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] search for only C-terminal degenerate motifs

Hi,
I'm not sure if this is the correct list, but I figured someone here would
be able to help me.
I'd like to use blast to search for a protein motif within a certain number
of residues of the C-terminus. What is the best way to go about doing this?
It seems like someone would have already had to do this, and written
software to do it. That's what made me think of bioperl.
-Lucas
_______________________________________________
Bioperl-l mailing list
Bioperl-l@portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


From amackey at pcbi.upenn.edu  Fri Oct 10 16:08:26 2003
From: amackey at pcbi.upenn.edu (Aaron J. Mackey)
Date: Fri Oct 10 16:05:54 2003
Subject: [Bioperl-l] search for only C-terminal degenerate motifs
In-Reply-To: 
Message-ID: <81E173BD-FB5D-11D7-9104-000A958C5008@pcbi.upenn.edu>

Yeah, the problem is you'd really like to *not* search all of the 
database (for both speed and statistical reasons), only the first n 
C-terminal residues of each sequence in the database.  Both BLAST and 
FASTA have mechanisms to allow you to focus the search on a given part 
of the query, but not on a given part of the library.  Unfortunately, I 
think the best/quickest answer is to make your own database of 
C-terminal sequences [perhaps using Bio::SeqIO and $seq->trunc()].

But you said "motif" - are you trying to find:

   a) exact matches to a given short sequence
   b) exact matches to a consensus regular expression (e.g.: CX[S|T]C)
   c) near-exact, homologous matches using a query sequence and a 
stringent, shallow scoring matrix
   d) high scoring matches to a position-specific profile/weight matrix

Depending on the answer, you should be able to use current tools, 
filter your output based on where hits occur, and then alter any 
statistical results (P, E()) to accomodate your effectively reduced 
search space.

-Aaron

On Friday, October 10, 2003, at 03:31 PM, Brian Osborne wrote:

> Lucas,
>
> I don't think a script exactly like this exists in Bioperl but 
> certainly the
> means to write this script does. A good start might be the SearchIO 
> HOWTO
> (bioperl.org/HOWTOs). The combination of SearchIO and StandAloneBlast
> (section III.4.5 of the bptutorial) enables you to run BLAST and parse 
> the
> results. The details of the C-terminal match should be 
> straightforward, I
> think, but it depends on your familiarity with Perl.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Lucas Carey
> Sent: Thursday, October 09, 2003 6:48 PM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] search for only C-terminal degenerate motifs
>
> Hi,
> I'm not sure if this is the correct list, but I figured someone here 
> would
> be able to help me.
> I'd like to use blast to search for a protein motif within a certain 
> number
> of residues of the C-terminus. What is the best way to go about doing 
> this?
> It seems like someone would have already had to do this, and written
> software to do it. That's what made me think of bioperl.
> -Lucas
> _______________________________________________
> 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 grossman at molgen.mpg.de  Fri Oct 10 16:45:39 2003
From: grossman at molgen.mpg.de (Steffen Grossmann)
Date: Fri Oct 10 16:42:05 2003
Subject: [Bioperl-l] Method dnaseq in EncodedSeq not working properly?
Message-ID: <3F871A73.7080908@molgen.mpg.de>

Dear all,

am I wrong or does the method "dnaseq" of Bio::Seq::EncodedSeq not do 
what is promised in the documentation? I understand the documentation 
such that e.g. with the command

@introns = $obj->$dnaseq(-encoding => 'I')

I would get a list of all the parts in the sequence which are coded with 
an 'I'. (From a look at the method's code I'd say it doesn't do anything 
at all...)

Actually, what I really need is a way to identify pieces of repeated X's 
or N's from DNA sequences in order to exclude them from a sequence-wide 
screening for good hits of a position-weight-matrix. Any hint concerning 
that problem is highly appreciated! Since I am a bioperl-newbie maybe I 
only suffer from a lack of overview...

Steffen
-- 
%---------------------------------------------%
%            Steffen Grossmann                %
%                                             %
% Max Planck Institute for Molecular Genetics %
%      Computational Molecular Biology        %
%---------------------------------------------%
%              Ihnestrasse 73                 %
%               14195 Berlin                  %
%                 Germany                     %
%---------------------------------------------%
%         Tel: (++49 +30) 8413-1167           %
%         Fax: (++49 +30) 8413-1152           %
%---------------------------------------------%

From lstein at cshl.edu  Fri Oct 10 16:59:47 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Fri Oct 10 16:57:23 2003
Subject: [BioPerl] Re: [Bioperl-l] load_gff.pl error
In-Reply-To: <1065732852.2767.29.camel@localhost.localdomain>
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
	<200310091626.59317.lstein@cshl.edu>
	<1065732852.2767.29.camel@localhost.localdomain>
Message-ID: <200310101659.47813.lstein@cshl.edu>

Hi Mark,

Oh dear.  I maligned you.  I personally broke the code in order to satisfy 
your request that load_gff() handle tied filehandles.  Now we both have to 
spend time in purgatory.

Lincoln

On Thursday 09 October 2003 04:54 pm, Mark Wilkinson wrote:
> Uh... no, you threatened me with purgatory if I broke the way data
> loading from filehandles worked - you said nothing about messing with
> ARGV ;-)
>
> .besides, it doesn't look like this error is my fault??  I don't see
> any code in there that came from my fingers.  do you know what bit of
> code I wrote that is causing that error?
>
> M
>
> On Thu, 2003-10-09 at 14:26, Lincoln Stein wrote:
> > The issue is fixed in bioperl live.
> >
> > Lincoln
> >
> > PS: Mark, remember when I told you that your soul would be consigned to
> > purgatory if you broke anything when you changed the ARGV handling? 
> > Well, it happened.
> >
> > On Thursday 09 October 2003 03:23 pm, Vamsi wrote:
> > > Hi,
> > >
> > > I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts
> > > directory of the bioperl-1.2.3 distribution.
> > >
> > > When I try
> > > "perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"
> > >
> > > I get the error
> > >
> > > Can't use string ("ARGV") as a symbol ref while "strict refs" in use at
> > > /usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.
> > >
> > > When I modify sub do_load_gff in GFF.pm by having as the first line
> > > "no strict 'refs';"
> > > the error disappears.
> > >
> > > Is this something anyone else has faced?
> > >
> > > Thanks,
> > > Vamsi
> > >
> > > _______________________________________________
> > > 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From amackey at pcbi.upenn.edu  Fri Oct 10 17:09:12 2003
From: amackey at pcbi.upenn.edu (Aaron J. Mackey)
Date: Fri Oct 10 17:06:40 2003
Subject: [Bioperl-l] Method dnaseq in EncodedSeq not working properly?
In-Reply-To: <3F871A73.7080908@molgen.mpg.de>
Message-ID: 

You're completely correct, it's entirely documented but entirely 
unimplemented.  Since you're the first to notice, you must also be the 
first to need it ;)  If you continue to need it, I'll see what I can do.

> Actually, what I really need is a way to identify pieces of repeated 
> X's or N's from DNA sequences in order to exclude them from a 
> sequence-wide screening for good hits of a position-weight-matrix.

If I understand you correctly, your weight matrix search results in 
hits that "align" against X/N's, and you want to filter out those hits. 
  I see two choices:

    1) alter your profile to give very bad scores to X/N (if you have 
this capability)
    2) use some Bio::Range objects representing hits and X/N stretches, 
and call
       $hit->overlap($xn) to see if they overlap.

-Aaron

From markw at illuminae.com  Fri Oct 10 18:36:50 2003
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri Oct 10 18:36:51 2003
Subject: [BioPerl] Re: [Bioperl-l] load_gff.pl error
In-Reply-To: <200310101659.47813.lstein@cshl.edu>
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
	<200310091626.59317.lstein@cshl.edu>
	<1065732852.2767.29.camel@localhost.localdomain>
	<200310101659.47813.lstein@cshl.edu>
Message-ID: <1065825558.1698.90.camel@localhost.localdomain>

hey... wait a minute!  

Why do *I* have to go to purgatory?!  I didn't do anything wrong - I
only *suggested* that the code be changed... and it wasn't even for ME! 
It was for Sheldon - damn HIM!

This just isn't fair at all... I hate divine thought-police   }-/

M


On Fri, 2003-10-10 at 14:59, Lincoln Stein wrote:
> Hi Mark,
> 
> Oh dear.  I maligned you.  I personally broke the code in order to satisfy 
> your request that load_gff() handle tied filehandles.  Now we both have to 
> spend time in purgatory.
> 
> Lincoln
> 
> On Thursday 09 October 2003 04:54 pm, Mark Wilkinson wrote:
> > Uh... no, you threatened me with purgatory if I broke the way data
> > loading from filehandles worked - you said nothing about messing with
> > ARGV ;-)
> >
> > .besides, it doesn't look like this error is my fault??  I don't see
> > any code in there that came from my fingers.  do you know what bit of
> > code I wrote that is causing that error?
> >
> > M
> >
> > On Thu, 2003-10-09 at 14:26, Lincoln Stein wrote:
> > > The issue is fixed in bioperl live.
> > >
> > > Lincoln
> > >
> > > PS: Mark, remember when I told you that your soul would be consigned to
> > > purgatory if you broke anything when you changed the ARGV handling? 
> > > Well, it happened.
> > >
> > > On Thursday 09 October 2003 03:23 pm, Vamsi wrote:
> > > > Hi,
> > > >
> > > > I am trying to use the load_gff.pl located in the Bio-DB-GFF/scripts
> > > > directory of the bioperl-1.2.3 distribution.
> > > >
> > > > When I try
> > > > "perl load_gff.pl --dsn dbi:mysql:XXX --user XXX --pass XXX a.gff"
> > > >
> > > > I get the error
> > > >
> > > > Can't use string ("ARGV") as a symbol ref while "strict refs" in use at
> > > > /usr/perl5/site_perl/5.005/Bio/DB/GFF.pm line 2130.
> > > >
> > > > When I modify sub do_load_gff in GFF.pm by having as the first line
> > > > "no strict 'refs';"
> > > > the error disappears.
> > > >
> > > > Is this something anyone else has faced?
> > > >
> > > > Thanks,
> > > > Vamsi
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@portal.open-bio.org
> > > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
Mark Wilkinson 
Illuminae

From smckay at bcgsc.bc.ca  Fri Oct 10 19:11:08 2003
From: smckay at bcgsc.bc.ca (Sheldon McKay)
Date: Fri Oct 10 19:08:35 2003
Subject: [BioPerl] Re: [Bioperl-l] load_gff.pl error
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
	<200310091626.59317.lstein@cshl.edu>
	<1065732852.2767.29.camel@localhost.localdomain>
	<200310101659.47813.lstein@cshl.edu>
	<1065825558.1698.90.camel@localhost.localdomain>
Message-ID: <001101c38f83$da88ec00$c201010a@celegans01>

Mark is indeed correct, it was I who wanted tied filehandles.  I don't think
third party damning is allowed, sorry Mark.
When you get released from purgatory, please don't remove the tied
filehandle functionality.

Sheldon

----- Original Message -----
From: "Mark Wilkinson" 
To: "Lincoln Stein" ; "Doreen Ware" ;
"Sheldon McKay" ; "me" 
Cc: 
Sent: Friday, October 10, 2003 3:39 PM
Subject: Re: [BioPerl] Re: [Bioperl-l] load_gff.pl error


> hey... wait a minute!
>
> Why do *I* have to go to purgatory?!  I didn't do anything wrong - I
> only *suggested* that the code be changed... and it wasn't even for ME!
> It was for Sheldon - damn HIM!
>
> This just isn't fair at all... I hate divine thought-police   }-/
>
> M
>
>


From bmadsen at mathworks.com  Fri Oct 10 11:29:35 2003
From: bmadsen at mathworks.com (Brian Madsen)
Date: Fri Oct 10 21:16:58 2003
Subject: [Bioperl-l] Suggestions for MATLAB-Bioperl Interface
Message-ID: 

I am studying Bioinformatics through the Master's program at
Northeastern and am working as a co-op at MathWorks on their
Bioinformatics Toolbox.

In August, I met a few researchers around Boston to get ideas on the
Toolbox. One of the best suggestions was from a current user, Dr. Vamsi
Mootha at the Whitehead Institute. He was interested in calling Bioperl
apps from MATLAB and calling MATLAB functions from Bioperl. While I
don't yet have a streamlined approach for calling MATLAB from Perl, I
have gone through the installation of Bioperl and tested calling Perl
apps from the toolbox (attached is an html of a demo).

2 questions:
1 - Are there any suggestions on the interface for MATLAB and
Bioperl--any procedures or issues I should research?
2 - What intellectual property issues might be involved? With the base
of Bioperl modules available, I thought it might be a good idea to
include an installation of Bioperl on the Bioinformatics Toolbox CD.

Thanks for any ideas.

-Brian Madsen
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From bio at masrao.homelinux.com  Sat Oct 11 06:07:24 2003
From: bio at masrao.homelinux.com (Koichi Minamijima)
Date: Sat Oct 11 05:49:26 2003
Subject: [Bioperl-l] Bio::Graphics HOWTO :: about of the color of graph
Message-ID: <20031011190724.D09D3770.bio@masrao.com>

Hi.
If it knows, please let me know.

I looked at the web page of "BioGraphics HOWTO."
It was used having edited "Example 4."
	http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html#parsing-
blast

[next unless $hit->significance < 1E-20;] 
of the 38th line was only changed into 
[next unless $hit->significance < 1;].

rscu.fas (ftp://ftp.ncbi.nlm.nih.gov/refseq/cumulative/rscu.fas.Z) 
and "One arrangement file" were used, and blastall was done.
The picture was generated when "Exsample 4." was performed using the 
result.

?The picture of a result?
	http://masrao.com/img/render4.png (total)
	 or
	 http://masrao.com/img/render4.jpg (A part)

?A part of result of BLAST?
//-------------------------------------------start--------------------
-----------------------//

	>gi|32563818|ref|NP_871912.1| (NM_182112) ROLler: helically 
twisted,animals roll when moving ROL-8, COLlagenstructural gene (rol-8)
 [Caenorhabdtis elegans]
           Length = 265

	  Score = 70.1 bits (170), Expect = 2e-11
	  Identities = 37/95 (38%), Positives = 56/95 (58%), Gaps = 8/
95 (8%)

	Query: 11  
EVGRFRRNAFSAVALSTSCILAIVVLTPIAYQAIQRIHSNLLNDAHFCQARNRDLWTETM 
	70
	            E  + RR AF AV +ST+ ++A VV  P+ Y  +Q   S+L+ +  +C+
AR+RD+W E
	Sbjct: 8   
EQRQMRRIAFVAVVVSTAAVIASVVTLPMLYNYVQSFQSHLMVETDYCKARSRDMWLEMT 
	67
	
	Query: 71  KMARSRGRDEELVARTKRAVKGTWLFGQYIPDRSS 105
	             +   +G       R KRA    WLFGQ+IP+ S+
	Sbjct: 68  ALQAGKGMGH----RMKRA----WLFGQWIPETSA 94



	  Score = 59.7 bits (143), Expect = 3e-08
	  Identities = 24/37 (64%), Positives = 25/37 (67%)

	Query: 291 PGPYGKPGQPGAPGPDGSAGEKGGCDHCPPPRTPPGY 327
	            PG  G+ G  G  GP G  GEKG C HCPPPRTPPGY
	Sbjct: 229 PGHEGRAGPNGPAGPPGDNGEKGDCGHCPPPRTPPGY 265

	 >gi|17533809|ref|NP_496362.1| (NM_063961) COLlagen 
structural gene(29.2 kD) (col-82) [Caenorhabditis elegans]Length = 306

	  Score = 57.8 bits (138), Expect = 1e-07
	  Identities = 23/36 (63%), Positives = 24/36 (66%)

	Query: 292 GPYGKPGQPGAPGPDGSAGEKGGCDHCPPPRTPPGY 327
	            G  G+PG  G  GP G  G  GGCDHCPPPRT PGY
	Sbjct: 271 GAAGQPGAAGEQGPAGEPGAGGGCDHCPPPRTAPGY 306



	  Score = 42.7 bits (99), Expect = 0.004
	  Identities = 20/76 (26%), Positives = 38/76 (50%)

	Query: 10 
LEVGRFRRNAFSAVALSTSCILAIVVLTPIAYQAIQRIHSNLLNDAHFCQARNRDLWTET 
	69
           +E    R+ AF  + +ST   L  +V  P+ Y  +Q + S L  +  FC+ R   L+ +
	Sbjct: 12 
VEAESLRKVAFFGICISTVATLTAIVAIPLLYNYMQHVQSTLQTEVDFCKHRTNGLFDQY 
	71

	Query: 70 MKMARSRGRDEELVAR 85
	            +M + +G   +L+ +
	Sbjct: 72 ERMQQLKGVRGKLIVK 87

//---------------------------------------------------end--------------
-----------------------//

Please compare the portions of 292-327 of NM_182112 and NM_063961.
Graph is white, although NM_182112 are higher as for a score and e-
value is low.

It pats, although it is written to "http://bioperl.org/HOWTOs/html/
Graphics-HOWTO.html#addingscale" as "We specify the base background 
color (-bgcolor => 'blue') and and the minimum and maximum scores to 
scale to. (-min_score and-max_score)", and it is ?
Is it different in HSP?

It is a long text and is pardon. 
Teach, if there are those who understand some.
It is it and English which is hard to read, and is pardon.

From letondal at pasteur.fr  Sat Oct 11 08:26:57 2003
From: letondal at pasteur.fr (Catherine Letondal)
Date: Sat Oct 11 08:24:27 2003
Subject: [Bioperl-l] Suggestions for MATLAB-Bioperl Interface
In-Reply-To: ;
	from bmadsen@mathworks.com on Fri, Oct 10, 2003 at 11:29:35AM -0400
References: 
Message-ID: <20031011142657.A13680@electre.pasteur.fr>

On Fri, Oct 10, 2003 at 11:29:35AM -0400, Brian Madsen wrote:
> I am studying Bioinformatics through the Master's program at
> Northeastern and am working as a co-op at MathWorks on their
> Bioinformatics Toolbox.
> 
> In August, I met a few researchers around Boston to get ideas on the
> Toolbox. One of the best suggestions was from a current user, Dr. Vamsi
> Mootha at the Whitehead Institute. He was interested in calling Bioperl
> apps from MATLAB and calling MATLAB functions from Bioperl. While I
> don't yet have a streamlined approach for calling MATLAB from Perl, I
> have gone through the installation of Bioperl and tested calling Perl
> apps from the toolbox (attached is an html of a demo).
> 
> 2 questions:
> 1 - Are there any suggestions on the interface for MATLAB and
> Bioperl--any procedures or issues I should research?
> 2 - What intellectual property issues might be involved? With the base
> of Bioperl modules available, I thought it might be a good idea to
> include an installation of Bioperl on the Bioinformatics Toolbox CD.
> 
> Thanks for any ideas.
> 

This is probably at a research stage only, but I came accross
"Lightweight Languages" which are (as far as I have understood) an
attempt to address complex programming situations such as this
one. Communication with differing subsystems is addresed also, but the
idea goes much further.

http://www.mail-archive.com/perl6-internals@perl.org/msg17089.html

A more detailed description of the field is provided here:
http://www.usenix.org/publications/library/proceedings/dsl97/full_papers/spinellis/spinellis_html/spinellis.html


-- 
Catherine Letondal -- Pasteur Institute Computing Center
From lcarey at odd.bio.sunysb.edu  Sun Oct 12 00:56:10 2003
From: lcarey at odd.bio.sunysb.edu (Lucas Carey)
Date: Sun Oct 12 00:53:38 2003
Subject: [Bioperl-l] search for only C-terminal degenerate motifs
In-Reply-To: <81E173BD-FB5D-11D7-9104-000A958C5008@pcbi.upenn.edu>
References: 
	<81E173BD-FB5D-11D7-9104-000A958C5008@pcbi.upenn.edu>
Message-ID: <20031012045610.GA18891@odd.bio.sunysb.edu>

On Fri, Oct 10, 2003 at 04:08:26PM -0400, Aaron J. Mackey wrote:
> Yeah, the problem is you'd really like to *not* search all of the 
> database (for both speed and statistical reasons), only the first n 
> C-terminal residues of each sequence in the database.  Both BLAST and 
Search time isn't an issue, I'll be using mpiBLAST on a 128cpu cluster. I don't think the statistics will matter, because I'm just looking for genes to test biologically, not to draw any conclusions from the db search alone.

> But you said "motif" - are you trying to find:
> 
>   a) exact matches to a given short sequence
exact matches to one of ~7 sequences located at : (C-3) - (C-2) - (C-1) - C
The query file would just be a FASTA file with 7 4aa query sequences.

>   b) exact matches to a consensus regular expression (e.g.: CX[S|T]C)
is this possible? can i search for [R|K][D|E] if I wanted to search for a negativly charged aa that follows a postitivly charged one?

My thought, because I'm fairly competent with perl but have never used bioperl before, was to do this:

>gi|17647257|ref|NP_523617.1|   Chitinase 1 [Drosophila melanogaster]
 gi|37078008|sp|Q9W5U3|CHI1_DROME   Probable chitinase 1
            Length = 508

				Score = 14.6 bits (27), Expect =  9048
				Identities = 4/4 (100%), Positives = 4/4 (100%)

				Query: 1   AGDK 4
				AGDK
				Sbjct: 226 AGDK 229

If my signal sequence is AGDK. I want to look for matches where XXX in
'Length = XXX' is equal to XXX in 'Sbjct: nnn AGDK XXX'.

I would not mind using this as an excuse to learn bioperl, assuming that there is a reasonable straight forward way to go about doing this in bioperl. In the BioSearch::IO HOWTO I see end('hit') and length('query') but no length('db_sequence') or something like that. Does this method exist?
I could do 
if( (end('hit') == length('db_sequence')) && (matches('query')[0] == 4)) { print 	query_description ;}
-Lucas
thank you for your assistance

From bounce at gaintrafficfast.com  Sun Oct 12 01:56:30 2003
From: bounce at gaintrafficfast.com (Sharon Brown)
Date: Sun Oct 12 02:03:40 2003
Subject: [Bioperl-l] www.bioperl.org
Message-ID: <3195CR1000034300@s2h6a0w3.trafficglue.com>

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From W.Kenworthy at murdoch.edu.au  Sun Oct 12 08:16:43 2003
From: W.Kenworthy at murdoch.edu.au (William Kenworthy)
Date: Sun Oct 12 08:14:16 2003
Subject: [Bioperl-l] bioperl-pipeline
Message-ID: <1065961003.8277.15.camel@rattus.localdomain>

the link to biopipe.org on the openbioinformatics website broke some
months back.  Has this project become "bioperl-pipeline"?

Also, is there a tutorial for bioperl-pipeline, or some document that
can give me a start on it? (what to install, module listing etc)

BillK


From ajm6q at virginia.edu  Sun Oct 12 09:58:51 2003
From: ajm6q at virginia.edu (Aaron J Mackey)
Date: Sun Oct 12 09:56:23 2003
Subject: [Bioperl-l] search for only C-terminal degenerate motifs
In-Reply-To: <20031012045610.GA18891@odd.bio.sunysb.edu>
Message-ID: 


Since you're looking for exact matches (in a defined location, no less),
why do you need BLAST, or any bioinfomatics tool?  Doesn't simple string
comparison, or regexp matching get you what you need with minimal fuss?

-Aaron

On Sun, 12 Oct 2003, Lucas Carey wrote:

> On Fri, Oct 10, 2003 at 04:08:26PM -0400, Aaron J. Mackey wrote:
> > Yeah, the problem is you'd really like to *not* search all of the
> > database (for both speed and statistical reasons), only the first n
> > C-terminal residues of each sequence in the database.  Both BLAST and
> Search time isn't an issue, I'll be using mpiBLAST on a 128cpu cluster. I don't think the statistics will matter, because I'm just looking for genes to test biologically, not to draw any conclusions from the db search alone.
>
> > But you said "motif" - are you trying to find:
> >
> >   a) exact matches to a given short sequence
> exact matches to one of ~7 sequences located at : (C-3) - (C-2) - (C-1) - C
> The query file would just be a FASTA file with 7 4aa query sequences.
>
> >   b) exact matches to a consensus regular expression (e.g.: CX[S|T]C)
> is this possible? can i search for [R|K][D|E] if I wanted to search for a negativly charged aa that follows a postitivly charged one?
>
> My thought, because I'm fairly competent with perl but have never used bioperl before, was to do this:
>
> >gi|17647257|ref|NP_523617.1|   Chitinase 1 [Drosophila melanogaster]
>  gi|37078008|sp|Q9W5U3|CHI1_DROME   Probable chitinase 1
>             Length = 508
>
> 				Score = 14.6 bits (27), Expect =  9048
> 				Identities = 4/4 (100%), Positives = 4/4 (100%)
>
> 				Query: 1   AGDK 4
> 				AGDK
> 				Sbjct: 226 AGDK 229
>
> If my signal sequence is AGDK. I want to look for matches where XXX in
> 'Length = XXX' is equal to XXX in 'Sbjct: nnn AGDK XXX'.
>
> I would not mind using this as an excuse to learn bioperl, assuming that there is a reasonable straight forward way to go about doing this in bioperl. In the BioSearch::IO HOWTO I see end('hit') and length('query') but no length('db_sequence') or something like that. Does this method exist?
> I could do
> if( (end('hit') == length('db_sequence')) && (matches('query')[0] == 4)) { print 	query_description ;}
> -Lucas
> thank you for your assistance
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu


From charles at gizmotronics.dyndns.org  Sun Oct 12 12:05:13 2003
From: charles at gizmotronics.dyndns.org (Charles Plessy)
Date: Sun Oct 12 12:02:42 2003
Subject: A script to automagically generate DocBook formatted references. (was
	: Re: [Bioperl-l] Re: Bio::Biblio)
In-Reply-To: 
References: 
Message-ID: <20031012160513.GC1237@gizmotronics.dyndns.org>

>    Here I am ataching an example doing hopefully what you wish (and few 
> explanations labelled by '(digit)' pattern:

Thank you very much! Your script is very useful to me!

I now search for the articles'pmid on pubmed, run the script with the
pmid as an argument, and cut-paste the output in my docbook
bibliography file.

Here are my modifications. I plan some cosmetic changes, and to make
this script able to process a list of pmids.

-- 
Charles Plessy



#!/usr/bin/perl -w

#$Revision: 1.1 $

# This script was originally written by Martin Senger.
# I adapted the output fo facilitate the writing of my biology thesis.
# Charles Plessy

use Bio::Biblio;       # to read data via SOAP
use Bio::Biblio::IO;   # to convert resulting XML to Biblio objects

# (1)
# --- taking citations from MEDLINE at EBI using SOAP

my $pmID = shift;
my $biblio = new Bio::Biblio;
my $citation = $biblio->get_by_id ("$pmID");

# (2)
# --- make an instance of a converter
my $io = new Bio::Biblio::IO ('-data' => $citation);

# (3)
# --- and make the conversion (use the citation)

while (my $bibref = $io->next_bibref) {

$bibref->{_date} =~ /(\d*)/;
my $year=$1 ;

print << "DOCBOOK_START";

  $bibref->{_authors}->[0]->{_lastname} et al, $year
  
    $bibref->{_journal}->{_medline_ta}
  
  
    
DOCBOOK_START

# To fix : no 'et al' if 1, 2 or 3 authors
#          if multiple pmids, check unicity of biblioentry ids
#          manage languages

    foreach (@ {$$bibref{'_authors'}} ) {
        print << "DOCBOOK_AUTHORS";
      
        $$_{_lastname}
        $$_{_forename}
      
DOCBOOK_AUTHORS
    }

print << "DOCBOOK_END";
    
    $bibref->{_title}
    $bibref->{_date}
    $bibref->{_volume}
    $bibref->{_issue}
    $bibref->{_medline_page}
  



DOCBOOK_END

# To fix    : put a nice &ndash: in 

}


__END__

From shawnh at stanford.edu  Sun Oct 12 13:18:00 2003
From: shawnh at stanford.edu (Shawn Hoon)
Date: Sun Oct 12 13:11:44 2003
Subject: [Bioperl-l] bioperl-pipeline
In-Reply-To: <1065961003.8277.15.camel@rattus.localdomain>
References: <1065961003.8277.15.camel@rattus.localdomain>
Message-ID: <07CD0901-FCD8-11D7-95C5-000A95783436@stanford.edu>

We are still trying to resolve some dns issues. See if  
biopipe-tmp.open-bio.org
or add

65.246.187.176 www.biopipe.org

to /etc/hosts
I recommend reading the INSTALL document and some of the HOWTOs
and use the bioperl-pipeline@bioperl.org mailing list for any queries.


cheers,

shawn

On Sunday, October 12, 2003, at 5:16AM, William Kenworthy wrote:

> the link to biopipe.org on the openbioinformatics website broke some
> months back.  Has this project become "bioperl-pipeline"?
>
> Also, is there a tutorial for bioperl-pipeline, or some document that
> can give me a start on it? (what to install, module listing etc)
>
> BillK
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From zayed at sanbi.ac.za  Mon Oct 13 09:17:38 2003
From: zayed at sanbi.ac.za (Zayed Albertyn)
Date: Mon Oct 13 09:15:11 2003
Subject: [Bioperl-l] [Bioperl] LocusLink
Message-ID: <20031013150113.C89754@fling.sanbi.ac.za>

Hi

I have been trying to use Bio::SeqIO to parse Locuslink format for
obtaining all RefSeq mRNAs associated with a Locuslink ID.

I receive the following error message when I use the hash_tree method from
Bio:Annotation:
Can't locate object method "each_synonym" via package "Bio::Annotation::OntologyTerm" at OntologyTerm.pm line 187,
 line 1.
The strange thing is that it does support the as_text() method and I can
pull values this way yet I would like to store and retrieve the values as
I like in a hash (as described in the Bio:Annotation documentation).

Is there some reason why I cannot access this "each_synonym" method and
how would I obtain the RefSeq entries if I could initialize the hash_tree()
method?

Thanks
Zayed
-----------------------------------------------
From: Zayed Albertyn
Electric Genetics PTY Ltd
Tel: +27 21 959 3645; Mobile: +2782 480 6097
www.egenetics.com
From lstein at cshl.edu  Mon Oct 13 11:14:06 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Mon Oct 13 11:11:44 2003
Subject: [BioPerl] Re: [Bioperl-l] load_gff.pl error
In-Reply-To: <001101c38f83$da88ec00$c201010a@celegans01>
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>
	<1065825558.1698.90.camel@localhost.localdomain>
	<001101c38f83$da88ec00$c201010a@celegans01>
Message-ID: <200310131114.06086.lstein@cshl.edu>

I think we're all going to purgatory together....

Lincoln

On Friday 10 October 2003 07:11 pm, Sheldon McKay wrote:
> Mark is indeed correct, it was I who wanted tied filehandles.  I don't
> think third party damning is allowed, sorry Mark.
> When you get released from purgatory, please don't remove the tied
> filehandle functionality.
>
> Sheldon
>
> ----- Original Message -----
> From: "Mark Wilkinson" 
> To: "Lincoln Stein" ; "Doreen Ware" ;
> "Sheldon McKay" ; "me" 
> Cc: 
> Sent: Friday, October 10, 2003 3:39 PM
> Subject: Re: [BioPerl] Re: [Bioperl-l] load_gff.pl error
>
> > hey... wait a minute!
> >
> > Why do *I* have to go to purgatory?!  I didn't do anything wrong - I
> > only *suggested* that the code be changed... and it wasn't even for ME!
> > It was for Sheldon - damn HIM!
> >
> > This just isn't fair at all... I hate divine thought-police   }-/
> >
> > M
>
> _______________________________________________
> 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From markw at illuminae.com  Mon Oct 13 13:40:23 2003
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon Oct 13 13:37:43 2003
Subject: [unclassified] Re: [BioPerl] Re: [Bioperl-l] load_gff.pl error
References: <200310091923.h99JN3k23009@warta.bio.psu.edu>	<1065825558.1698.90.camel@localhost.localdomain>	<001101c38f83$da88ec00$c201010a@celegans01>
	<200310131114.06086.lstein@cshl.edu>
Message-ID: <3F8AE387.5080605@illuminae.com>

I think the correct ideom is "going to hell in a handbasket"...

Happy Thanksgiving everyone!

M

Lincoln Stein wrote:

>I think we're all going to purgatory together....
>
>Lincoln
>  
>


From hlapp at gnf.org  Mon Oct 13 16:02:39 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Mon Oct 13 15:59:59 2003
Subject: [Bioperl-l] [Bioperl] LocusLink
In-Reply-To: <20031013150113.C89754@fling.sanbi.ac.za>
Message-ID: 

This is due to a bug that was fixed on the main trunk in May already but not
migrated to the stable branch. I migrated (and corrected) the fix. Either
wait a few hours and update from anonymous cvs, or pull up
Bio/Annotation/OntologyTerm.pm in your favorite editor change the call to
each_synonym to get_synonyms.

The refseq Ids are not ontology terms though, they are dbxrefs. In order to
get at them you need to extract the correct dbxrefs.

    -hilmar

On 10/13/03 6:17 AM, "Zayed  Albertyn"  wrote:

> Hi
> 
> I have been trying to use Bio::SeqIO to parse Locuslink format for
> obtaining all RefSeq mRNAs associated with a Locuslink ID.
> 
> I receive the following error message when I use the hash_tree method from
> Bio:Annotation:
> Can't locate object method "each_synonym" via package
> "Bio::Annotation::OntologyTerm" at OntologyTerm.pm line 187,
>  line 1.
> The strange thing is that it does support the as_text() method and I can
> pull values this way yet I would like to store and retrieve the values as
> I like in a hash (as described in the Bio:Annotation documentation).
> 
> Is there some reason why I cannot access this "each_synonym" method and
> how would I obtain the RefSeq entries if I could initialize the hash_tree()
> method?
> 
> Thanks
> Zayed
> -----------------------------------------------
> From: Zayed Albertyn
> Electric Genetics PTY Ltd
> Tel: +27 21 959 3645; Mobile: +2782 480 6097
> www.egenetics.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 shawnh at stanford.edu  Mon Oct 13 21:18:13 2003
From: shawnh at stanford.edu (Shawn Hoon)
Date: Mon Oct 13 21:11:41 2003
Subject: [Bioperl-l] Bio::Index::PDB
Message-ID: <4837EE60-FDE4-11D7-95C5-000A95783436@stanford.edu>

Hi,
I wrote an indexer along the lines of the sequence index modules  for 
PDB structure files.
Basically a lot of copying from Bio::Index::Fasta

Basically 2 modules added:

Bio::Index::AbstractStructure (which inherits from Bio::Index::Abstract)
Bio::Index::PDB

Usage:

     use Bio::Index::PDB;
     use strict;

     my $Index_File_Name = shift;
     my $inx = Bio::Index::PDB->new('-filename' => $Index_File_Name);
     my $out = Bio::Structure::IO->new('-format' => 'pdb','-fh' => 
\*STDOUT);

     foreach my $id (@ARGV) {
         my $struct= $inx->fetch($id); # Returns Bio::Structure object
         $out->write_structure($struct);
     }

Is this along the lines of how indexers are implemented? If so, I will 
go ahead and commit them.


shawn

From brian_osborne at cognia.com  Tue Oct 14 08:18:56 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Tue Oct 14 08:20:50 2003
Subject: [Bioperl-l] Bio::Index::PDB
In-Reply-To: <4837EE60-FDE4-11D7-95C5-000A95783436@stanford.edu>
Message-ID: 

Shawn,

Both Bio::Index::Fasta and Bio::DB::Fasta allow you to stipulate the key you
want to use, as in:

my $inx = Bio::Index::Fasta->new( -filename   => $file_name . ".idx",
                                    -write_flag => 1 );
$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);

# where get_id() could look like:

# here is where the retrieval key is specified
  sub get_id {
     my $header = shift;
     $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
     $1;
  }

I've found this capability to be very useful myself.

Brian O.


-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Shawn Hoon
Sent: Monday, October 13, 2003 9:18 PM
To: BioPerl List
Subject: [Bioperl-l] Bio::Index::PDB

Hi,
I wrote an indexer along the lines of the sequence index modules  for
PDB structure files.
Basically a lot of copying from Bio::Index::Fasta

Basically 2 modules added:

Bio::Index::AbstractStructure (which inherits from Bio::Index::Abstract)
Bio::Index::PDB

Usage:

     use Bio::Index::PDB;
     use strict;

     my $Index_File_Name = shift;
     my $inx = Bio::Index::PDB->new('-filename' => $Index_File_Name);
     my $out = Bio::Structure::IO->new('-format' => 'pdb','-fh' =>
\*STDOUT);

     foreach my $id (@ARGV) {
         my $struct= $inx->fetch($id); # Returns Bio::Structure object
         $out->write_structure($struct);
     }

Is this along the lines of how indexers are implemented? If so, I will
go ahead and commit them.


shawn

_______________________________________________
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Bioperl-l@portal.open-bio.org
http://portal.open-bio.org/mailman/listinfo/bioperl-l


From jerome.eteve at it-omics.com  Tue Oct 14 11:42:07 2003
From: jerome.eteve at it-omics.com (=?ISO-8859-1?Q?J=E9r=F4me_Et=E9v=E9?=)
Date: Tue Oct 14 11:42:09 2003
Subject: [Bioperl-l] [OBDA] proxy settings.
Message-ID: <1066146197.22653.142.camel@neuron.itomics.local>

Hi everyone.
 I wonder if it is possible to set OBDA in order to make it use an http
proxy for the biofetch database flavour. This would be a great help
since many organisations do use a proxy to access the web.

On my linuxbox, I've set the 
HTTP_PROXY and the http_proxy environment variables to
'http://myproxy:8080/' and it don't seem to work.

Thanx for your help !
Regards.

-- 
--
Of course there's no reason for it, it's just our policy.
----------------------------
jerome.eteve_at_it-omics.com

From michael.watson at bbsrc.ac.uk  Tue Oct 14 12:03:01 2003
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Tue Oct 14 12:02:34 2003
Subject: [Bioperl-l] Codon Table
Message-ID: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>

Hi

I want to use a different codon table than any that are present in CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I have to hack CodonTable.pm?

Thanks
Mick
From cf2 at ualberta.ca  Tue Oct 14 15:58:13 2003
From: cf2 at ualberta.ca (Carlos Fernandez-Patron)
Date: Tue Oct 14 15:53:12 2003
Subject: [Bioperl-l] carlos
Message-ID: <5.1.0.14.0.20031014135619.028e6e50@pop.srv.ualberta.ca>

Lobvi,
Deje tu tarjeta en la casa.
No se si este es tu email.
Respondeme ASAP y pasame por fax una copia de los permisos de trabajos tuyo 
y de tu esposa para human resources de la Universidad.

Gracias,

Carlos

Dr. Carlos Fernandez-Patron
Heart and Stroke Foundation New Investigator
Assistant Professor
Department of Biochemistry
3-08 Medical Sciences Building
The University of Alberta
Edmonton, Alberta T6G 2H7,
Canada
--------------------------------
Lab phone: (780) 492 9540
Fax:           (780) 492 0095
e-mail:        cf2@ualberta.ca
http://www.biochem.ualberta.ca/Biochem/Faculty/CFPatron/cfp.html


From shawnh at stanford.edu  Tue Oct 14 16:11:58 2003
From: shawnh at stanford.edu (Shawn Hoon)
Date: Tue Oct 14 16:05:32 2003
Subject: [Bioperl-l] Bio::Index::PDB
In-Reply-To: 
References: 
Message-ID: 

Yeah, but I needed to have it return a Bio::Structure type object so I 
needed to inherit
from a Bio::Index::AbstractStructure as opposed to a 
Bio::Index::AbstractSeq

But yes, definitely this looks like a good feature to have especially 
as I'm now finding,
some of the astral pdb type files have different headers from the 
normal pdb files..

shawn


On Tuesday, October 14, 2003, at 5:18AM, Brian Osborne wrote:

> Shawn,
>
> Both Bio::Index::Fasta and Bio::DB::Fasta allow you to stipulate the 
> key you
> want to use, as in:
>
> my $inx = Bio::Index::Fasta->new( -filename   => $file_name . ".idx",
>                                     -write_flag => 1 );
> $inx->id_parser(\&get_id);
> # make the index
> $inx->make_index($file_name);
>
> # where get_id() could look like:
>
> # here is where the retrieval key is specified
>   sub get_id {
>      my $header = shift;
>      $header =~ /^>.*\bsp\|([A-Z]\d{5}\b)/;
>      $1;
>   }
>
> I've found this capability to be very useful myself.
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces@portal.open-bio.org
> [mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Shawn Hoon
> Sent: Monday, October 13, 2003 9:18 PM
> To: BioPerl List
> Subject: [Bioperl-l] Bio::Index::PDB
>
> Hi,
> I wrote an indexer along the lines of the sequence index modules  for
> PDB structure files.
> Basically a lot of copying from Bio::Index::Fasta
>
> Basically 2 modules added:
>
> Bio::Index::AbstractStructure (which inherits from 
> Bio::Index::Abstract)
> Bio::Index::PDB
>
> Usage:
>
>      use Bio::Index::PDB;
>      use strict;
>
>      my $Index_File_Name = shift;
>      my $inx = Bio::Index::PDB->new('-filename' => $Index_File_Name);
>      my $out = Bio::Structure::IO->new('-format' => 'pdb','-fh' =>
> \*STDOUT);
>
>      foreach my $id (@ARGV) {
>          my $struct= $inx->fetch($id); # Returns Bio::Structure object
>          $out->write_structure($struct);
>      }
>
> Is this along the lines of how indexers are implemented? If so, I will
> go ahead and commit them.
>
>
> shawn
>
> _______________________________________________
> 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 babenko at ncbi.nlm.nih.gov  Tue Oct 14 09:32:18 2003
From: babenko at ncbi.nlm.nih.gov (babenko)
Date: Tue Oct 14 22:15:15 2003
Subject: [Bioperl-l] Abandoned GBentries
Message-ID: <002001c39257$96a6f500$78140e82@ncbi.nlm.nih.gov>

     Hi, 

I'm using the somewhat old version of genbank. So when I assess the
results on the ncbi list, I could often see the red title:

This record was replaced or removed

E.g.:


1: AAF56887
 [gi:7301776] This
record was replaced or removed. See revision

history for details.

 

       Is

Is there any means to automatically trace that?

    Thanks,

        Vladimir

 

From zayed at sanbi.ac.za  Wed Oct 15 04:27:23 2003
From: zayed at sanbi.ac.za (Zayed Albertyn)
Date: Wed Oct 15 04:24:54 2003
Subject: [Bioperl-l] Bioperl parser for Gene Expression Omnibus
Message-ID: <20031015102227.I43095@fling.sanbi.ac.za>

Hi

I know that there exists a biopython module for handling GEO's SOFT format
but is there a similar module in development for bioperl. It would be
really great to have objects that handle experiment results.

Thanks
Zayed

-----------------------------------------------
From: Zayed Albertyn
Electric Genetics PTY Ltd
Tel: +27 21 959 3645; Mobile: +2782 480 6097
www.egenetics.com
From tania at egenetics.com  Wed Oct 15 06:06:10 2003
From: tania at egenetics.com (Tania Broveak Hide)
Date: Wed Oct 15 06:03:35 2003
Subject: [Bioperl-l] BioPerl programmer opening at Electric Genetics
Message-ID: <023b01c39303$f5c3f130$6402a8c0@boing>



Want to...
  live in one of the most beautiful cities in the world, 
    develop open source software
      and get PAID for it???
 
If you have:
  - 3+ years Perl coding experience
  - 1+ year experience with another programming language widely used 
    in bioinformatics open source projects (e.g., Java, Python, etc)
  - 3+ years UNIX experience (Linux or *BSD a plus)
  - participated actively in open source projects, preferably as a 
    core developer
  - great productivity and enthusiasm
  - a (community) service attitude
  - good written and verbal communication skills
 
Then you qualify for this unique position!
 
Your application is strengthen with any of the following:
  - experience with the BioPerl project
  - familiarity or existing relationship with key open source developers

    in bioinformatics
  - training or exposure to bioinformatics, genetics, molecular biology 
    or other life science discipline
  - experience using UML modeling techniques and tools.
 
Job description follows:
 
Open Source Programmer
----------------------
Build and maintain relationship with Bioinformatics open source
community through active participation (i.e., programming) in open
source projects relevant to the company's strategic aims.  Participate
actively in Bioinformatics open source community and key open source
events such as BOSC and Biohackathon.  It is expected that the Open
Source Programmer will become a 'major contributor' on the BioPerl
project and, as time permits, participate in other application or
platform projects. The open source programmer will implement the
company's BioPerl Support offering as well as provide support internally
to programming and documentation staff interacting heavily with BioPerl
and other open source projects.

 
Who are we?
-----------
Electric Genetics is an international leader in the development of
Bioinformatics tools and services, specializing in tools and techniques
for making the most of transcriptomic and gene expression data.
Electric Genetics has a strong philosophy of using and supporting open
source programs and open standards and are currently preparing technical
and user documentation for the Ensembl system.  With offices in the USA
and South Africa, Electric Genetics' software is used by over 300 key
research sites around the world.

The Open Source Programmer will be located at Electric Genetics' Cape
Town R&D centre.  

How to apply
------------
To apply, please send a CV and one example of your Perl work to
recruit@egenetics.com.  Be sure to tell us why you think you are the
best candidate for this "ideal job".  Applications are open until 10
November 2003.

From janenerz at web.de  Wed Oct 15 06:44:56 2003
From: janenerz at web.de (Christiane Nerz)
Date: Wed Oct 15 06:42:03 2003
Subject: [Bioperl-l] Does bioperl is the answer?
Message-ID: <3F8D2528.1050105@web.de>

Hi everybody!
I never worked with bioperl and even worse: I'm an absolute perl-newbie.
Does bioperl provides the key to the following problem:
I have a list with positions on bacterial-DNA. (Start-Stop-Positions of 
patterns, about 600 hits) and would like to know if the patterns are 
located within orfs or outside. So I need a programm to search hit by 
hit in an Genome-Database.
Any idea?
Jane


From jason at cgt.duhs.duke.edu  Wed Oct 15 06:55:05 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 15 06:52:23 2003
Subject: [Bioperl-l] Codon Table
In-Reply-To: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>
References: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>
Message-ID: 

If the table is not there then you obviously have to hack CodonTable - you
need to add values to the @NAMES, @TABLES, @STARTS

You specify which table you want to use as
$table->id($n)
where $n is 1->23 - so you would want to add them to the bottom I suppose
but we

Is this table avaialble at
     http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c

perhaps we need to update the module for new tables?


If this is a LOCAL only think you can add values to the available tables
by directly updating the value of these variables in your script

push @Bio::Tools::CodonTable::NAMES, 'NewName';
... etc (update the other values)
-jason
On Tue, 14 Oct 2003, michael watson (IAH-C) wrote:

> Hi
>
> I want to use a different codon table than any that are present in
> CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I
> have to hack CodonTable.pm?
>
> Thanks
> Mick
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From daniel.lang at biologie.uni-freiburg.de  Wed Oct 15 09:15:54 2003
From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Wed Oct 15 09:13:00 2003
Subject: [Bioperl-l] Bio::DB::Registry
Message-ID: <3F8D488A.2080401@biologie.uni-freiburg.de>

Hi,
I encountered problems using the obda registry system...
Sequence retrieval with the example script fails:
	use Bio::DB::Registry();
	my $reg = new Bio::DB::Registry();
	my $db = $reg->get_database("ppp");
	my $seq = $db->get_Seq_by_acc("PPP_3085_C1");
	print $seq->seq,"\n";
With following Exception:
	-------------------- WARNING ---------------------
	MSG: Couldn't call new_from_registry on [Bio::DB::Flat]
	
	------------- EXCEPTION  -------------
	MSG: you must specify an indexing scheme
	STACK Bio::DB::Flat::new 		
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:163
	STACK Bio::DB::Flat::new_from_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:250
	STACK (eval) /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:194
	STACK Bio::DB::Registry::_load_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:193
	STACK Bio::DB::Registry::new
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:96
	STACK toplevel fetch_test.pl:8

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

	---------------------------------------------------
	Can't call method "seq" on an undefined value at fetch_test.pl line 11,
 line 14.

I?m using latest tarball with Linux/Perl 5.61.
I indexed a flat fasta file using the bioflat_index.pl from the recent
tarball  with BDB. No Errors and warning.
I also created a /etc/bioinformatics/seqdatabase.ini as follows:
	VERSION=1.00

	[ppp]
	protocol=flat
	location=/export/flatfiles/ppp/
	dbname=ppp
The permissions for the corresponding directories should be ok also..
Any hints for me?

Thanks in advance,
	Daniel


-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

From brian_osborne at cognia.com  Wed Oct 15 10:31:44 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Wed Oct 15 10:33:44 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: <3F8D488A.2080401@biologie.uni-freiburg.de>
Message-ID: 

Daniel,

* MSG: you must specify an indexing scheme

My guess is that you need to set the variable OBDA_INDEX. A value of "flat"
means use the built-in scheme, a value of "bdb" means use BerkeleyDB, which
you'll have to install if it's not installed. Check out the file
doc/howto/FLAT-DATABASES-HOWTO.txt.

We probably should convert this to Docbook, make it more accessible. Did you
take a look at the OBDA_Access HOWTO
(http://bioperl.org/HOWTOs/html/OBDA_Access.html)?

Brian O.



-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Daniel Lang
Sent: Wednesday, October 15, 2003 9:16 AM
To: Bioperl-List
Subject: [Bioperl-l] Bio::DB::Registry

Hi,
I encountered problems using the obda registry system...
Sequence retrieval with the example script fails:
        use Bio::DB::Registry();
        my $reg = new Bio::DB::Registry();
        my $db = $reg->get_database("ppp");
        my $seq = $db->get_Seq_by_acc("PPP_3085_C1");
        print $seq->seq,"\n";
With following Exception:
        -------------------- WARNING ---------------------
        MSG: Couldn't call new_from_registry on [Bio::DB::Flat]

        ------------- EXCEPTION  -------------
        MSG: you must specify an indexing scheme
        STACK Bio::DB::Flat::new
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:163
        STACK Bio::DB::Flat::new_from_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Flat.pm:250
        STACK (eval) /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:194
        STACK Bio::DB::Registry::_load_registry
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:193
        STACK Bio::DB::Registry::new
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/Registry.pm:96
        STACK toplevel fetch_test.pl:8

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

        ---------------------------------------------------
        Can't call method "seq" on an undefined value at fetch_test.pl line
11,
 line 14.

I?m using latest tarball with Linux/Perl 5.61.
I indexed a flat fasta file using the bioflat_index.pl from the recent
tarball  with BDB. No Errors and warning.
I also created a /etc/bioinformatics/seqdatabase.ini as follows:
        VERSION=1.00

        [ppp]
        protocol=flat
        location=/export/flatfiles/ppp/
        dbname=ppp
The permissions for the corresponding directories should be ok also..
Any hints for me?

Thanks in advance,
        Daniel


--
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

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


From daniel.lang at biologie.uni-freiburg.de  Wed Oct 15 10:52:39 2003
From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Wed Oct 15 10:49:40 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: 
References: 
Message-ID: <200310151652.43405.daniel.lang@biologie.uni-freiburg.de>

Thanks Brian, but still not working:(

On Wednesday 15 October 2003 16:31, Brian Osborne wrote:
> My guess is that you need to set the variable OBDA_INDEX. A value of "flat"
> means use the built-in scheme, a value of "bdb" means use BerkeleyDB, which
I tried both flat and bdb with the corresponding  OBDA_INDEX enviroment 
variable  setting.
 
> (http://bioperl.org/HOWTOs/html/OBDA_Access.html)?
Yes I configured everything correspondingly.

I was also confused, that in the current cvs the bioflat_index.pl script can 
only be found in scripts/DB/attic and not in examples/db?
So the version I?m using is the one from attic...

Maybe somehing is wrong with my config.dat:
index   flat/1
fileid_0        /export/flatfiles/ppp.seq       13155893
primary_namespace       ACC
secondary_namespaces    ID
format  URN:LSID:open-bio.org:fasta

Thanks in advance,
Daniel

  
-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
>REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################


From brian_osborne at cognia.com  Wed Oct 15 11:13:09 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Wed Oct 15 11:15:08 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: <200310151652.43405.daniel.lang@biologie.uni-freiburg.de>
Message-ID: 

Daniel,

Hmm. Here's a config.dat that worked for me:

index   BerkeleyDB/1
format  URN:LSID:open-bio.org:fasta/protein
fileid_0        /home/bosborne/programming/perl/Bioperl/out.fa  7405
primary_namespace       ACC
secondary_namespaces

Note that I'm saying "fasta/protein", not simply "fasta". Don't know if it's
important.

I'll look into bioflat_index.pl.

Brian O.



-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Daniel Lang
Sent: Wednesday, October 15, 2003 10:53 AM
To: Brian Osborne; Bioperl-List
Subject: Re: [Bioperl-l] Bio::DB::Registry

Thanks Brian, but still not working:(

On Wednesday 15 October 2003 16:31, Brian Osborne wrote:
> My guess is that you need to set the variable OBDA_INDEX. A value of
"flat"
> means use the built-in scheme, a value of "bdb" means use BerkeleyDB,
which
I tried both flat and bdb with the corresponding  OBDA_INDEX enviroment
variable  setting.

> (http://bioperl.org/HOWTOs/html/OBDA_Access.html)?
Yes I configured everything correspondingly.

I was also confused, that in the current cvs the bioflat_index.pl script can
only be found in scripts/DB/attic and not in examples/db?
So the version I?m using is the one from attic...

Maybe somehing is wrong with my config.dat:
index   flat/1
fileid_0        /export/flatfiles/ppp.seq       13155893
primary_namespace       ACC
secondary_namespaces    ID
format  URN:LSID:open-bio.org:fasta

Thanks in advance,
Daniel


--
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
>REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################


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


From rjdrouse at patentinformatics.com  Wed Oct 15 17:36:10 2003
From: rjdrouse at patentinformatics.com (Richard Rouse)
Date: Wed Oct 15 17:33:30 2003
Subject: [Bioperl-l] installation problems
Message-ID: 

Dear bioperl-db,

I have mysql 3.23, slackware 8.1 and bioperl-1.2.2 I recently installed
bioperl-db and it was working nicely until I updated perl from 5.8.0 to
5.8.1. Now I get errors when running make test and have problems with the
load_seqdatabase.pl script:

Using this command I get the following problem:

perl ./load_seqdatabase.pl --host localhost --dbname biosql2 --dbuser
richard --dbpass xxxx --lookup --safe --format genbank patent
/home/richard/bioperl-1.2.2/bioperl-db/scripts/biosql/db/gbpat1.seq



-------------------- WARNING ---------------------
MSG: failed to load dbadaptor:
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::DB::BioSQL::DBAdaptor. Can't locate
Bio/DB/DBAdaptorI.pm in @INC (@INC contains:
/usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
/usr/local/lib/perl5/site_perl/5.8.1/i686-linux
/usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
BEGIN failed--compilation aborted at
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
Compilation failed in require at
/usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.

STACK Bio::Root::Root::_load_module
/usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
STACK Bio::DB::BioDB::_load_dbadaptor
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
STACK Bio::DB::BioDB::new
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
STACK toplevel ./load_seqdatabase.pl:353

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


------------- EXCEPTION  -------------
MSG: Failed to load module Bio::DB::BioSQL::dbadaptor. Can't locate
Bio/DB/BioSQL/dbadaptor.pm in @INC (@INC contains:
/usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
/usr/local/lib/perl5/site_perl/5.8.1/i686-linux
/usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
/usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.

STACK Bio::Root::Root::_load_module
/usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
STACK Bio::DB::BioDB::_load_dbadaptor
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
STACK Bio::DB::BioDB::new
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
STACK toplevel ./load_seqdatabase.pl:353

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

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

------------- EXCEPTION  -------------
MSG: fatal: unable to load DBAdaptor for database:
Bio::DB::BioSQL::{DBAdaptor,dbadaptor} all failed to load
STACK Bio::DB::BioDB::new
/usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:122
STACK toplevel ./load_seqdatabase.pl:353

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

Richard Rouse JD
Rouse Patent Services
USPTO Registered Patent Agent
P.O. Box 948586
La Jolla, CA 92037
web: www.patentinformatics.com
email: rjdrouse@patentinformatics.com
phone: 619-846-8291



From jason at cgt.duhs.duke.edu  Wed Oct 15 17:41:53 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 15 17:39:02 2003
Subject: [Bioperl-l] installation problems
In-Reply-To: 
References: 
Message-ID: 

You upgraded your perl - did you reinstall Bioperl?

You might as well get bioperl 1.2.3 as well as it has several bugfixes.

-jason
On Wed, 15 Oct 2003, Richard Rouse wrote:

> Dear bioperl-db,
>
> I have mysql 3.23, slackware 8.1 and bioperl-1.2.2 I recently installed
> bioperl-db and it was working nicely until I updated perl from 5.8.0 to
> 5.8.1. Now I get errors when running make test and have problems with the
> load_seqdatabase.pl script:
>
> Using this command I get the following problem:
>
> perl ./load_seqdatabase.pl --host localhost --dbname biosql2 --dbuser
> richard --dbpass xxxx --lookup --safe --format genbank patent
> /home/richard/bioperl-1.2.2/bioperl-db/scripts/biosql/db/gbpat1.seq
>
>
>
> -------------------- WARNING ---------------------
> MSG: failed to load dbadaptor:
> ------------- EXCEPTION  -------------
> MSG: Failed to load module Bio::DB::BioSQL::DBAdaptor. Can't locate
> Bio/DB/DBAdaptorI.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
> /usr/local/lib/perl5/site_perl/5.8.1/i686-linux
> /usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
> BEGIN failed--compilation aborted at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioSQL/DBAdaptor.pm line 58.
> Compilation failed in require at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.
>
> STACK Bio::Root::Root::_load_module
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
> STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
> STACK Bio::DB::BioDB::_load_dbadaptor
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
>
> ------------- EXCEPTION  -------------
> MSG: Failed to load module Bio::DB::BioSQL::dbadaptor. Can't locate
> Bio/DB/BioSQL/dbadaptor.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.8.1/i686-linux /usr/local/lib/perl5/5.8.1
> /usr/local/lib/perl5/site_perl/5.8.1/i686-linux
> /usr/local/lib/perl5/site_perl/5.8.1 /usr/local/lib/perl5/site_perl .) at
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm line 407.
>
> STACK Bio::Root::Root::_load_module
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/Root/Root.pm:409
> STACK (eval) /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:155
> STACK Bio::DB::BioDB::_load_dbadaptor
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:154
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:121
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: fatal: unable to load DBAdaptor for database:
> Bio::DB::BioSQL::{DBAdaptor,dbadaptor} all failed to load
> STACK Bio::DB::BioDB::new
> /usr/local/lib/perl5/site_perl/5.8.1/Bio/DB/BioDB.pm:122
> STACK toplevel ./load_seqdatabase.pl:353
>
> --------------------------------------
>
> Richard Rouse JD
> Rouse Patent Services
> USPTO Registered Patent Agent
> P.O. Box 948586
> La Jolla, CA 92037
> web: www.patentinformatics.com
> email: rjdrouse@patentinformatics.com
> phone: 619-846-8291
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From hlapp at gmx.net  Thu Oct 16 03:12:27 2003
From: hlapp at gmx.net (Hilmar Lapp)
Date: Thu Oct 16 03:09:44 2003
Subject: [Bioperl-l] installation problems
In-Reply-To: 
Message-ID: <195AB679-FFA8-11D7-AD4B-000A959EB4C4@gmx.net>


On Wednesday, October 15, 2003, at 02:41  PM, Jason Stajich wrote:

> You upgraded your perl - did you reinstall Bioperl?
>

You'll also need to reinstall bioperl-db obviously.

	-hilmar

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From William.Cannon at pnl.gov  Thu Oct 16 18:28:50 2003
From: William.Cannon at pnl.gov (Cannon, William R)
Date: Thu Oct 16 18:26:17 2003
Subject: [Bioperl-l] RemoteBlast: can't get a TaxBlast report
Message-ID: <62AE0CF1D4875C4BBDEC29DB9924ACE88B1D44@pnlmse25.pnl.gov>

Hi,
I tried running RemoteBlast using the synopsis script found on at http://doc.bioperl.org/releases/bioperl-1.2/Bio/Tools/Run/RemoteBlast.html. Everything worked fine, as is. However, when I try to get a Taxonomy report by adding the line:
$Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'TaxBlast';

I still get the alignment report back. Anybody know what else I should be doing?

Thanks.
Bill

(Using :
perl 5.6
bioperl 1.2.3 on redhat linux 7.2.

Here is the full script:
#! /msrc/apps/perl-5.6/bin/perl

  #Remote-blast "factory object" creation and blast-parameter initialization

  use Bio::Tools::Run::RemoteBlast;
  use strict;
  my $prog = 'blastp';
  my $db   = 'nr';
  my $e_val= '1.0';

  my @params = ( '-prog' => $prog,
         '-data' => $db,
         '-expect' => $e_val,
         '-readmethod' => 'SearchIO' );

  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

  #change a paramter
  $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
  $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'TaxBlast';

  #remove a parameter
  delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENT_VIEW'};
  delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'};
  delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'};

  my $v = 1;
  #$v is just to turn on and off the messages
  
#  my $str = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 'fasta' );
  my $str = Bio::SeqIO->new(-file=>'roa1.fasta' , '-format' => 'fasta' );

  while (my $input = $str->next_seq()){
    #Blast a sequence against a database:

    #Alternatively, you could  pass in a file with many
    #sequences rather than loop through sequence one at a time
    #Remove the loop starting 'while (my $input = $str->next_seq())'
    #and swap the two lines below for an example of that.
    print STDERR "%s\n", $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'};
    my $r = $factory->submit_blast($input);
    #my $r = $factory->submit_blast('amino.fa');

    print STDERR "waiting..." if( $v > 0 );
    while ( my @rids = $factory->each_rid ) {
      foreach my $rid ( @rids ) {
        my $rc = $factory->retrieve_blast($rid);
        if( !ref($rc) ) {
          if( $rc < 0 ) {
            $factory->remove_rid($rid);
          }
          print STDERR "." if ( $v > 0 );
          sleep 5;
        } else {
          my $result = $rc->next_result();
          #save the output
          my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
          $factory->remove_rid($rid);
          print "\nQuery Name: ", $result->query_name(), "\n";
          while ( my $hit = $result->next_hit ) {
            next unless ( $v > 0);
            print "\thit name is ", $hit->name, "\n";
            while( my $hsp = $hit->next_hsp ) {
              print "\t\tscore is ", $hsp->score, "\n";
            }
          }
        }
      }
    }
  }




From jason at cgt.duhs.duke.edu  Thu Oct 16 20:19:13 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Oct 16 20:16:19 2003
Subject: [Bioperl-l] need a devloper for RemoteBlast (was RemoteBlast: can't
 get a TaxBlast report)
In-Reply-To: <62AE0CF1D4875C4BBDEC29DB9924ACE88B1D44@pnlmse25.pnl.gov>
References: <62AE0CF1D4875C4BBDEC29DB9924ACE88B1D44@pnlmse25.pnl.gov>
Message-ID: 

I really have no idea how to parse this so I suspect SearchIO doesn't
either.  This is not something we have ever tried to support because it
isn't in part of the standard output from stand alone blast reports.

Frankly this module started as a hack to provide and illustrate minimal
access just to running BLAST on a remote server such as NCBI when the cgi
page itsself was pretty minimal.

If people want to do more complicated stuff the module needs a dedicated
soul actively developing it who will adapt it to the new features NCBI is
providing.  In case it isn't clear, I am not going to be that person any
time soon.

Currently there are also new features which allow sending multiple
sequences in and using discontinuous megablast which will allow, for
example, in parallel searching of multiple sequences reducing the total
search time to a fraction of the time versus compared to each query
in-serial.  This would be a big time save against things like dbest.

(I bang this drum every few months so it isn't directed at you Bill.)

-jason
On Thu, 16 Oct 2003, Cannon, William R wrote:

> Hi, I tried running RemoteBlast using the synopsis script found on at
> http://doc.bioperl.org/releases/bioperl-1.2/Bio/Tools/Run/RemoteBlast.html.
> Everything worked fine, as is. However, when I try to get a Taxonomy
> report by adding the line:
> $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'TaxBlast';
>
> I still get the alignment report back. Anybody know what else I should
> be doing?
>
> Thanks.
> Bill
>
> (Using :
> perl 5.6
> bioperl 1.2.3 on redhat linux 7.2.
>
> Here is the full script:
> #! /msrc/apps/perl-5.6/bin/perl
>
>   #Remote-blast "factory object" creation and blast-parameter initialization
>
>   use Bio::Tools::Run::RemoteBlast;
>   use strict;
>   my $prog = 'blastp';
>   my $db   = 'nr';
>   my $e_val= '1.0';
>
>   my @params = ( '-prog' => $prog,
>          '-data' => $db,
>          '-expect' => $e_val,
>          '-readmethod' => 'SearchIO' );
>
>   my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
>   #change a paramter
>   $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
>   $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'} = 'TaxBlast';
>
>   #remove a parameter
>   delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENT_VIEW'};
>   delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'};
>   delete $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'};
>
>   my $v = 1;
>   #$v is just to turn on and off the messages
>
> #  my $str = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 'fasta' );
>   my $str = Bio::SeqIO->new(-file=>'roa1.fasta' , '-format' => 'fasta' );
>
>   while (my $input = $str->next_seq()){
>     #Blast a sequence against a database:
>
>     #Alternatively, you could  pass in a file with many
>     #sequences rather than loop through sequence one at a time
>     #Remove the loop starting 'while (my $input = $str->next_seq())'
>     #and swap the two lines below for an example of that.
>     print STDERR "%s\n", $Bio::Tools::Run::RemoteBlast::HEADER{'FORMAT_OBJECT'};
>     my $r = $factory->submit_blast($input);
>     #my $r = $factory->submit_blast('amino.fa');
>
>     print STDERR "waiting..." if( $v > 0 );
>     while ( my @rids = $factory->each_rid ) {
>       foreach my $rid ( @rids ) {
>         my $rc = $factory->retrieve_blast($rid);
>         if( !ref($rc) ) {
>           if( $rc < 0 ) {
>             $factory->remove_rid($rid);
>           }
>           print STDERR "." if ( $v > 0 );
>           sleep 5;
>         } else {
>           my $result = $rc->next_result();
>           #save the output
>           my $filename = $result->query_name()."\.out";
>           $factory->save_output($filename);
>           $factory->remove_rid($rid);
>           print "\nQuery Name: ", $result->query_name(), "\n";
>           while ( my $hit = $result->next_hit ) {
>             next unless ( $v > 0);
>             print "\thit name is ", $hit->name, "\n";
>             while( my $hsp = $hit->next_hsp ) {
>               print "\t\tscore is ", $hsp->score, "\n";
>             }
>           }
>         }
>       }
>     }
>   }
>
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From wes.barris at csiro.au  Fri Oct 17 01:48:17 2003
From: wes.barris at csiro.au (Wes Barris)
Date: Fri Oct 17 01:45:57 2003
Subject: [Bioperl-l] How do you create a genbank file?
Message-ID: <3F8F82A1.5060504@csiro.au>

Hi,

I need to convert a set of fasta sequences into a set of genbank entries.
This is easy to do except that there are a few subtle parts of the genbank
format that I have not figured out how to set yet using bioperl.

Here is an example of what I have been able to produce:

LOCUS       AB050006                 588 bp    dna     linear   UNK
DEFINITION  Bos taurus bASC mRNA for apoptosis-associated speck-like protein
             containing a CARD, complete cds.
ACCESSION   AB050006
FEATURES             Location/Qualifiers
      source          1..588
                      /organism="Bos taurus"
.
.
.

Here is an example of what I would like it too look like:

LOCUS       AB050006                 588 bp    mRNA     linear   MAM
DEFINITION  Bos taurus bASC mRNA for apoptosis-associated speck-like protein
             containing a CARD, complete cds.
ACCESSION   AB050006
VERSION     AB050006.1  GI:26453358
SOURCE      Bos taurus (cow)
   ORGANISM  Bos taurus
FEATURES             Location/Qualifiers
      source          1..588
                      /organism="Bos taurus"
.
.
.

My question is how do I set the following?

mRNA (instead of dna)
MAM (instead of UNK)
VERSION     AB050006.1  GI:26453358		<- I can't get this line to appear
SOURCE      Bos taurus (cow)
   ORGANISM  Bos taurus


Here is a portion of my code:

my $seq_in  = Bio::SeqIO->new( -format => 'fasta', -file => $infile);
my $seq_out = Bio::SeqIO->new( -format => 'genbank',   -file => ">$outfile");
while (my $seq = $seq_in->next_seq()) {
    my ($gi, $accession, $clone, $clonelib, $length, $file, $direction, $description, 
$tissuetype, $organism) = &parseStackDefline($seq->description());
    $seq->desc($description);
    $seq->accession_number($accession);
    $seq->primary_id($gi);
    my $feat = Bio::SeqFeature::Generic->new(-primary=>'source', -start=>1, -end=>$length);
    $feat->add_tag_value('clone',$clone)           if ($clone ne 'unknown');
    $feat->add_tag_value('clonelib',$clonelib)     if ($clonelib ne 'unknown');
    $feat->add_tag_value('tissuetype',$tissuetype) if ($tissuetype ne 'unknown');
    $feat->add_tag_value('organism',$organism)     if ($organism ne 'unknown');
    $seq->add_SeqFeature($feat);

    $seq_out->write_seq($seq);
    }

-- 
Wes Barris
E-Mail: Wes.Barris@csiro.au


From Marc.Logghe at devgen.com  Fri Oct 17 05:49:03 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri Oct 17 05:46:23 2003
Subject: [Bioperl-l] How do you create a genbank file?
Message-ID: 

> My question is how do I set the following?
> 
> mRNA (instead of dna)
> MAM (instead of UNK)
> VERSION     AB050006.1  GI:26453358		<- I can't get 
> this line to appear
> SOURCE      Bos taurus (cow)
>    ORGANISM  Bos taurus
> 
> 
To set the version you should use:
$seq->seq_version($version);  # $version is e.g. 1
Problem is, it is not possible to set the GI number. As far as I know, when you pass a genbank file, Bio::SeqIO does not even  parse it, at least it does not show up when you Data::Dump the resulting Bio::Seq::RichSeq object.
There is no slot for that information, because it does not exist in e.g. an EMBL sequence record.
Concerning the organism, first create the Bio::Species object. In case you only have the string 'Bos taurus' in your fasta, of course you can not generate the full classification. At least not using only your fasta data.
my $species = Bio::Species->new([reverse split /\s/, $organism]);
$seq->species($species);

gives you:
SOURCE      Bos taurus
  ORGANISM  Bos taurus
            Bos.

HTH,
Marc

From heikki at ebi.ac.uk  Fri Oct 17 06:20:34 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Fri Oct 17 06:18:04 2003
Subject: [Bioperl-l] Bioperl Developer snapshot 1.3.02
Message-ID: <1066386033.2446.128.camel@localhost>


   Bioperl developer snap shot  1.3.02
   ---------------------------------


This is the second developer snap shot from the BioPerl CVS head
that will eventually lead to release 1.4.

http://bioperl.org/DIST/current_core_unstable.tar.gz
http://bioperl.org/DIST/bioperl-1.3.02.tar.gz


Last fortnight has been dominated by bug fixing (but more is needed; see
bugzilla). The only new stuff added has been on comparison matrix
modules by Stafan Kirov.

The most important fixes have been tweaks in ontology handling, GFF
histograms, some Bio::Graphics glyphs, feature table output and
Gene/Genomewise parsing. The full list is below.

Enjoy,

	-Heikki




NEW DIRECTORIES and FILES
=========================

Bio::Matrix::PSM
  IO InstanceSite InstanceSiteI Psm PsmHeader 
  PsmHeaderI PsmI SiteMatrix SiteMatrixI 

  Added DNA PSM (Position Scoring Matrix) modules This includes meme,
  mast and transfac parsers

examples/rnai_finder.cgi 
  cgi script for RNAi reagent design


CHANGES
=======

Bio::DB::GFF::Adaptor::dbi 
  fixed bug 1384; histograms not working

Bio::DB::GFF::Feature
bulk_load_gff.PLS fast_load_gff.PLS load_gff.PLS
  fixed overly-promiscuous regexp for detecting FASTA files

Bio::DB::Query::WebQuery 
  quell undef warnings

Bio::DB::WebDBSeqI 
  reset MODVERSION to use Packagewide Version system - change agent
  string to be 'bioperl-Bio_DB_GenBank/1.3' for example

Bio::Graphics::FeatureFile 
  All functionality moved to Bio::DB::GFF->split_group, however still
  see major perf problems, not sure if this is localized to
  FeatureFile or not

Bio::Graphics::Glyph::Factory 
  fixed implementation of user-defined glyph sort routines

Bio::Graphics::Glyph::arrow
Bio::Graphics::Glyph
  partial fix for incorrectly-rendered half-open intervals

Bio::Index::Abstract 
  don't warn if we set verbose to -1

Bio::Location::Simple::to_FTstring()
  was never returning a location of the form "complement(12345)

Bio::Ontology::SimpleGOEngine 
Bio::OntologyIO::dagflat 
Bio::Expression::FeatureGroup 
  allowing an underscore in ontology IDs.  this is necessary to be
  able to parse cjm's OBO_REL relationship ontology, which otherwise
  observes DAG-Edit format

Bio::Ontology::SimpleGOEngine
Bio::OntologyIO::dagflat.pm 
  MPATH ontology doesn't have at least 3 digits in all identifiers

Bio::SearchIO::(chado&chadosxpr)
  removed as redundant

Bio::SeqFeature::Tools::TypeMapper 
  updated type sequence_variant to reflect SO

Bio::SeqIO::chadoxml 
  fix bug of null srcfeature_id for featureloc when srcfeature is not
  given on write_seq() invocation; fix bug of not calling unflattener
  when -seq_so_type is explicitly supplied.

  fixed bug 1532 with regard to filehandle; modified code to eliminate
  warnings when run with 'perl -w'.
  debugging code clean up

Bio::SearchIO::wise 
  was swapping query/target improperly

Bio::Restriction::IO::base 
  fix suggested in bug report #1538, correctly parse negative cut site
  locations

Bio::Tools::Phylo::PAML::Result
  doc fixes

+ several minor fixes to quiet warnings when Test::Harness runs tests
with 'use warnings'


-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From heikki at ebi.ac.uk  Fri Oct 17 06:47:35 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Fri Oct 17 06:45:02 2003
Subject: [Bioperl-l] bioperl mirror at iubio.bio.indiana.edu now daily
	updated
In-Reply-To: <01993920-E940-11D7-AB8B-000393B8D01C@indiana.edu>
References: <01993920-E940-11D7-AB8B-000393B8D01C@indiana.edu>
Message-ID: <1066387655.7927.4.camel@localhost>

Thanks Don,

I changed the text on the page. Sorry for not reacting earlier.
Your mirror is much appreciated.

	-Heikki

On Wed, 2003-09-17 at 19:51, Don Gilbert wrote:
> Re: http://www.bioperl.org/Core/Latest/index.shtml
> MIRRORS:
> iubio.bio.indiana.edu - Updates on a 20 day cycle so may not always be 
> current.
> 
> I updated IUBio mirroring of this to daily, in case you all start 
> cranking
> out new revisions.
> 
> -- Don
> 
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gilbertd@indiana.edu -- http://marmot.bio.indiana.edu/
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From jason at cgt.duhs.duke.edu  Fri Oct 17 08:27:27 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 17 08:25:00 2003
Subject: [Bioperl-l] How do you create a genbank file?
In-Reply-To: 
References: 
Message-ID: 

If you are parsing Fasta files with properly set NCBI headers I thought we
had added a way to make this all get set properly, perhaps not...

You can set GI number with
$seq->primary_id($ginumber);

If you want to be creating RichSeq instead of Bio::Seq objects (in the
event you want to set some fields which are only available in RichSeq
objects, initialize your  Bio::SeqIO fasta parser like this:

use Bio::SeqIO;
use Bio::Seq::SeqFactory;
my $seqio = new Bio::SeqIO(-format => 'fasta',
			   -file   => $file,
			   -seqfactory => new Bio::Seq::SeqFactory
			( -type => 'Bio::Seq::RichSeq'));

(Or alternatively you can set the seqfactory after you have initialized
the SeqIO object with
$seqio->sequence_factory(new Bio::Seq::SeqFactory(-type =>
'Bio::Seq::RichSeq'));

-jason

On Fri, 17 Oct 2003, Marc Logghe wrote:

> > My question is how do I set the following?
> >
> > mRNA (instead of dna)
> > MAM (instead of UNK)
> > VERSION     AB050006.1  GI:26453358		<- I can't get
> > this line to appear
> > SOURCE      Bos taurus (cow)
> >    ORGANISM  Bos taurus
> >
> >
> To set the version you should use:
> $seq->seq_version($version);  # $version is e.g. 1
> Problem is, it is not possible to set the GI number. As far as I know, when you pass a genbank file, Bio::SeqIO does not even  parse it, at least it does not show up when you Data::Dump the resulting Bio::Seq::RichSeq object.
> There is no slot for that information, because it does not exist in e.g. an EMBL sequence record.
> Concerning the organism, first create the Bio::Species object. In case you only have the string 'Bos taurus' in your fasta, of course you can not generate the full classification. At least not using only your fasta data.
> my $species = Bio::Species->new([reverse split /\s/, $organism]);
> $seq->species($species);
>
> gives you:
> SOURCE      Bos taurus
>   ORGANISM  Bos taurus
>             Bos.
>
> HTH,
> Marc
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From Marc.Logghe at devgen.com  Fri Oct 17 08:38:06 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri Oct 17 08:35:23 2003
Subject: [Bioperl-l] How do you create a genbank file?
Message-ID: 


> You can set GI number with
> $seq->primary_id($ginumber);

True. You can set it up in the object but it is not shown in the genbank dump. And, also the way around, when a genbank record is parsed containing the line 'VERSION     AB050006.1  GI:26453358' it does not get into the Bio::Seq::RichSeq object. As far as I can see.

> 
> If you want to be creating RichSeq instead of Bio::Seq objects (in the
> event you want to set some fields which are only available in RichSeq
> objects, initialize your  Bio::SeqIO fasta parser like this:
> 
> use Bio::SeqIO;
> use Bio::Seq::SeqFactory;
> my $seqio = new Bio::SeqIO(-format => 'fasta',
> 			   -file   => $file,
> 			   -seqfactory => new Bio::Seq::SeqFactory
> 			( -type => 'Bio::Seq::RichSeq'));
That is a really cool one. Never used it like this. Thanks
ML

From jason at cgt.duhs.duke.edu  Fri Oct 17 08:58:08 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 17 08:55:25 2003
Subject: [Bioperl-l] How do you create a genbank file?
In-Reply-To: 
References: 
Message-ID: 

The should all be captured when you parse a genbank file (and be
available when you write a genbank file) that is how we can round trip
the format and have it be 99% identical.

gi number goes to primary_id()
accession number goes to accession_number()
version goes to seq_version() and version() (not sure why we have 2 methods here???)

  # From Bio::SeqIO::genbank
  if( /^ACCESSION\s+(\S.*\S)/ ) {
	      push(@acc, split(/\s+/,$1));
	      while( defined($_ = $self->_readline) ) {
		  /^\s+(.*)/ && do { push (@acc, split(/\s+/,$1)); next };
		  last;
	      }
	      $buffer = $_;
	      next;
	  }
  ....
  elsif( /^VERSION\s+(.+)$/ ) {
	      my ($acc,$gi) = split(' ',$1);
	      if($acc =~ /^\w+\.(\d+)/) {
		  $params{'-version'} = $1;
		  $params{'-seq_version'} = $1;
	      }
	      if($gi && (index($gi,"GI:") == 0)) {
		  $params{'-primary_id'} = substr($gi,3);
	      }
	  }

   the first item in @acc is passed to the appropriate accession_number
   slot and the rest are passed to secondard accessions slot.

   The %params hash gets passed to the appropriate Seq object
through the factory.  The arguments are passed through the hierarchy

   SEQ_VERSION is consumed by Seq::RichSeq
   VERSION     is consumed by Seq::PrimarySeq
   PRIMARY_ID  is consumed by Seq::PrimarySeq

-jason

On Fri, 17 Oct 2003, Marc Logghe wrote:

>
> > You can set GI number with
> > $seq->primary_id($ginumber);
>
> True. You can set it up in the object but it is not shown in the genbank
> dump. And, also the way around, when a genbank record is parsed
> containing the line 'VERSION AB050006.1 GI:26453358' it does not get
> into the Bio::Seq::RichSeq object. As far as I can see.
>
> >
> > If you want to be creating RichSeq instead of Bio::Seq objects (in the
> > event you want to set some fields which are only available in RichSeq
> > objects, initialize your  Bio::SeqIO fasta parser like this:
> >
> > use Bio::SeqIO;
> > use Bio::Seq::SeqFactory;
> > my $seqio = new Bio::SeqIO(-format => 'fasta',
> > 			   -file   => $file,
> > 			   -seqfactory => new Bio::Seq::SeqFactory
> > 			( -type => 'Bio::Seq::RichSeq'));
> That is a really cool one. Never used it like this. Thanks
> ML
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From Marc.Logghe at devgen.com  Fri Oct 17 09:23:42 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Fri Oct 17 09:21:00 2003
Subject: [Bioperl-l] How do you create a genbank file?
Message-ID: 

I must have had huge flies in my eyes: the GI is there indeed, in the object *and* in the genbank dump.
Thanks for your patience, Jason !!
Cheers,
Marc

> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
> Sent: Friday, October 17, 2003 2:58 PM
> To: Marc Logghe
> Cc: Wes Barris; Bioperl Mailing List
> Subject: RE: [Bioperl-l] How do you create a genbank file?
> 
> 
> The should all be captured when you parse a genbank file (and be
> available when you write a genbank file) that is how we can round trip
> the format and have it be 99% identical.
> 
> gi number goes to primary_id()
> accession number goes to accession_number()
> version goes to seq_version() and version() (not sure why we 
> have 2 methods here???)
> 
>   # From Bio::SeqIO::genbank
>   if( /^ACCESSION\s+(\S.*\S)/ ) {
> 	      push(@acc, split(/\s+/,$1));
> 	      while( defined($_ = $self->_readline) ) {
> 		  /^\s+(.*)/ && do { push (@acc, 
> split(/\s+/,$1)); next };
> 		  last;
> 	      }
> 	      $buffer = $_;
> 	      next;
> 	  }
>   ....
>   elsif( /^VERSION\s+(.+)$/ ) {
> 	      my ($acc,$gi) = split(' ',$1);
> 	      if($acc =~ /^\w+\.(\d+)/) {
> 		  $params{'-version'} = $1;
> 		  $params{'-seq_version'} = $1;
> 	      }
> 	      if($gi && (index($gi,"GI:") == 0)) {
> 		  $params{'-primary_id'} = substr($gi,3);
> 	      }
> 	  }
> 
>    the first item in @acc is passed to the appropriate 
> accession_number
>    slot and the rest are passed to secondard accessions slot.
> 
>    The %params hash gets passed to the appropriate Seq object
> through the factory.  The arguments are passed through the hierarchy
> 
>    SEQ_VERSION is consumed by Seq::RichSeq
>    VERSION     is consumed by Seq::PrimarySeq
>    PRIMARY_ID  is consumed by Seq::PrimarySeq
> 
> -jason
> 
> On Fri, 17 Oct 2003, Marc Logghe wrote:
> 
> >
> > > You can set GI number with
> > > $seq->primary_id($ginumber);
> >
> > True. You can set it up in the object but it is not shown 
> in the genbank
> > dump. And, also the way around, when a genbank record is parsed
> > containing the line 'VERSION AB050006.1 GI:26453358' it does not get
> > into the Bio::Seq::RichSeq object. As far as I can see.
> >
> > >
> > > If you want to be creating RichSeq instead of Bio::Seq 
> objects (in the
> > > event you want to set some fields which are only 
> available in RichSeq
> > > objects, initialize your  Bio::SeqIO fasta parser like this:
> > >
> > > use Bio::SeqIO;
> > > use Bio::Seq::SeqFactory;
> > > my $seqio = new Bio::SeqIO(-format => 'fasta',
> > > 			   -file   => $file,
> > > 			   -seqfactory => new Bio::Seq::SeqFactory
> > > 			( -type => 'Bio::Seq::RichSeq'));
> > That is a really cool one. Never used it like this. Thanks
> > ML
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 

From heikki at ebi.ac.uk  Fri Oct 17 09:51:21 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Fri Oct 17 09:48:44 2003
Subject: [Bioperl-l] Codon Table
In-Reply-To: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>
References: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>
Message-ID: <1066398681.7861.47.camel@localhost>

Mick,

I really have not thought about this possibility. CodonTable can easily
be modified, but there is no way of passing the modified codontable
object to sequence::translate. The translate function has really complex
argument list already, so there is no way we can add anything in there. 

Depending what you want to do, it might be enough to modify the
codontable object and use its translate function. Compare it to
Bio::PrimarySeqI::translate to see what I mean. If you need full
seq::translate functionality, Bio::SeqUtils is the place to put the
code, e.g. $polypept = Bio::SeqUtils::translate($seq, $codontable);

I wrote the following method to be added into Bio::Tools::CodonTable. If
you think it is useful, I can commit it.

Yours,
	-Heikki


=head2 add_table

 Title   : add_table
 Usage   : $newid = $ct->add_table($name, $table, $starts)
 Function: Add a custom Codon Table into the object.
           Know what you are doing, only the length of
           the argument strings is checked!
 Returns : the id of the new codon table
 Args    : name, a string, optional (can be empty)
           table, a string of 64 characters
           startcodons, a string of 64 characters, defaults to standard

=cut

sub add_table {
    my ($self, $name, $table, $starts) = @_;

    $name ||= 'Custom'. scalar @NAMES + 1;
    $starts ||= $STARTS[0]; 
    $self->throw('Suspect input!')
        unless length($table) == 64 and length($starts) == 64;

    push @NAMES, $name;
    push @TABLES, $table;
    push @STARTS, $starts;

    return scalar @NAMES;

}

usage:

$ct_id = $ct->add_table(@custom_table);
$ct->id($ct_id);
$string = $ct->translate($nt_string);


 



On Tue, 2003-10-14 at 17:03, michael watson (IAH-C) wrote:
> Hi
> 
> I want to use a different codon table than any that are present in CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I have to hack CodonTable.pm?
> 
> Thanks
> Mick
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From hyupaik at indiana.edu  Fri Oct 17 14:15:52 2003
From: hyupaik at indiana.edu (Henry Hyun-il Paik)
Date: Fri Oct 17 14:13:10 2003
Subject: [Bioperl-l] (no subject)
In-Reply-To: 
Message-ID: 


 Hello list,

 It is impossible to have a space in Feature key, Right?

 I downlaoded some data from embl cpgisle. They look like below.

---------------------------------------------------------------------------
ID   GAPDHG
AC   J04038;
LE   5378
DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, complete
cds.
DE   7/95
EX   Gene expression widespread
FT   CpG island      871..1673
FT                   /size=803
FT                   /%(C+G)=69.12
FT                   /Obs/Exp CpG=0.82
FT   CpG island      1683..2063
FT                   /size=381
FT                   /%(C+G)=67.19
FT                   /Obs/Exp CpG=0.77
XX
FT                   /CAAT-box.1="884"
FT                   /CAAT-box.2_complement="2156"
FT                   /GC-box="1064"
FT                   /E2F_CS.1="1785"
FT                   /SpI="158,1198,1244,1290,1310,1314"
FT                   /SpI_complement="174,584,1519,1668,1736,2271"
FT                   /SpI_complement="2625"
FT                   /AccII="717,727,1093,1268,1334,1423"
FT                   /AccII="1489,1531,1788,2006,3650,4278"
//
------------------------------------------------------------------------
 
 I tried to parse this by using SeqIO. It didn't work.

 I got an error message like below.

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

Argument "island" isn't numeric in numeric gt (>) at
/home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
Argument "island" isn't numeric in numeric gt (>) at
/home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.

------------- EXCEPTION  -------------
MSG: Got a sequence with no letters in - cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet
/home/hy1001/bin/Bio/PrimarySeq.pm:817
STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
STACK Bio::Seq::SeqFactory::create
/home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
STACK toplevel extracted.pl:13

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

 So I changed 'CpG island' to 'CpG_island'. Then it worked fine.

 I am using perl 5.8.0 and bioperl 1.2.3 on linux.

 Thank you.

 - Henry.

 

From hyupaik at indiana.edu  Fri Oct 17 14:18:37 2003
From: hyupaik at indiana.edu (hyupaik@indiana.edu)
Date: Fri Oct 17 14:15:54 2003
Subject: [Bioperl-l] a space in Feature key in the Feature Table.
Message-ID: <1066414717.3f90327d3f8eb@webmail.iu.edu>




 Hello list,

 It is impossible to have a space in Feature key, Right?

 I downlaoded some data from embl cpgisle. They look like below.

---------------------------------------------------------------------------
ID   GAPDHG
AC   J04038;
LE   5378
DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, complete
cds.
DE   7/95
EX   Gene expression widespread
FT   CpG island      871..1673
FT                   /size=803
FT                   /%(C+G)=69.12
FT                   /Obs/Exp CpG=0.82
FT   CpG island      1683..2063
FT                   /size=381
FT                   /%(C+G)=67.19
FT                   /Obs/Exp CpG=0.77
XX
FT                   /CAAT-box.1="884"
FT                   /CAAT-box.2_complement="2156"
FT                   /GC-box="1064"
FT                   /E2F_CS.1="1785"
FT                   /SpI="158,1198,1244,1290,1310,1314"
FT                   /SpI_complement="174,584,1519,1668,1736,2271"
FT                   /SpI_complement="2625"
FT                   /AccII="717,727,1093,1268,1334,1423"
FT                   /AccII="1489,1531,1788,2006,3650,4278"
//
------------------------------------------------------------------------
 
 I tried to parse this by using SeqIO. It didn't work.

 I got an error message like below.

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

Argument "island" isn't numeric in numeric gt (>) at
/home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
Argument "island" isn't numeric in numeric gt (>) at
/home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.

------------- EXCEPTION  -------------
MSG: Got a sequence with no letters in - cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet
/home/hy1001/bin/Bio/PrimarySeq.pm:817
STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
STACK Bio::Seq::SeqFactory::create
/home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
STACK toplevel extracted.pl:13

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

 So I changed 'CpG island' to 'CpG_island'. Then it worked fine.

 I am using perl 5.8.0 and bioperl 1.2.3 on linux.

 Thank you.

 - Henry.

From birney at ebi.ac.uk  Fri Oct 17 14:31:11 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Fri Oct 17 14:28:23 2003
Subject: [Bioperl-l] (no subject)
In-Reply-To: 
Message-ID: <15052214-00D0-11D8-919D-000393CBD5AE@ebi.ac.uk>


On Friday, October 17, 2003, at 07:15  pm, Henry Hyun-il Paik wrote:

>
>  Hello list,
>
>  It is impossible to have a space in Feature key, Right?
>
>  I downlaoded some data from embl cpgisle. They look like below.
>

I don't think you are allowed spaces. Where did you get this from?



> ----------------------------------------------------------------------- 
> ----
> ID   GAPDHG
> AC   J04038;
> LE   5378
> DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene,  
> complete
> cds.
> DE   7/95
> EX   Gene expression widespread
> FT   CpG island      871..1673
> FT                   /size=803
> FT                   /%(C+G)=69.12
> FT                   /Obs/Exp CpG=0.82
> FT   CpG island      1683..2063
> FT                   /size=381
> FT                   /%(C+G)=67.19
> FT                   /Obs/Exp CpG=0.77
> XX
> FT                   /CAAT-box.1="884"
> FT                   /CAAT-box.2_complement="2156"
> FT                   /GC-box="1064"
> FT                   /E2F_CS.1="1785"
> FT                   /SpI="158,1198,1244,1290,1310,1314"
> FT                   /SpI_complement="174,584,1519,1668,1736,2271"
> FT                   /SpI_complement="2625"
> FT                   /AccII="717,727,1093,1268,1334,1423"
> FT                   /AccII="1489,1531,1788,2006,3650,4278"
> //
> ----------------------------------------------------------------------- 
> -
>
>  I tried to parse this by using SeqIO. It didn't work.
>
>  I got an error message like below.
>
>   
> -----------------------------------------------------------------------
>
> Argument "island" isn't numeric in numeric gt (>) at
> /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
> Argument "island" isn't numeric in numeric gt (>) at
> /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
>
> ------------- EXCEPTION  -------------
> MSG: Got a sequence with no letters in - cannot guess alphabet []
> STACK Bio::PrimarySeq::_guess_alphabet
> /home/hy1001/bin/Bio/PrimarySeq.pm:817
> STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
> STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
> STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
> STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
> STACK Bio::Seq::SeqFactory::create
> /home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
> STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
> STACK toplevel extracted.pl:13
>
>   
> -----------------------------------------------------------------------
>
>  So I changed 'CpG island' to 'CpG_island'. Then it worked fine.
>
>  I am using perl 5.8.0 and bioperl 1.2.3 on linux.
>
>  Thank you.
>
>  - Henry.
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From hyupaik at indiana.edu  Fri Oct 17 16:03:15 2003
From: hyupaik at indiana.edu (Henry Hyun-il Paik)
Date: Fri Oct 17 16:00:41 2003
Subject: [Bioperl-l] a space in Feature key
In-Reply-To: <15052214-00D0-11D8-919D-000393CBD5AE@ebi.ac.uk>
Message-ID: 



 Hello Ewan,

 I downloaded data from 

	ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/

 the file name is cpgisle.dat

 - Henry

On Fri, 17 Oct 2003, Ewan Birney wrote:

> 
> On Friday, October 17, 2003, at 07:15  pm, Henry Hyun-il Paik wrote:
> 
> >
> >  Hello list,
> >
> >  It is impossible to have a space in Feature key, Right?
> >
> >  I downlaoded some data from embl cpgisle. They look like below.
> >
> 
> I don't think you are allowed spaces. Where did you get this from?
> 
> 
> 
> > ----------------------------------------------------------------------- 
> > ----
> > ID   GAPDHG
> > AC   J04038;
> > LE   5378
> > DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene,  
> > complete
> > cds.
> > DE   7/95
> > EX   Gene expression widespread
> > FT   CpG island      871..1673
> > FT                   /size=803
> > FT                   /%(C+G)=69.12
> > FT                   /Obs/Exp CpG=0.82
> > FT   CpG island      1683..2063
> > FT                   /size=381
> > FT                   /%(C+G)=67.19
> > FT                   /Obs/Exp CpG=0.77
> > XX
> > FT                   /CAAT-box.1="884"
> > FT                   /CAAT-box.2_complement="2156"
> > FT                   /GC-box="1064"
> > FT                   /E2F_CS.1="1785"
> > FT                   /SpI="158,1198,1244,1290,1310,1314"
> > FT                   /SpI_complement="174,584,1519,1668,1736,2271"
> > FT                   /SpI_complement="2625"
> > FT                   /AccII="717,727,1093,1268,1334,1423"
> > FT                   /AccII="1489,1531,1788,2006,3650,4278"
> > //
> > ----------------------------------------------------------------------- 
> > -
> >
> >  I tried to parse this by using SeqIO. It didn't work.
> >
> >  I got an error message like below.
> >
> >   
> > -----------------------------------------------------------------------
> >
> > Argument "island" isn't numeric in numeric gt (>) at
> > /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
> > Argument "island" isn't numeric in numeric gt (>) at
> > /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
> >
> > ------------- EXCEPTION  -------------
> > MSG: Got a sequence with no letters in - cannot guess alphabet []
> > STACK Bio::PrimarySeq::_guess_alphabet
> > /home/hy1001/bin/Bio/PrimarySeq.pm:817
> > STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
> > STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
> > STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
> > STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
> > STACK Bio::Seq::SeqFactory::create
> > /home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
> > STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
> > STACK toplevel extracted.pl:13
> >
> >   
> > -----------------------------------------------------------------------
> >
> >  So I changed 'CpG island' to 'CpG_island'. Then it worked fine.
> >
> >  I am using perl 5.8.0 and bioperl 1.2.3 on linux.
> >
> >  Thank you.
> >
> >  - Henry.
> >
> >
> >
> > _______________________________________________
> > 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 muratet at hiwaay.net  Fri Oct 17 20:03:47 2003
From: muratet at hiwaay.net (Michael Muratet)
Date: Fri Oct 17 18:32:28 2003
Subject: [Bioperl-l] 'Suspicious' headers
Message-ID: <20031017190347.139d2cb9.muratet@hiwaay.net>

Greetings

I sent an email to the list regarding modules in bioperl that would
format data for phylip (other than simple file format changes) from a
Windows machine and it bounced to the moderator for a 'suspicious
header'. Can anyone tell me what was suspicious, so I can fix it?

Regarding the original question: I'm trying to format data from a
clustalw alignment for use in a phylogeny program. There must be a
simple way to clip the ends of the sequences so they're all the same
length, pick a region without gaps, etc., but I can't find it in the
documentation. Does anybody have any suggestions?

Thanks

Mike
From cvelasc at gwdg.de  Wed Oct 15 08:52:32 2003
From: cvelasc at gwdg.de (velasco)
Date: Fri Oct 17 18:36:14 2003
Subject: [Bioperl-l] (no subject)
Message-ID: <000001c3931b$33eebd70$277b4c86@helsinki>

To whom it concern
 
I'm strongly interested in bioperl. I have not any bioinformatics
experience and I would like to start with bioperl.
I have already installed Perl (ActiveState Perl 5.6) on Windows. I have
already downloaded the bioperl modules by Perl Package Maneger and from
http://bioperl.org/Core/external.shtml . I have read many tutorials
available on internet, but I cannot access to the bioperl programs.
Maybe I miss some important details. I hope to get help.
 
Best Regards
 
 
Velasco Cimica
velasco.cimica@virgilio.it
cvelasc@gwdg.de
+49/551/396365 (Lab)
 
Clinic of Goettingen
Departement of Gastroenterology 
2.D4 675 
Roberth Koch Str 40
37075 Goettingen
Germany
 
From mike.muratet at torchtechnologies.com  Fri Oct 17 09:38:31 2003
From: mike.muratet at torchtechnologies.com (Mike Muratet)
Date: Fri Oct 17 18:36:37 2003
Subject: [Bioperl-l] Phylip format for phylogeny
Message-ID: <016801c394b3$f55ebf70$5301a8c0@TORCHQR1Q6JDEG>

Greetings

In the "there must be a way to do this" department, I am working on a phylogeny project, and I would like to take clustalw output, find the common aligned region (i.e., the region without gaps) write it out in phylip format and use it in one or more of the available phylogeny tools. Converting clustalw to phylip format is trivial, but is there a way to find and extract a region from all of the sequences in an alignment? (I can't find it in the documentation.)

Thanks

Mike
From dag at sonsorol.org  Fri Oct 17 19:09:49 2003
From: dag at sonsorol.org (chris dagdigian)
Date: Fri Oct 17 19:08:17 2003
Subject: [Bioperl-l] 'Suspicious' headers
In-Reply-To: <20031017190347.139d2cb9.muratet@hiwaay.net>
References: <20031017190347.139d2cb9.muratet@hiwaay.net>
Message-ID: <3F9076BD.5060203@sonsorol.org>


For spam and virus reasons just about any email sent to our mailing 
lists that _is not_ written in plain ASCII text will be caught and held 
for moderation (one of our admin volunteers looks at the message and 
makes an approve/discard decision).

These are the most common scenarios for people getting their messages 
held up:

  o Email written in HTML (ie Outlook users)
  o Email with any sort of attachment
  o Any sort of MIME-encoded email, inline or attachment
  o Odd character encoding

We do quite a bit of behind the scenes mail filtering and we still can't 
stop all of the spam from leaking through. Right now any incoming email 
that has a spamassasin score of >= 8.0 is deleted pretty much instantly 
at the server level.

Messages that pass that first step get to our Mailman mailing list 
software which will also 'hold for moderation' any messages that have 
odd encoding or attachment issues.

-Chris



Michael Muratet wrote:

> Greetings
> 
> I sent an email to the list regarding modules in bioperl that would
> format data for phylip (other than simple file format changes) from a
> Windows machine and it bounced to the moderator for a 'suspicious
> header'. Can anyone tell me what was suspicious, so I can fix it?
> 
> Regarding the original question: I'm trying to format data from a
> clustalw alignment for use in a phylogeny program. There must be a
> simple way to clip the ends of the sequences so they're all the same
> length, pick a region without gaps, etc., but I can't find it in the
> documentation. Does anybody have any suggestions?
> 
> Thanks
> 
> Mike
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Chris Dagdigian, 
Independent life science IT & informatics consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net

From brian_osborne at cognia.com  Fri Oct 17 09:11:19 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Fri Oct 17 21:09:37 2003
Subject: [Bioperl-l] (no subject)
In-Reply-To: <000001c3931b$33eebd70$277b4c86@helsinki>
Message-ID: 

Velasco,

Please send us an example of the code you've written and the error messages
that you're seeing.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of velasco
Sent: Wednesday, October 15, 2003 8:53 AM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] (no subject)

To whom it concern

I'm strongly interested in bioperl. I have not any bioinformatics
experience and I would like to start with bioperl.
I have already installed Perl (ActiveState Perl 5.6) on Windows. I have
already downloaded the bioperl modules by Perl Package Maneger and from
http://bioperl.org/Core/external.shtml . I have read many tutorials
available on internet, but I cannot access to the bioperl programs.
Maybe I miss some important details. I hope to get help.

Best Regards


Velasco Cimica
velasco.cimica@virgilio.it
cvelasc@gwdg.de
+49/551/396365 (Lab)

Clinic of Goettingen
Departement of Gastroenterology
2.D4 675
Roberth Koch Str 40
37075 Goettingen
Germany


From kvddrift at earthlink.net  Sat Oct 18 15:05:57 2003
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Sat Oct 18 15:03:25 2003
Subject: [Bioperl-l] some tests fail on Mac OS X and Bioperl 1.302
Message-ID: <1AB133AF-019E-11D8-BA0B-003065A5FDCC@earthlink.net>

Hi,

The Bioperl install of 1.3 (release October 17) gave some errors during
the test phase. I am using perl 5.8.0 on Mac OS X 10.2.8.

Most errors came from the fact that the test was done while my Mac
was off-line (I have dialup). All these tests passed with version 1.2.3
Is it now necessary to be online for the tests? I didn't see anything
about this in the docs.

These tests gave errors while online:

in DBCUTG.t :

# Test 9 got: '10.06' (t/DBCUTG.t at line 67)
#   Expected: '10.07'

# Test 14 got: '10.06' (t/DBCUTG.t at line 75)
#    Expected: '10.07'


in psm.t:

# Failed test 7 in t/psm.t at line 39

# Test 25 got: '1' (t/psm.t at line 89)
#    Expected: '0'
a is 13

# Test 29 got: 'NNNNNNNNNNNNN' (t/psm.t at line 102)
#    Expected: 'VVDCAGGTGBYD'

# Failed test 34 in t/psm.t at line 117



thanks,

- Koen.

From redwards at utmem.edu  Sat Oct 18 21:34:43 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Sat Oct 18 21:31:58 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: <1065025847.2553.112.camel@localhost>
Message-ID: <6A819219-01D4-11D8-9995-000A959E1622@utmem.edu>

Building bioperl-1.302 on Mac OSX with perl 5.8.0

Failed Test        Stat Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------------ 
-------
t/Coalescent.t                   11    1   9.09%  9
t/DBCUTG.t                       23    2   8.70%  9 14
t/psm.t                          41    4   9.76%  7 25 29 34
t/simpleGOparser.t               88    1   1.14%  11
27 subtests skipped.
Failed 4/174 test scripts, 97.70% okay. 8/7953 subtests failed, 99.90%  
okay.

Building bioperl-1.302 on Debian linux with perl 5.8.0

Failed Test        Stat Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------------ 
-------
t/DBCUTG.t                       23    2   8.70%  9 14
t/psm.t                          41    4   9.76%  7 25 29 34
t/simpleGOparser.t               88    1   1.14%  11
27 subtests skipped.
Failed 3/174 test scripts, 98.28% okay. 7/7953 subtests failed, 99.91%  
okay.
make: *** [test_dynamic] Error 29

Note that t/Coalescent.t  only fails on OS X.

Rob

From redwards at utmem.edu  Sat Oct 18 22:52:47 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Sat Oct 18 22:50:02 2003
Subject: [Bioperl-l] New modules
Message-ID: <5204FDB8-01DF-11D8-9995-000A959E1622@utmem.edu>

I have written a couple of modules that are bioperl-ish. They are by no 
means finished, polished objects, and there is not t/ scripts at the 
moment. (But there are some docs!).

Bio::Tools::RepeatFinder for finding direct and indirect, perfect, and 
imperfect repeats in DNA sequences.

It is not necessarily speed-optimized, but it works well for sequences 
upto several hundred kb. The imperfect repeats part of it (a) just 
joins other repeats that it finds, so there is a limitation on the 
minimum length of imperfect repeats (2n+1 where n is the user-defined 
length of one half of a repeat); (b) in the current implementation 
requires Tie::RefHash; (c) the distance between repeats can be 
specified; and (d) this really slows things down because all the 
repeats are compared to all other repeats. You don't have to calculate 
these though, if you are only looking for perfect repeats.

Bio::SearchIO::Blink is a parser for BLINK from NCBI

Blink is NCBI's Blast Link - precalculated BLAST searches for every 
protein in the NR database (I believe). Unfortunately these reports 
don't contain useful things like starts and stops of matches so at the 
moment this doesn't return a very bioperl-ish result, but I am hoping 
that as NCBI develop BLINK this module can evolve into something. Its 
useful as is, though, depending on what you need.

The modules are available from http://www.salmonella.org/bioperl/

Take a look and let me know what you think or if you find bugs.

Rob

From brian_osborne at cognia.com  Sun Oct 19 02:01:56 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Sun Oct 19 14:00:35 2003
Subject: [Bioperl-l] New modules
In-Reply-To: <5204FDB8-01DF-11D8-9995-000A959E1622@utmem.edu>
Message-ID: 

Rob,

Can the repeats overlap? There was a recent feature request for something
like this...

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards
Sent: Saturday, October 18, 2003 10:53 PM
To: Bioperl
Subject: [Bioperl-l] New modules

I have written a couple of modules that are bioperl-ish. They are by no
means finished, polished objects, and there is not t/ scripts at the
moment. (But there are some docs!).

Bio::Tools::RepeatFinder for finding direct and indirect, perfect, and
imperfect repeats in DNA sequences.

It is not necessarily speed-optimized, but it works well for sequences
upto several hundred kb. The imperfect repeats part of it (a) just
joins other repeats that it finds, so there is a limitation on the
minimum length of imperfect repeats (2n+1 where n is the user-defined
length of one half of a repeat); (b) in the current implementation
requires Tie::RefHash; (c) the distance between repeats can be
specified; and (d) this really slows things down because all the
repeats are compared to all other repeats. You don't have to calculate
these though, if you are only looking for perfect repeats.

Bio::SearchIO::Blink is a parser for BLINK from NCBI

Blink is NCBI's Blast Link - precalculated BLAST searches for every
protein in the NR database (I believe). Unfortunately these reports
don't contain useful things like starts and stops of matches so at the
moment this doesn't return a very bioperl-ish result, but I am hoping
that as NCBI develop BLINK this module can evolve into something. Its
useful as is, though, depending on what you need.

The modules are available from http://www.salmonella.org/bioperl/

Take a look and let me know what you think or if you find bugs.

Rob

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


From redwards at utmem.edu  Sun Oct 19 14:25:05 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Sun Oct 19 14:22:20 2003
Subject: [Bioperl-l] New modules
In-Reply-To: 
Message-ID: <8FC39619-0261-11D8-9995-000A959E1622@utmem.edu>


On Sunday, October 19, 2003, at 01:01  AM, Brian Osborne wrote:

> Rob,
>
> Can the repeats overlap? There was a recent feature request for 
> something
> like this...
>
> Brian O.
>
>


Yep, the repeats can and do overlap. I suppose I could add something to 
not allow this, but I haven't yet.

there is a known "issue" that if you have repeats like this

GGAAAAAAAGG  and CCAAAAAAATTAAAAAAACC

and ask it to merge the nearby repeats the left half will have length 7 
and the right half will have length 16. I just keep forgetting to add 
something to make sure the left and right halves of the repeats are the 
same length. (Note: this is only with merged repeats; if you don't 
merge things together you'll get two separate repeats).

The most recent queries I remember about repeats had to do with 
repeatmasking sequences. I haven't given this much thought but I don't 
see why you couldn't use this module for that, but I'd set the minimum 
lengths of the repeats to be quite long to start with otherwise it will 
be horribly slow. The speed is really determined by the length of the 
sequence and the length of the repeats (obviously-a short sequence will 
have fewer repeats, and longer repeats will occur less frequently).

What was the other request ? I couldn't find anything in a search 
through the mailing archive.

Rob

From letondal at pasteur.fr  Sun Oct 19 17:11:16 2003
From: letondal at pasteur.fr (Catherine Letondal)
Date: Sun Oct 19 17:08:31 2003
Subject: [Bioperl-l] Pise: control on submissions
Message-ID: <20031019231116.A219070@electre.pasteur.fr>

Hi,

This is just an information for those of you who use the bioperl Pise
API. It's about a new type of error that can happen
when running programs under Pise: recently, we had difficulties to
cope with the growing number of requests (mainly from interactive
users) and I had to add a limit on the number of submissions - even
queued ones. So, it's really a good idea to check for the job
status when using the bioperl Pise API, for the server may be too busy
and reject the request.

my $job = $fastdnaml->run(-alignment => $ARGV[0]);
if ($job->error) {
    print $job->error_message, "\n";
    # exit or whatever
}

In this case, a possibility is to use an alternative Pise servers (such as
kun.homelinux.com - which is faster, see examples).

-- 
Catherine Letondal -- Pasteur Institute Computing Center
From jason at cgt.duhs.duke.edu  Sun Oct 19 19:56:54 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Sun Oct 19 19:53:54 2003
Subject: [Bioperl-l] Phylip format for phylogeny
In-Reply-To: <016801c394b3$f55ebf70$5301a8c0@TORCHQR1Q6JDEG>
References: <016801c394b3$f55ebf70$5301a8c0@TORCHQR1Q6JDEG>
Message-ID: 

You'd need to write something that would determine where the cutoffs of
your sub-alignment need to be if you are talking about a contiguous slice
of the alignment you want to preserve.

I have something I wrote a long time ago which basically walked out from
the start and end of the alignment and identify the part I want to
include.  This might be something like setting a cutoff % of sequences in
a column which are gapped and then finding either a single or multiple
regions which were of a minimum length and met the gap restriction cutoff.
This seemed to work for my needs - it reduced some of the noise for later
analyses but it definitely an alg that needs tweaking for a specific
question.

Anyways, you can get a slice of contiguous columns with
$aln->slice($start,$end)

There are also cmds to get non-contiguous columns but I'm not sure if that
is what you want.

-jason

On Fri, 17 Oct 2003, Mike Muratet wrote:

> Greetings
>
> In the "there must be a way to do this" department, I am working on a
> phylogeny project, and I would like to take clustalw output, find the
> common aligned region (i.e., the region without gaps) write it out in
> phylip format and use it in one or more of the available phylogeny
> tools. Converting clustalw to phylip format is trivial, but is there a
> way to find and extract a region from all of the sequences in an
> alignment? (I can't find it in the documentation.)
>
> Thanks
>
> Mike

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From copley at well.ox.ac.uk  Mon Oct 20 04:30:49 2003
From: copley at well.ox.ac.uk (Richard Copley)
Date: Mon Oct 20 04:28:02 2003
Subject: [Bioperl-l] Phylip format for phylogeny
In-Reply-To: <016801c394b3$f55ebf70$5301a8c0@TORCHQR1Q6JDEG>
References: <016801c394b3$f55ebf70$5301a8c0@TORCHQR1Q6JDEG>
Message-ID: <3F939D39.1010601@well.ox.ac.uk>


> In the "there must be a way to do this" department, I am working on a phylogeny project, and I would like to take clustalw output, find the common aligned region (i.e., the region without gaps) write it out in phylip format and use it in one or more of the available phylogeny tools. Converting clustalw to phylip format is trivial, but is there a way to find and extract a region from all of the sequences in an alignment? (I can't find it in the documentation.)

Jose Castresana's Gblocks program is a useful way to extract well 
aligned blocks for phylogenetic analysis.

http://monstre1.imim.es/~castresa/Gblocks/Gblocks.html


-- 
Richard Copley      | Wellcome Trust Centre for Human Genetics
tel +44 1865 287597 | Roosevelt Drive
fax +44 1865 287664 | Oxford OX3 7BN, England

From brian_osborne at cognia.com  Sun Oct 19 20:01:13 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Mon Oct 20 07:59:30 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: 
Message-ID: 

Daniel,

I've made a change that fixes the OBDA/Registry system for me, but only when
I create "flat" indices with bioflat_index.pl, not "bdb". Now I'll take a
look at why "bdb" doesn't work, it has to do with the code's inability to
direct the search properly to BinarySearch.pm or BDB.pm, I think.
Anotherwords, using Bio::DB::Flat directly using "flat" (or "binarysearch")
or "bdb" works, but when you use Registry with "bdb" the search is
incorrectly directed to BinarySearch.

If you'd like to try this then get the latest Bioperl from CVS. I don't
think there's anything wrong with your config.dat, and no, I didn't make any
changes to bioflat_index.pl.


Brian O.

-----Original Message-----
From: Daniel Lang [mailto:daniel.lang@biologie.uni-freiburg.de]
Sent: Friday, October 17, 2003 3:29 PM
To: Brian Osborne
Subject: Re: [Bioperl-l] Bio::DB::Registry

Hi Brian,
No, I?ve tried it with the enviroment variable using both
methods(flat and bsd), but the error remains:(
I?v posted my config.dat to the list(Wed Oct 15 10:52:39
EDT 2003 ), maybe there is something wrong?
As I?ve mentioned, I?ve downladed the bioflat_index.pl
seperately from the attic...
I see you moved it back to examples, did you change
anything?

Thanks for your help!
Enjoy your weekend:)
Daniel


From brian_osborne at cognia.com  Sun Oct 19 20:58:39 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Mon Oct 20 08:56:56 2003
Subject: [Bioperl-l] New modules
In-Reply-To: <8FC39619-0261-11D8-9995-000A959E1622@utmem.edu>
Message-ID: 

Rob,

>What was the other request ? I couldn't find anything in a search
>through the mailing archive.

Perhaps not exactly what you've done, it was a request to make SeqWords
collect overlapping matches.

Brian O.

-----Original Message-----
From: Rob Edwards [mailto:redwards@utmem.edu]
Sent: Sunday, October 19, 2003 2:25 PM
To: Brian Osborne
Cc: Bioperl
Subject: Re: [Bioperl-l] New modules


On Sunday, October 19, 2003, at 01:01  AM, Brian Osborne wrote:

> Rob,
>
> Can the repeats overlap? There was a recent feature request for
> something
> like this...
>
> Brian O.
>
>


Yep, the repeats can and do overlap. I suppose I could add something to
not allow this, but I haven't yet.

there is a known "issue" that if you have repeats like this

GGAAAAAAAGG  and CCAAAAAAATTAAAAAAACC

and ask it to merge the nearby repeats the left half will have length 7
and the right half will have length 16. I just keep forgetting to add
something to make sure the left and right halves of the repeats are the
same length. (Note: this is only with merged repeats; if you don't
merge things together you'll get two separate repeats).

The most recent queries I remember about repeats had to do with
repeatmasking sequences. I haven't given this much thought but I don't
see why you couldn't use this module for that, but I'd set the minimum
lengths of the repeats to be quite long to start with otherwise it will
be horribly slow. The speed is really determined by the length of the
sequence and the length of the repeats (obviously-a short sequence will
have fewer repeats, and longer repeats will occur less frequently).

What was the other request ? I couldn't find anything in a search
through the mailing archive.

Rob


From mike.muratet at torchtechnologies.com  Mon Oct 20 13:34:17 2003
From: mike.muratet at torchtechnologies.com (Mike Muratet)
Date: Mon Oct 20 13:30:49 2003
Subject: [Bioperl-l] Sequence from PDB
Message-ID: <01dc01c39730$6461a0d0$5301a8c0@TORCHQR1Q6JDEG>

Greetings

Is there a method associated with the Bio::Structure family that will
extract the sequence (primary structure) from PDB files? I don't see one in
the documentation.

Thanks

Mike

From brian_osborne at cognia.com  Mon Oct 20 01:47:29 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Mon Oct 20 13:46:11 2003
Subject: [Bioperl-l] Sequence from PDB
In-Reply-To: <01dc01c39730$6461a0d0$5301a8c0@TORCHQR1Q6JDEG>
Message-ID: 

Mike,

>From bptutorial:

  $structio = Bio::Structure::IO->new( -file => "1XYZ.pdb");
  $struc = $structio->next_structure; # returns an Entry object
  $pseq = $struc->seqres;             # returns a PrimarySeq object, thus
  $pseq->subseq(1,20);                # returns a sequence string

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Mike Muratet
Sent: Monday, October 20, 2003 1:34 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] Sequence from PDB

Greetings

Is there a method associated with the Bio::Structure family that will
extract the sequence (primary structure) from PDB files? I don't see one in
the documentation.

Thanks

Mike

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


From allenday at ucla.edu  Mon Oct 20 21:46:36 2003
From: allenday at ucla.edu (Allen Day)
Date: Mon Oct 20 21:43:47 2003
Subject: [Bioperl-l] Bio::SeqIO::kegg
Message-ID: 

Hi all,

I just added a parser for KEGG sequence records, available from:

ftp://ftp.genome.ad.jp/pub/kegg/genomes/genes/

I've parsed all tags except CODON_USAGE and POSITION into a 
Bio::Seq::RichSeq.  I didn't implement CODON_USAGE because I wasn't sure 
what class would hold it, and also because the codon frequencies can be 
recalculated from the primary sequence.

For the POSITION tag, I didn't implement it because I wasn't sure how to 
deal with the reference sequence and exon positions for a spliced mRNA.  
If someone wants to explain to me how to do this, I'd be happy to 
implement it.  Or if someone wants to DIY, please feel free.

I'm in the process of writing a parser for KGML:

ftp://ftp.genome.ad.jp/pub/kegg/pathways/KGML_v0.3/

to read in KEGG's pathway data, are people interested in representing
metabolic networks in bioperl, or am I better off doing this as a separate
project?  Or better yet, has someone already done this?

-Allen

From birney at ebi.ac.uk  Tue Oct 21 03:54:46 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Tue Oct 21 04:43:26 2003
Subject: [Bioperl-l] Bio::SeqIO::kegg
In-Reply-To: 
Message-ID: 


On Tuesday, October 21, 2003, at 02:46  am, Allen Day wrote:

> Hi all,
>
> I just added a parser for KEGG sequence records, available from:
>
> ftp://ftp.genome.ad.jp/pub/kegg/genomes/genes/
>
> I've parsed all tags except CODON_USAGE and POSITION into a
> Bio::Seq::RichSeq.  I didn't implement CODON_USAGE because I wasn't 
> sure
> what class would hold it, and also because the codon frequencies can be
> recalculated from the primary sequence.
>
> For the POSITION tag, I didn't implement it because I wasn't sure how 
> to
> deal with the reference sequence and exon positions for a spliced mRNA.
> If someone wants to explain to me how to do this, I'd be happy to
> implement it.  Or if someone wants to DIY, please feel free.
>
> I'm in the process of writing a parser for KGML:
>
> ftp://ftp.genome.ad.jp/pub/kegg/pathways/KGML_v0.3/
>
> to read in KEGG's pathway data, are people interested in representing
> metabolic networks in bioperl, or am I better off doing this as a 
> separate
> project?  Or better yet, has someone already done this?
>

Allen - whatever happens in Kegg parsing in bioperl, over at GK we'd 
like to
make sure that we can provide similar information and try to round trip
information. Imre Vastrik is the technical lead on GK and possibly
has some ideas about a generic "pathway" object model (GK has a rich
pathway object model which is defined in Protege and then Perl and
Java code run-time bind to the protege-generated and manipulated
datastructures).



> -Allen
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From chauser at duke.edu  Tue Oct 21 13:34:56 2003
From: chauser at duke.edu (Charles Hauser)
Date: Tue Oct 21 16:49:36 2003
Subject: [Bioperl-l] Bio::SeqFeature::Generic
Message-ID: <1066757868.17682.40.camel@pandorina.biology.duke.edu>

Don't know if this is a bug or a problem on my end.

Using Bio::SeqFeature::Generic to generate gff:

	my $feat = new Bio::SeqFeature::Generic();
	$feat->seq_id($seq->id);
	$feat->source_tag('assembly');
	$feat->primary_tag('contig');
	$feat->start('1');
	$feat->end($seq->length);
	$feat->add_tag_value('Contig',$seq->id);
	$out->write_feature($feat);

I end up with 2 extra spaces following the group tag ('Contig
scaffold_1') which results in gbrowse returning: ...landmark not
recognized...

deleting these spaces makes all right with the world.

Is the problem in my code or in  Bio::SeqFeature::Generic?

Charles

-------------- next part --------------
scaffold_1	assembly	contig	1	2159858	.	.	.	Contig scaffold_1  
scaffold_1	ace	match	50886	52846	.	+	.	Target "ACE:20021010.8753.1"  9 687  
scaffold_1	ace	HSP	50886	51245	.	+	.	Target "ACE:20021010.8753.1"  9 368  
scaffold_1	ace	HSP	51578	51703	.	+	.	Target "ACE:20021010.8753.1"  369 494  
scaffold_1	ace	HSP	52280	52345	.	+	.	Target "ACE:20021010.8753.1"  495 560  
scaffold_1	ace	HSP	52719	52834	.	+	.	Target "ACE:20021010.8753.1"  561 676  
scaffold_1	ace	HSP	52836	52846	.	+	.	Target "ACE:20021010.8753.1"  677 687  
scaffold_1	ace	match	2852	3829	.	+	.	Target "ACE:20021010.432.1"  948 1577  
scaffold_1	ace	HSP	2852	2998	.	+	.	Target "ACE:20021010.432.1"  948 1094  
scaffold_1	ace	HSP	3175	3218	.	+	.	Target "ACE:20021010.432.1"  1095 1138  
scaffold_1	ace	HSP	3219	3305	.	+	.	Target "ACE:20021010.432.1"  1140 1226  
scaffold_1	ace	HSP	3479	3829	.	+	.	Target "ACE:20021010.432.1"  1227 1577  
scaffold_1	ace	match	47657	48119	.	+	.	Target "ACE:20021010.1025.1"  5 484  
scaffold_1	ace	HSP	47657	47746	.	+	.	Target "ACE:20021010.1025.1"  5 94  
scaffold_1	ace	HSP	47747	48119	.	+	.	Target "ACE:20021010.1025.1"  112 484  
scaffold_1	ace	match	44560	45221	.	+	.	Target "ACE:20021010.3151.1"  8 669  
scaffold_1	ace	HSP	44560	45221	.	+	.	Target "ACE:20021010.3151.1"  8 669  
scaffold_1	ace	match	47550	50747	.	+	.	Target "ACE:20021010.8359.1"  9 1212  
scaffold_1	ace	HSP	47550	48210	.	+	.	Target "ACE:20021010.8359.1"  9 669  
scaffold_1	ace	HSP	48741	48862	.	+	.	Target "ACE:20021010.8359.1"  670 791  
scaffold_1	ace	HSP	49384	49502	.	+	.	Target "ACE:20021010.8359.1"  792 910  
scaffold_1	ace	HSP	50261	50383	.	+	.	Target "ACE:20021010.8359.1"  911 1033  
scaffold_1	ace	HSP	50569	50747	.	+	.	Target "ACE:20021010.8359.1"  1034 1212  
From hlapp at gnf.org  Tue Oct 21 21:37:40 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Oct 21 21:34:34 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: <6A819219-01D4-11D8-9995-000A959E1622@utmem.edu>
Message-ID: 

On 10/18/03 6:34 PM, "Rob Edwards"  wrote:

> t/simpleGOparser.t               88    1   1.14%  11

Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
5.6.0.

    -hilmar
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From jason at cgt.duhs.duke.edu  Tue Oct 21 21:57:54 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Oct 21 21:55:03 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: 
References: 
Message-ID: 

I also get this on perl 5.8.0

not ok 11
# Test 11 got:  (t/simpleGOparser.t at line 82)
#    Expected: 'EC:5.3.99.5'


and perl 5.6.0
not ok 11
# Test 11 got:  (t/simpleGOparser.t at line 82)
#    Expected: 'EC:5.3.99.5'


On Tue, 21 Oct 2003, Hilmar Lapp wrote:

> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
>
> > t/simpleGOparser.t               88    1   1.14%  11
>
> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
> 5.6.0.
>
>     -hilmar
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From hlapp at gnf.org  Tue Oct 21 22:01:27 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Tue Oct 21 21:58:22 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: 
Message-ID: 

Will check. This used to work; somebody changed the parser lately though.

    -hilmar

On 10/21/03 6:57 PM, "Jason Stajich"  wrote:

> I also get this on perl 5.8.0
> 
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
> 
> 
> and perl 5.6.0
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
> 
> 
> On Tue, 21 Oct 2003, Hilmar Lapp wrote:
> 
>> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
>> 
>>> t/simpleGOparser.t               88    1   1.14%  11
>> 
>> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
>> 5.6.0.
>> 
>>     -hilmar
>> 
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From redwards at utmem.edu  Tue Oct 21 22:28:55 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Tue Oct 21 22:26:08 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: 
Message-ID: <7BB5C6EE-0437-11D8-9995-000A959E1622@utmem.edu>

I'm probably just going to confuse things here:

When I run make test
It fails on OSX/perl 5.8.0 and Debian/perl 5.8.0
It passes on Redhat/perl 5.6.1
($dblinks[0] is undef as Jason got)


However, it passes on all systems if you run 'perl -w 
t/simpleGOparser.t' and $dblinks[0] has the right value.

See, I warned you I'd confuse you.

Rob


On Tuesday, October 21, 2003, at 08:57  PM, Jason Stajich wrote:

> I also get this on perl 5.8.0
>
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
>
>
> and perl 5.6.0
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
>
>
> On Tue, 21 Oct 2003, Hilmar Lapp wrote:
>
>> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
>>
>>> t/simpleGOparser.t               88    1   1.14%  11
>>
>> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
>> 5.6.0.
>>
>>     -hilmar
>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu

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Date: Wed Oct 22 00:04:27 2003
Subject: [Bioperl-l] Orion BioSolutions Kits, $25 to you with Purchase
Message-ID: <20031022035750.8874.qmail@crm.orionbiosolutions.com>


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From daniel.lang at biologie.uni-freiburg.de  Wed Oct 22 03:27:40 2003
From: daniel.lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Wed Oct 22 03:24:23 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: 
References: 
Message-ID: <3F96316C.3080107@biologie.uni-freiburg.de>

Hi Brian,
I hope I?m not getting on your nerves...
Now, there occurs a new problem when using flat indices:(
When I call services on the Registry object, it returns the list of the
available services, but when I want to "get_databases" on one of them I
get a Bio::DB::Failover Object...
I?ve registered a nt (FASTA) and an aa (SWISSPROT) flat file...
Of course, I?m still interested in using the bdb indices:)

Thanks again,
Daniel

-- 
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

From hlapp at gnf.org  Wed Oct 22 03:56:14 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct 22 03:53:09 2003
Subject: [Bioperl-l] Bio::SeqIO::kegg
In-Reply-To: 
Message-ID: <35B1A9DE-0465-11D8-B5E7-000A959EB4C4@gnf.org>

t/SeqIO......................ok 48/230"my" variable $annotation masks 
earlier declaration in same scope at blib/lib/Bio/SeqIO/kegg.pm line 
202,  line 235

	-hilmar

On Monday, October 20, 2003, at 06:46  PM, Allen Day wrote:

> Hi all,
>
> I just added a parser for KEGG sequence records, available from:
>
> ftp://ftp.genome.ad.jp/pub/kegg/genomes/genes/
>
> I've parsed all tags except CODON_USAGE and POSITION into a
> Bio::Seq::RichSeq.  I didn't implement CODON_USAGE because I wasn't 
> sure
> what class would hold it, and also because the codon frequencies can be
> recalculated from the primary sequence.
>
> For the POSITION tag, I didn't implement it because I wasn't sure how 
> to
> deal with the reference sequence and exon positions for a spliced mRNA.
> If someone wants to explain to me how to do this, I'd be happy to
> implement it.  Or if someone wants to DIY, please feel free.
>
> I'm in the process of writing a parser for KGML:
>
> ftp://ftp.genome.ad.jp/pub/kegg/pathways/KGML_v0.3/
>
> to read in KEGG's pathway data, are people interested in representing
> metabolic networks in bioperl, or am I better off doing this as a 
> separate
> project?  Or better yet, has someone already done this?
>
> -Allen
>
> _______________________________________________
> 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 gnf.org  Wed Oct 22 04:25:20 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct 22 04:22:14 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: 
Message-ID: <4609B7E9-0469-11D8-ABB3-000A959EB4C4@gnf.org>

Allen, your recent change to require only 1 digit instead of 3 after 
the colon broke the parser. The change makes the regular expressions 
pick up EC numbers as secondary GO accessions. Did the test quoted 
below not fail on your machine?

I'm going to reverse that change. The MPATH ontology needs to be 
accommodated in a way that doesn't break the parser, possibly by having 
its own.

Also, I should urge you to add test cases for all the ontologies for 
which you found yourself having to adapt the parser. Otherwise the 
ability to parse those too may be abolished silently at any time by 
anyone changing the code.

	-hilmar

On Tuesday, October 21, 2003, at 06:57  PM, Jason Stajich wrote:

> I also get this on perl 5.8.0
>
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
>
>
> and perl 5.6.0
> not ok 11
> # Test 11 got:  (t/simpleGOparser.t at line 82)
> #    Expected: 'EC:5.3.99.5'
>
>
> On Tue, 21 Oct 2003, Hilmar Lapp wrote:
>
>> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
>>
>>> t/simpleGOparser.t               88    1   1.14%  11
>>
>> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
>> 5.6.0.
>>
>>     -hilmar
>>
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------


From brian_osborne at cognia.com  Wed Oct 22 08:28:19 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Wed Oct 22 08:27:13 2003
Subject: [Bioperl-l] Bio::DB::Registry
In-Reply-To: <3F96316C.3080107@biologie.uni-freiburg.de>
Message-ID: 

Daniel,

No problem, you're not bugging me. I have both BinarySearch and BDB working
with Registry and DB/Flat on my machine now. I'll take a look at your
get_databases() problem. Then I have to add some BDB/DB_File tests to
Registry.t. I'll tell you when this is all done, probably after the weekend.

What you should do is submit this get_databases() error into the tracking
system at bugzilla.bioperl.org with details, that would help.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Daniel Lang
Sent: Wednesday, October 22, 2003 3:28 AM
To: Brian Osborne
Cc: bioperl-l@bioperl.org
Subject: Re: [Bioperl-l] Bio::DB::Registry

Hi Brian,
I hope I?m not getting on your nerves...
Now, there occurs a new problem when using flat indices:(
When I call services on the Registry object, it returns the list of the
available services, but when I want to "get_databases" on one of them I
get a Bio::DB::Failover Object...
I?ve registered a nt (FASTA) and an aa (SWISSPROT) flat file...
Of course, I?m still interested in using the bdb indices:)

Thanks again,
Daniel

--
Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang@biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

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


From heikki at ebi.ac.uk  Wed Oct 22 09:11:45 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Wed Oct 22 09:08:58 2003
Subject: Bio::Tools::GFF [Re: [Bioperl-l] Bio::SeqFeature::Generic]
In-Reply-To: <1066757868.17682.40.camel@pandorina.biology.duke.edu>
References: <1066757868.17682.40.camel@pandorina.biology.duke.edu>
Message-ID: <1066828304.2631.18.camel@localhost>

Charles,

Your code should be fine.

I can see the extra spaces in the output by running the
following script as 'gfftest.pl |od'.

The method that needs changing is Bio::Tools::GFF::_gff2_string(), I'd
rather have feedback from GFF people first. Lincoln or someone from his
group should be able to say what is the correct way to solve this
problem.

Yours,
	-Heikki

---------------------gfftest.pl--------------------------------
use Bio::Tools::GFF;
use Bio::SeqFeature::Generic;
use Data::Dumper;

my $gffout = Bio::Tools::GFF->new(-gff_version => 2);

my $feat = new Bio::SeqFeature::Generic();
$feat->seq_id('111');
$feat->source_tag('assembly');
$feat->primary_tag('contig');
$feat->start('1');
$feat->end(123);
$feat->add_tag_value('Contig','111');
$gffout->write_feature($feat);
#print Dumper $feat;
--------------------------------------------------------

On Tue, 2003-10-21 at 18:37, Charles Hauser wrote:
> Don't know if this is a bug or a problem on my end.
> 
> Using Bio::SeqFeature::Generic to generate gff:
> 
> 	my $feat = new Bio::SeqFeature::Generic();
> 	$feat->seq_id($seq->id);
> 	$feat->source_tag('assembly');
> 	$feat->primary_tag('contig');
> 	$feat->start('1');
> 	$feat->end($seq->length);
> 	$feat->add_tag_value('Contig',$seq->id);
> 	$out->write_feature($feat);
> 
> I end up with 2 extra spaces following the group tag ('Contig
> scaffold_1') which results in gbrowse returning: ...landmark not
> recognized...
> 
> deleting these spaces makes all right with the world.
> 
> Is the problem in my code or in  Bio::SeqFeature::Generic?
> 
> Charles
> 
> 
> ______________________________________________________________________
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From jason at cgt.duhs.duke.edu  Wed Oct 22 09:39:09 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 22 09:36:36 2003
Subject: Bio::Tools::GFF [Re: [Bioperl-l] Bio::SeqFeature::Generic]
In-Reply-To: <1066828304.2631.18.camel@localhost>
References: <1066757868.17682.40.camel@pandorina.biology.duke.edu>
	<1066828304.2631.18.camel@localhost>
Message-ID: 

I've got a fix - this code really needed to be written better.  I'm using
arrays and joins instead of chop-ing strings post-hoc.

Index: Bio/Tools/GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GFF.pm,v
retrieving revision 1.29
diff -r1.29 GFF.pm
570c570
<    my $valuestr;
---
>
571a572
>    my @group;
573,575d573
<        $str .= "\t"; # my interpretation of the GFF2
<                      # specification suggests the need
<                      # for this additional TAB character...??
577,579c575
< 	   my $valuestr; # a string which will hold one or more values
< 	                 # for this tag, with quoted free text and
< 	                 # space-separated individual values.
---
> 	   my @v;
585c581,582
< 		   $value = '"' . $value . '" '} # if the value contains
---
> 		   $value = '"' . $value . '" ';
> 	       }                                 # if the value contains
589c586
< 	       $value = "\"\"" unless defined $value;
---
> 	       $value = '\""' unless defined $value;
593,595c590,591
< 	       $valuestr .=  $value . " "; # with a trailing space in case
< 	                                   # there are multiple values
< 	       # for this tag (allowed in GFF2 and .ace format)
---
> 	       push @v, $value;
> 	       # for this tag (allowed in GFF2 and .ace format)
597c593
< 	   $str .= "$tag $valuestr ; ";	# semicolon delimited with no '='
sign
---
> 	   push @group, "$tag ".join(" ", @v);
599d594
<        chop $str; chop $str;  # remove the trailing semicolon and space
600a596
>    $str .= "\t" . join(' ; ', @group);

-jason

-jason
On Wed, 22 Oct 2003, Heikki Lehvaslaiho wrote:

> Charles,
>
> Your code should be fine.
>
> I can see the extra spaces in the output by running the
> following script as 'gfftest.pl |od'.
>
> The method that needs changing is Bio::Tools::GFF::_gff2_string(), I'd
> rather have feedback from GFF people first. Lincoln or someone from his
> group should be able to say what is the correct way to solve this
> problem.
>
> Yours,
> 	-Heikki
>
> ---------------------gfftest.pl--------------------------------
> use Bio::Tools::GFF;
> use Bio::SeqFeature::Generic;
> use Data::Dumper;
>
> my $gffout = Bio::Tools::GFF->new(-gff_version => 2);
>
> my $feat = new Bio::SeqFeature::Generic();
> $feat->seq_id('111');
> $feat->source_tag('assembly');
> $feat->primary_tag('contig');
> $feat->start('1');
> $feat->end(123);
> $feat->add_tag_value('Contig','111');
> $gffout->write_feature($feat);
> #print Dumper $feat;
> --------------------------------------------------------
>
> On Tue, 2003-10-21 at 18:37, Charles Hauser wrote:
> > Don't know if this is a bug or a problem on my end.
> >
> > Using Bio::SeqFeature::Generic to generate gff:
> >
> > 	my $feat = new Bio::SeqFeature::Generic();
> > 	$feat->seq_id($seq->id);
> > 	$feat->source_tag('assembly');
> > 	$feat->primary_tag('contig');
> > 	$feat->start('1');
> > 	$feat->end($seq->length);
> > 	$feat->add_tag_value('Contig',$seq->id);
> > 	$out->write_feature($feat);
> >
> > I end up with 2 extra spaces following the group tag ('Contig
> > scaffold_1') which results in gbrowse returning: ...landmark not
> > recognized...
> >
> > deleting these spaces makes all right with the world.
> >
> > Is the problem in my code or in  Bio::SeqFeature::Generic?
> >
> > Charles
> >
> >
> > ______________________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From allenday at ucla.edu  Wed Oct 22 14:40:42 2003
From: allenday at ucla.edu (Allen Day)
Date: Wed Oct 22 14:37:50 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: <4609B7E9-0469-11D8-ABB3-000A959EB4C4@gnf.org>
Message-ID: 

> Allen, your recent change to require only 1 digit instead of 3 after 
> the colon broke the parser. The change makes the regular expressions 
> pick up EC numbers as secondary GO accessions. Did the test quoted 
> below not fail on your machine?

i tested my changes on Ontology.t and OntologyEngine.t, i didn't see
simpleGOparser.t, and so didn't run it before i checked in.  it does fail 
on my machine.

> I'm going to reverse that change. The MPATH ontology needs to be 
> accommodated in a way that doesn't break the parser, possibly by having 
> its own.

i keep loosening the regular expression to accommodate the different 
DAG-Edit IDs i enounter.  how about i write a regular expression that is 
as strict as possible but still matches everything that DAG-Edit allows?

> Also, I should urge you to add test cases for all the ontologies for 
> which you found yourself having to adapt the parser. Otherwise the 
> ability to parse those too may be abolished silently at any time by 
> anyone changing the code.
> 

sure.

-allen

> 	-hilmar
> 
> On Tuesday, October 21, 2003, at 06:57  PM, Jason Stajich wrote:
> 
> > I also get this on perl 5.8.0
> >
> > not ok 11
> > # Test 11 got:  (t/simpleGOparser.t at line 82)
> > #    Expected: 'EC:5.3.99.5'
> >
> >
> > and perl 5.6.0
> > not ok 11
> > # Test 11 got:  (t/simpleGOparser.t at line 82)
> > #    Expected: 'EC:5.3.99.5'
> >
> >
> > On Tue, 21 Oct 2003, Hilmar Lapp wrote:
> >
> >> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
> >>
> >>> t/simpleGOparser.t               88    1   1.14%  11
> >>
> >> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
> >> 5.6.0.
> >>
> >>     -hilmar
> >>
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
> 



From hlapp at gnf.org  Wed Oct 22 15:25:40 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Wed Oct 22 15:22:33 2003
Subject: [Bioperl-l] 1.3.02 failed tests
In-Reply-To: 
Message-ID: 

On 10/22/03 11:40 AM, "Allen Day"  wrote:

>> Allen, your recent change to require only 1 digit instead of 3 after
>> the colon broke the parser. The change makes the regular expressions
>> pick up EC numbers as secondary GO accessions. Did the test quoted
>> below not fail on your machine?
> 
> i tested my changes on Ontology.t and OntologyEngine.t, i didn't see
> simpleGOparser.t, and so didn't run it before i checked in.  it does fail
> on my machine.

It's generally not a bad idea to run *all* tests before checking in, as
bioperl is so complex meanwhile that it is difficult to predict with
certainty what knock-on effects a change may or may not have. Yes I know
running all tests takes a while and is painful, but I don't think there is a
good reason not to.

> 
>> I'm going to reverse that change. The MPATH ontology needs to be
>> accommodated in a way that doesn't break the parser, possibly by having
>> its own.
> 
> i keep loosening the regular expression to accommodate the different
> DAG-Edit IDs i enounter.  how about i write a regular expression that is
> as strict as possible but still matches everything that DAG-Edit allows?

Sure, you'd be welcome. Note though that non-conforming or
not-so-well-conforming formats may clearly justify their own parser in order
to avoid making a brittle one-catch-all monolithic parser. Also, complex
regular expressions have a tendency to become arcane and impossible to
maintain, so I'm actually not a big fan of coming up with ever more
sophisticated patterns with all kinds of subtle recognition features.

Rather, I'd try to find a pattern that identifies the token as an ID,
whether seconday ID or dbxref ID, and then leave it up to a method that may
be overridden to actually parse the ID and assign it to one of the term's
properties. (You'd then have 2 parsers, which would share most of the code
though.)

Event-based parsing may also be a way out, but that'd be big change.

    -hilmar

> 
>> Also, I should urge you to add test cases for all the ontologies for
>> which you found yourself having to adapt the parser. Otherwise the
>> ability to parse those too may be abolished silently at any time by
>> anyone changing the code.
>> 
> 
> sure.
> 
> -allen
> 
>> -hilmar
>> 
>> On Tuesday, October 21, 2003, at 06:57  PM, Jason Stajich wrote:
>> 
>>> I also get this on perl 5.8.0
>>> 
>>> not ok 11
>>> # Test 11 got:  (t/simpleGOparser.t at line 82)
>>> #    Expected: 'EC:5.3.99.5'
>>> 
>>> 
>>> and perl 5.6.0
>>> not ok 11
>>> # Test 11 got:  (t/simpleGOparser.t at line 82)
>>> #    Expected: 'EC:5.3.99.5'
>>> 
>>> 
>>> On Tue, 21 Oct 2003, Hilmar Lapp wrote:
>>> 
>>>> On 10/18/03 6:34 PM, "Rob Edwards"  wrote:
>>>> 
>>>>> t/simpleGOparser.t               88    1   1.14%  11
>>>> 
>>>> Do these just fail under Mac OSX perl 5.8.x? I can only check for perl
>>>> 5.6.0.
>>>> 
>>>>     -hilmar
>>>> 
>>> 
>>> --
>>> Jason Stajich
>>> Duke University
>>> jason at cgt.mc.duke.edu
>>> 
>> 
> 
> 
> 
> 

-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From ryan.doherty at mrc.ac.za  Thu Oct 23 04:30:15 2003
From: ryan.doherty at mrc.ac.za (Ryan Doherty)
Date: Thu Oct 23 04:24:45 2003
Subject: [Bioperl-l] Retrieve mail
Message-ID: 

Hello,

Can anyone recommend a module (either BioPerl module or other Perl module) that
will assist me in retrieving e-mail messages from a POP3 mail-server?

Much appreciated,


Ryan Doherty

From heikki at ebi.ac.uk  Thu Oct 23 04:41:31 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Thu Oct 23 04:38:40 2003
Subject: [Bioperl-l] a space in Feature key
In-Reply-To: 
References: 
Message-ID: <1066898490.2226.51.camel@localhost>

Checking with EMBL databank guys, I find out that since feature table 
format is defined in characters, space characters are not specifically
banned in feature keys, but they are actively avoided.

Also, I talked to Rodrigo Lopez who promised to release an updated
CpGIsle database soon (next week?) and remove the offending space.

Yours,

	-Heikki


On Fri, 2003-10-17 at 21:03, Henry Hyun-il Paik wrote:
>  Hello Ewan,
> 
>  I downloaded data from 
> 
> 	ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/
> 
>  the file name is cpgisle.dat
> 
>  - Henry
> 
> On Fri, 17 Oct 2003, Ewan Birney wrote:
> 
> > 
> > On Friday, October 17, 2003, at 07:15  pm, Henry Hyun-il Paik wrote:
> > 
> > >
> > >  Hello list,
> > >
> > >  It is impossible to have a space in Feature key, Right?
> > >
> > >  I downlaoded some data from embl cpgisle. They look like below.
> > >
> > 
> > I don't think you are allowed spaces. Where did you get this from?
> > 
> > 
> > 
> > > ----------------------------------------------------------------------- 
> > > ----
> > > ID   GAPDHG
> > > AC   J04038;
> > > LE   5378
> > > DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene,  
> > > complete
> > > cds.
> > > DE   7/95
> > > EX   Gene expression widespread
> > > FT   CpG island      871..1673
> > > FT                   /size=803
> > > FT                   /%(C+G)=69.12
> > > FT                   /Obs/Exp CpG=0.82
> > > FT   CpG island      1683..2063
> > > FT                   /size=381
> > > FT                   /%(C+G)=67.19
> > > FT                   /Obs/Exp CpG=0.77
> > > XX
> > > FT                   /CAAT-box.1="884"
> > > FT                   /CAAT-box.2_complement="2156"
> > > FT                   /GC-box="1064"
> > > FT                   /E2F_CS.1="1785"
> > > FT                   /SpI="158,1198,1244,1290,1310,1314"
> > > FT                   /SpI_complement="174,584,1519,1668,1736,2271"
> > > FT                   /SpI_complement="2625"
> > > FT                   /AccII="717,727,1093,1268,1334,1423"
> > > FT                   /AccII="1489,1531,1788,2006,3650,4278"
> > > //
> > > ----------------------------------------------------------------------- 
> > > -
> > >
> > >  I tried to parse this by using SeqIO. It didn't work.
> > >
> > >  I got an error message like below.
> > >
> > >   
> > > -----------------------------------------------------------------------
> > >
> > > Argument "island" isn't numeric in numeric gt (>) at
> > > /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
> > > Argument "island" isn't numeric in numeric gt (>) at
> > > /home/hy1001/bin/Bio/Location/Atomic.pm line 91,  line 15.
> > >
> > > ------------- EXCEPTION  -------------
> > > MSG: Got a sequence with no letters in - cannot guess alphabet []
> > > STACK Bio::PrimarySeq::_guess_alphabet
> > > /home/hy1001/bin/Bio/PrimarySeq.pm:817
> > > STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
> > > STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
> > > STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
> > > STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
> > > STACK Bio::Seq::SeqFactory::create
> > > /home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
> > > STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
> > > STACK toplevel extracted.pl:13
> > >
> > >   
> > > -----------------------------------------------------------------------
> > >
> > >  So I changed 'CpG island' to 'CpG_island'. Then it worked fine.
> > >
> > >  I am using perl 5.8.0 and bioperl 1.2.3 on linux.
> > >
> > >  Thank you.
> > >
> > >  - Henry.
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From ak at ebi.ac.uk  Thu Oct 23 04:51:12 2003
From: ak at ebi.ac.uk (Andreas Kahari)
Date: Thu Oct 23 04:48:18 2003
Subject: [offtopic] Re: [Bioperl-l] Retrieve mail
In-Reply-To: 
References: 
Message-ID: <20031023085112.GA32526@ebi.ac.uk>

On Thu, Oct 23, 2003 at 10:30:15AM +0200, Ryan Doherty wrote:
> Hello,
>
> Can anyone recommend a module (either BioPerl module or other
> Perl module) that will assist me in retrieving e-mail messages
> from a POP3 mail-server?

Search for POP3 at search.cpan.org

-- 
a n d r e (  Andreas K?h?ri                           ) 0 1 0 0 0
a s . k a  ) EMBL, European Bioinformatics Institute (  1 0 0 0 1
h a r i @ (  Wellcome Trust Genome Campus, Hinxton    ) 0 0 1 1 1
e b i . a  ) Cambridge, CB10 1SD                     (  0 0 1 0 0
c . u k   (  United Kingdom                           ) 0 0 0 1
From andreas.boehm at virchow.uni-wuerzburg.de  Thu Oct 23 05:10:48 2003
From: andreas.boehm at virchow.uni-wuerzburg.de (Andreas Boehm)
Date: Thu Oct 23 05:12:44 2003
Subject: [Bioperl-l] modified Fasta-Headers?
In-Reply-To: 
References: 
Message-ID: <3F979B18.2000302@virchow.uni-wuerzburg.de>

Hello,

analyzing fasta-files distributed with software from thermo, we found 
some undocumented characters in the header. There are some 0x01 (chr(1)) 
as field separator.
Is the meaning of theses chars known?

regards,
Andreas Boehm

From andreas.boehm at virchow.uni-wuerzburg.de  Thu Oct 23 05:16:25 2003
From: andreas.boehm at virchow.uni-wuerzburg.de (Andreas Boehm)
Date: Thu Oct 23 05:18:22 2003
Subject: [Bioperl-l] modified Fasta-Headers?
Message-ID: <3F979C69.3090105@virchow.uni-wuerzburg.de>

Hello,

analyzing fasta-files distributed with software from thermo, we found
some undocumented characters in the header. There are some 0x01 (chr(1))
as field separator.
Is the meaning of theses chars known?

regards,
Andreas Boehm

From Martin.Schenker at ogs.co.uk  Thu Oct 23 05:41:51 2003
From: Martin.Schenker at ogs.co.uk (Martin Schenker)
Date: Thu Oct 23 05:39:01 2003
Subject: [Bioperl-l] modified Fasta-Headers?
Message-ID: <934C1A6D9596D511B59E0002B34BC52A02F1394B@selene.ogs.co.uk>

Hi Andreas,

Are your sure that's not the "normal" nr header with ^A (^A => oct001 =>
\001) seperated chunks from different sources?

Best, Martin

> -----Original Message-----
> From: Andreas Boehm [mailto:andreas.boehm@virchow.uni-wuerzburg.de] 
> Sent: 23 October 2003 10:16
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] modified Fasta-Headers?
> 
> 
> Hello,
> 
> analyzing fasta-files distributed with software from thermo, we found
> some undocumented characters in the header. There are some 
> 0x01 (chr(1))
> as field separator.
> Is the meaning of theses chars known?
> 
> regards,
> Andreas Boehm
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 


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From andreas.boehm at virchow.uni-wuerzburg.de  Thu Oct 23 06:28:21 2003
From: andreas.boehm at virchow.uni-wuerzburg.de (Andreas Boehm)
Date: Thu Oct 23 06:30:18 2003
Subject: [Bioperl-l] modified Fasta-Headers?
In-Reply-To: <934C1A6D9596D511B59E0002B34BC52A02F1394B@selene.ogs.co.uk>
References: <934C1A6D9596D511B59E0002B34BC52A02F1394B@selene.ogs.co.uk>
Message-ID: <3F97AD45.5070703@virchow.uni-wuerzburg.de>

Hi,

> Are your sure that's not the "normal" nr header with ^A (^A => oct001 =>
> \001) seperated chunks from different sources?

No. Take a look:
 >gi|84670|pir||B27257 coagulogen II precursor - horseshoe crab =
(Tachypleus tridentatus)=01gi|10809 (X04192) coagulogen type II =
[Tachypleus tridentatus]=01gi|217395|gnl|PID|d1000491 (D00077) =
coagulogen type 2 [Tachypleus tridentatus]=01gi|356167|prf||1208319A =
coagulogen [Tachypleus sp.] [MASS=3D21826]
MEKKLFGIALLLTTVASVLAADTNAPICLCDEPGVLGRTQIVTTEIKDKIEKAVEAVAQESGVSGRGFSIFSH=
HPVFREC
GKYECRTVRPEHSRCYNFPPFIHFKSECPVSTRDCEPVFGYTVAGEFRVIVQAPRAGFRQCVWQHKCRFGSNS=
CGYNGRC
TQQRSVVRLVTYNLEKDGFLCESFRTCCGCPCRSF

from horse.fasta

I do not know, what the meaning of these chr(1) should be.
Any help?


regards,
Andreas Boehm

From deejoe at iastate.edu  Thu Oct 23 10:18:16 2003
From: deejoe at iastate.edu (D. Joe Anderson)
Date: Thu Oct 23 10:15:23 2003
Subject: [Bioperl-l] bioperl-pipeline
In-Reply-To: <07CD0901-FCD8-11D7-95C5-000A95783436@stanford.edu>
References: <1065961003.8277.15.camel@rattus.localdomain>
	<07CD0901-FCD8-11D7-95C5-000A95783436@stanford.edu>
Message-ID: <20031023141816.GM23429@iastate.edu>

On Sun, Oct 12, 2003 at 10:18:00AM -0700, Shawn Hoon wrote:
> We are still trying to resolve some dns issues. See if  
> biopipe-tmp.open-bio.org
> or add
> 
> 65.246.187.176 www.biopipe.org
> 
> to /etc/hosts
 
Just for the record, it looks like the DNS resolution problems have been
cleared up.

http://www.biopipe.org now just works (at least for me).



--Joe


From jason at cgt.duhs.duke.edu  Thu Oct 23 11:26:26 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Oct 23 11:23:30 2003
Subject: [Bioperl-l] [Bioperl-guts-l] [Bug 1544] New: Trouble dissecting
 problem Bio::SeqIO (fwd)
Message-ID: 

It is just a warning because the tag line doesn't wrap the way the parser
expects it to - it isn't a big deal.  If you don't want to see the
warnings you can set -verbose => -1 when you instantiate a
Bio::DB::GenBank.

my $db = Bio::DB::GenBank(-verbose => -1);


-jason
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Thu, 23 Oct 2003 09:24:59 -0400
From: bugzilla-daemon@portal.open-bio.org
To: bioperl-guts-l@bioperl.org
Subject: [Bioperl-guts-l] [Bug 1544] New: Trouble dissecting problem
    Bio::SeqIO

http://bugzilla.bioperl.org/show_bug.cgi?id=1544

           Summary: Trouble dissecting problem Bio::SeqIO
           Product: Bioperl
           Version: 1.2 branch
          Platform: PC
               URL: http://www.smd.qmul.ac.uk/gc/homepages/dbuchan/
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::SeqIO
        AssignedTo: bioperl-guts-l@bioperl.org
        ReportedBy: d.w.a.buchan@qmul.ac.uk


I assume this is a problem with Bio::SeqIO but may be a problem with
Bio::DB::GenBank (but I doubt it). Currently I'm trying to download a file
~67,000 est from genbank, however upon trying to download and output some of the
records bioperl throws the following error (depending on the est record)

-------------------- WARNING ---------------------
MSG: trouble dissecting
"IPISGKPLPKVTLSRDGVPLKATMRFNTEITAENLTINLKESVTADAGRYEITAANSSGTTKAFINI VVLDRPGPPT
GPVVISDITEESVTLKWEPPKYDGGSQVTNYILLKRETSTAVWTEVSATVARTMMKVMKL ... ;, mRNA
sequence." into chunks of 66 chars or less - this tag won't print right
---------------------------------------------------

or

-------------------- WARNING ---------------------
MSG: trouble dissecting
"TGTTACCAATCTGAAGTGGGAGCGGCCGCATTGCTTTTTTTTTTTTTTTTTTTTTTTT T 3'];
double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia),  digested with
Not I and cloned into the Not I and Eco RI sites of  the modified pT7T3 vector.
Library is normalized, and was constructed  by Bento Soares and M.Fatima
Bonaldo."" into chunks of 57 chars or less - this tag won't print right
---------------------------------------------------

In exchange it prints outputs nothing.  Unfortunately I can't give specific
accession numbers as I'm using the get_stream_by_id() method.  Although I will
gladly foward the file of accessions that I'm using and the script I'm using to
do this.

The perl version I'm using is 5.8.0, the Bio version I'm using is 1.2.3 both
running in RedHat 8.  We are experiencing the same problem when trying to
accomplish the same task on a Sun Solaris 8 machine



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From chauser at duke.edu  Thu Oct 23 12:09:34 2003
From: chauser at duke.edu (Charles Hauser)
Date: Thu Oct 23 12:09:35 2003
Subject: [Bioperl-l] GFF3: preliminary or implemented?
Message-ID: <1066925550.20083.4.camel@pandorina.biology.duke.edu>

My last notes re:GFF3 were that it was in the 'preliminary' stage, but
it appears as though Jason update Tools::GFF to handle '='.

Question: is GFF3 a supported version now & is  GBrowse happy w/ GFF3
formatting?


Charles


From lstein at cshl.edu  Thu Oct 23 12:33:07 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Oct 23 12:30:16 2003
Subject: [Bioperl-l] GFF3: preliminary or implemented?
In-Reply-To: <1066925550.20083.4.camel@pandorina.biology.duke.edu>
References: <1066925550.20083.4.camel@pandorina.biology.duke.edu>
Message-ID: <200310231233.07501.lstein@cshl.edu>

Essentially the answer is yes.  A few details need to be worked out, most 
importantly handling the CIGAR gap lines.

Lincoln

On Thursday 23 October 2003 12:12 pm, Charles Hauser wrote:
> My last notes re:GFF3 were that it was in the 'preliminary' stage, but
> it appears as though Jason update Tools::GFF to handle '='.
>
> Question: is GFF3 a supported version now & is  GBrowse happy w/ GFF3
> formatting?
>
>
> Charles
>
>
> _______________________________________________
> 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
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================


From cjm at fruitfly.org  Thu Oct 23 12:48:27 2003
From: cjm at fruitfly.org (Chris Mungall)
Date: Thu Oct 23 12:46:02 2003
Subject: [Bioperl-l] GFF3: preliminary or implemented?
In-Reply-To: <1066925550.20083.4.camel@pandorina.biology.duke.edu>
Message-ID: 


It seems to me that we need to extend Bio::Tools::GFF to read/write the
seqfeature nesting hierarchy using ID= and Parent= tags

This seems a little problemmatic because it requires the notion of a
unique id for features, which is lacking in bioperl

How should we progress here? Should we add add a unique_id method to
SeqFeature? Should this be autogenerated?

On 23 Oct 2003, Charles Hauser wrote:

> My last notes re:GFF3 were that it was in the 'preliminary' stage, but
> it appears as though Jason update Tools::GFF to handle '='.
>
> Question: is GFF3 a supported version now & is  GBrowse happy w/ GFF3
> formatting?
>
>
> Charles
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

From michael at galton.ucl.ac.uk  Thu Oct 23 16:01:59 2003
From: michael at galton.ucl.ac.uk (michael)
Date: Thu Oct 23 15:59:05 2003
Subject: [Bioperl-l] What's that number?
In-Reply-To: <200309241917.h8OJGoMj031893@portal.open-bio.org>
Message-ID: 



	Is there any code out there that can make an educated guess to the
origin of any given (biological) ID/accession number?

	X93993 AJ010957 are both valid EMBL accession numbers, P47202
looks similar but is from swissprot (a bit of digging reveals the
swissprot patten as /[OPQ]\d[A-Z\d][A-Z\d][A-Z\d]\d/ ).  Failing code is
there a biological name space document out there?

	I'm writing a public gene symbol submission form and want it to do
the right thing regardless of where the data is pasted in.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Michael John Lush PhD		 	 Tel:44-20-7679-5027
Nomenclature Bioinformatics Support 	 Fax:44-20-7387-3496
HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
The Galton Laboratory
University College London, UK
URL: http://www.gene.ucl.ac.uk/nomenclature/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

From o02u at unb.ca  Thu Oct 23 19:42:59 2003
From: o02u at unb.ca (Cooper, Marc Emmerson)
Date: Thu Oct 23 19:40:06 2003
Subject: [Bioperl-l] Question re: Phred Base Quality Data & Bio::SeqIO::scf 
Message-ID: <1066952579.3f986783186c9@webmail1.unb.ca>

Hi everyone, 

I'm looking for some information on base quality data via the Bio::SeqIO::scf package. 
Specifically, I recognize that there are methods to extract the base qualities for both
called and uncalled bases within the SCF file using _dump_base_qualities() or
_dump_base_qualities_incoming().  

I have generated an SCF file using phred and have written a small portion of perl code
to extract the quality data from the SCF file.  However upon examination of the output
I noticed that only the quality data for called bases is available and zero values are
assigned to the quality data for the three other potential bases at each base position.
   

Could anyone tell me whether it is possible to export quality data for the uncalled
bases using phred?  Or do SCF files generated by phred only contain quality data for
called bases?

Cheers,

Marc Cooper
Master's Candidate
Bioinformatics Research Group
Faculty of Computer Science
University of New Brunswick
Fredericton, NB  Canada  
E3B 5A3
email: marc.cooper@unb.ca

From pwilkinson at videotron.ca  Thu Oct 23 21:41:56 2003
From: pwilkinson at videotron.ca (Peter Wilkinson)
Date: Thu Oct 23 21:39:03 2003
Subject: [Bioperl-l] What's that number?
In-Reply-To: 
References: <200309241917.h8OJGoMj031893@portal.open-bio.org>
Message-ID: <5.2.0.9.0.20031023213506.00b242b8@pop.videotron.ca>

Well it would be nice if there existed some type of global namespace 
management for that sort of thing, however there is none.

I am afraid that we will have to put up with the mountainous clutter of 
sequences and annotations.

Now if someone wants to start some type of public registry for defining 
theses namespaces .... which would not be such a bad idea if one could 
prove how it would help the community. GO is an attempt for function, and 
HUGO for gene names ... no reason not to do it for namespaces 
(databasenamespaces ;) ).

Peter

p.s. perhaps a big pair of billy boots is good enough to wade through it all.





At 09:01 PM 23/10/2003 +0100, michael wrote:


>         Is there any code out there that can make an educated guess to the
>origin of any given (biological) ID/accession number?
>
>         X93993 AJ010957 are both valid EMBL accession numbers, P47202
>looks similar but is from swissprot (a bit of digging reveals the
>swissprot patten as /[OPQ]\d[A-Z\d][A-Z\d][A-Z\d]\d/ ).  Failing code is
>there a biological name space document out there?
>
>         I'm writing a public gene symbol submission form and want it to do
>the right thing regardless of where the data is pasted in.
>
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>Michael John Lush PhD                   Tel:44-20-7679-5027
>Nomenclature Bioinformatics Support     Fax:44-20-7387-3496
>HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
>The Galton Laboratory
>University College London, UK
>URL: http://www.gene.ucl.ac.uk/nomenclature/
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l@portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l


-------------------------------------
Peter Wilkinson
Bioinformatics Consultant

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


From lstein at cshl.edu  Thu Oct 23 22:23:30 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Oct 23 22:20:51 2003
Subject: [Gmod-gbrowse] Re: [Bioperl-l] GFF3: preliminary or implemented?
In-Reply-To: 
References: 
Message-ID: <200310232223.30051.lstein@cshl.edu>

The idea of the ID is that it is just unique within the GFF3 file.  It does 
not necessarily translate into an ID for the feature itself.  I did some work 
on Bio::Tools::GFF so that it would deal with this correctly, but it hasn't 
been torture tested.  GBrowse handles the IDs correctly, but doesn't rely on 
Bio::Tools::GFF.

Lincoln


On Thursday 23 October 2003 12:48 pm, Chris Mungall wrote:
> It seems to me that we need to extend Bio::Tools::GFF to read/write the
> seqfeature nesting hierarchy using ID= and Parent= tags
>
> This seems a little problemmatic because it requires the notion of a
> unique id for features, which is lacking in bioperl
>
> How should we progress here? Should we add add a unique_id method to
> SeqFeature? Should this be autogenerated?
>
> On 23 Oct 2003, Charles Hauser wrote:
> > My last notes re:GFF3 were that it was in the 'preliminary' stage, but
> > it appears as though Jason update Tools::GFF to handle '='.
> >
> > Question: is GFF3 a supported version now & is  GBrowse happy w/ GFF3
> > formatting?
> >
> >
> > Charles
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
> -------------------------------------------------------
> This SF.net email is sponsored by: The SF.net Donation Program.
> Do you like what SourceForge.net is doing for the Open
> Source Community?  Make a contribution, and help us add new
> features and functionality. Click here: http://sourceforge.net/donate/
> _______________________________________________
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> Gmod-gbrowse@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From zbigk at yahoo.com  Thu Oct 23 23:09:43 2003
From: zbigk at yahoo.com (ADV; . Energy Systems & Electrical Design)
Date: Fri Oct 24 02:09:31 2003
Subject: [Bioperl-l] ADV:  .  Resume for JOB or Service
Message-ID: <200310240609.h9O69Bdb004596@portal.open-bio.org>



Rich' S 	Resume	

							Santa Clara, CA 95050


  (408) 482-2840          rrsiek@yahoo.com
 



Electrical Designer &  Drafting


Electro-Mechanical Designer & Drafting



Drafting & Design Shopping Centers; grocery stores, hardware stores, restaurants & residential - housing areas, computer business & fast food units installation & testing; 

Energy systems; Solar Panels, Wind Energy, portable & emergency generators; Factory production lines, food & mechanical process machinery Installations & trouble shooting.  

Equipment & production line installations, MCC, Sensors, Wiring, Alarm, Network, Security, Electrical Design & Installations;  Network Sketches, one line diagrams, and "as is" drawings update. 

Customizing Electronic and Electrical Components & Parts, Layouts electronic and electrical schematic, connectors and mechanical detailing. Use CAD, Windows and applications; Programming & Detailing, Production Equipment, Machinery, Conveyors Spiral Elevator, Fast Cannery Transportation, Electronic and Electrical Components, Parts, Schematics & Layouts, Master Control Center, Can Sheet Metal Oven Rebuilding Project, Combustion Remodeling, PD 5,  PLC setup. 

Designing Electric Cars using AutoCAD, Spreadsheet, Basic, dB; electronic and electrical schematic, Layouts, mechanical detailing & redesigning components for manufacturing, Assembly drawings, Customizing Electronic, Mechanical and Electrical Equipment.

Quotes, supply, bids and job estimating. Customers contact, inspection, project mgmt & supervision of electricians & material handling; Commercial & Residential Project; Mgr. for satellite office & shop. 

Commercial, Industrial, Residential, Fire Alarms, Smoke Detectors, Lights, Plugs, Panels, Power Supply, Electro-Solar Installations, Emergency Generators, Transformers, Power Lines, Fire sprinklers design / control, CAD automation. Foreman, Estimator, Designer & CAD Operator (New & "as is" drawings update)

Hands on electrical installation performing, fitting wires & power lines;  Panels, Light, receptacles & Fuse boxes, emergency power supply, parking lighting & post installation; Installing lamps, switches, alarms, plugs, receptacles, fire alarms, smoke detectors, fire & safety installations; Computer & data network wiring; underground installations & conduit layout, bending and mounting; Job Estimating & bid preparation.

Environmental Energy Systems and Green Building Coordinating Programs;  P E C,  C E C,  PG&E training, Solar Living Institute, High Performance Schools, Health Analyzing, using Solar and Wind Energy Friendly Systems, Savings by Design recommendations & new Title 24 Standards - LEED, CEC, AIA & COTE Ratings. 

Electrical & Electrical Drafting, Electrical Design & management, Site Inspection and Quality Control, coordination with General Contractor, Estimating and Supplying, Document Control & Upgrade, daily performance checking & schedule update. 


Electrical Installations & Service

Solar Energy Installations & Service

Electro-Mechanical Assembly & Service

ELECTRICAL PROJECT MANAGER -  COORDINATOR

ELECTRICAL & MAINTENANCE SERVICE

HANDS ON WIRING & INSTALLATION

ELECTRICAL AND MECHANICAL PROJECTS 



Electrical Installations & Service

Solar Energy Installations & Service

Electro-Mechanical Assembly & Service

ELECTRICAL PROJECT MANAGER -  COORDINATOR

ELECTRICAL & MAINTENANCE SERVICE

HANDS ON WIRING & INSTALLATION

ELECTRICAL AND MECHANICAL PROJECTS 

Sun Tracking  double  SOLAR ENERGY



SOLAR ENERGY SYSTEMS

WIND ENERGY SYSTEMS

SUN TRACKING SYSTEMS

SOLAR PALETTE SYSTEMS

FLYWHEEL STORAGE SYSTEMS



Solar Engineer





From zbigk at yahoo.com  Thu Oct 23 23:09:43 2003
From: zbigk at yahoo.com (ADV; . Energy Systems & Electrical Design)
Date: Fri Oct 24 02:09:37 2003
Subject: [Bioperl-l] ADV:  .  Resume for JOB or Service
Message-ID: <200310240609.h9O69Bdb004597@portal.open-bio.org>



Rich' S 	Resume	

							Santa Clara, CA 95050


  (408) 482-2840          rrsiek@yahoo.com
 



Electrical Designer &  Drafting


Electro-Mechanical Designer & Drafting



Drafting & Design Shopping Centers; grocery stores, hardware stores, restaurants & residential - housing areas, computer business & fast food units installation & testing; 

Energy systems; Solar Panels, Wind Energy, portable & emergency generators; Factory production lines, food & mechanical process machinery Installations & trouble shooting.  

Equipment & production line installations, MCC, Sensors, Wiring, Alarm, Network, Security, Electrical Design & Installations;  Network Sketches, one line diagrams, and "as is" drawings update. 

Customizing Electronic and Electrical Components & Parts, Layouts electronic and electrical schematic, connectors and mechanical detailing. Use CAD, Windows and applications; Programming & Detailing, Production Equipment, Machinery, Conveyors Spiral Elevator, Fast Cannery Transportation, Electronic and Electrical Components, Parts, Schematics & Layouts, Master Control Center, Can Sheet Metal Oven Rebuilding Project, Combustion Remodeling, PD 5,  PLC setup. 

Designing Electric Cars using AutoCAD, Spreadsheet, Basic, dB; electronic and electrical schematic, Layouts, mechanical detailing & redesigning components for manufacturing, Assembly drawings, Customizing Electronic, Mechanical and Electrical Equipment.

Quotes, supply, bids and job estimating. Customers contact, inspection, project mgmt & supervision of electricians & material handling; Commercial & Residential Project; Mgr. for satellite office & shop. 

Commercial, Industrial, Residential, Fire Alarms, Smoke Detectors, Lights, Plugs, Panels, Power Supply, Electro-Solar Installations, Emergency Generators, Transformers, Power Lines, Fire sprinklers design / control, CAD automation. Foreman, Estimator, Designer & CAD Operator (New & "as is" drawings update)

Hands on electrical installation performing, fitting wires & power lines;  Panels, Light, receptacles & Fuse boxes, emergency power supply, parking lighting & post installation; Installing lamps, switches, alarms, plugs, receptacles, fire alarms, smoke detectors, fire & safety installations; Computer & data network wiring; underground installations & conduit layout, bending and mounting; Job Estimating & bid preparation.

Environmental Energy Systems and Green Building Coordinating Programs;  P E C,  C E C,  PG&E training, Solar Living Institute, High Performance Schools, Health Analyzing, using Solar and Wind Energy Friendly Systems, Savings by Design recommendations & new Title 24 Standards - LEED, CEC, AIA & COTE Ratings. 

Electrical & Electrical Drafting, Electrical Design & management, Site Inspection and Quality Control, coordination with General Contractor, Estimating and Supplying, Document Control & Upgrade, daily performance checking & schedule update. 


Electrical Installations & Service

Solar Energy Installations & Service

Electro-Mechanical Assembly & Service

ELECTRICAL PROJECT MANAGER -  COORDINATOR

ELECTRICAL & MAINTENANCE SERVICE

HANDS ON WIRING & INSTALLATION

ELECTRICAL AND MECHANICAL PROJECTS 



Electrical Installations & Service

Solar Energy Installations & Service

Electro-Mechanical Assembly & Service

ELECTRICAL PROJECT MANAGER -  COORDINATOR

ELECTRICAL & MAINTENANCE SERVICE

HANDS ON WIRING & INSTALLATION

ELECTRICAL AND MECHANICAL PROJECTS 

Sun Tracking  double  SOLAR ENERGY



SOLAR ENERGY SYSTEMS

WIND ENERGY SYSTEMS

SUN TRACKING SYSTEMS

SOLAR PALETTE SYSTEMS

FLYWHEEL STORAGE SYSTEMS



Solar Engineer





From david.konopnicki at hp.com  Fri Oct 24 05:47:06 2003
From: david.konopnicki at hp.com (Konopnicki, David)
Date: Fri Oct 24 05:44:13 2003
Subject: [Bioperl-l] Netwok problem?
Message-ID: <711B92DC11556E428989346ECC5D9E0C028350B7@raaexc01.emea.cpqcorp.net>

Hi,
I just installed BioPerl and am trying to run:

get_sequence('swissprot',"ROA1_HUMAN");

I receive an error: can't connect to www.ebi.ac.uk:80 (connection refused)
My proxy settings look fine and I get run lwp-download to get www.ebi.ac.uk:80
Any ideas? 
Thanks
-David

From walsh at cenix-bioscience.com  Fri Oct 24 07:25:07 2003
From: walsh at cenix-bioscience.com (Andrew Walsh)
Date: Fri Oct 24 08:39:54 2003
Subject: [Bioperl-l] What's that number?
In-Reply-To: <5.2.0.9.0.20031023213506.00b242b8@pop.videotron.ca>
References: <200309241917.h8OJGoMj031893@portal.open-bio.org>
	<5.2.0.9.0.20031023213506.00b242b8@pop.videotron.ca>
Message-ID: <3F990C13.3040806@cenix-bioscience.com>

There had been work done on something like that for seq retrievals- 
Bio::DB::Universal.  It probably still wouldn't help with the ambiguous 
identifiers though.

Andrew



Peter Wilkinson wrote:
> Well it would be nice if there existed some type of global namespace 
> management for that sort of thing, however there is none.
> 
> I am afraid that we will have to put up with the mountainous clutter of 
> sequences and annotations.
> 
> Now if someone wants to start some type of public registry for defining 
> theses namespaces .... which would not be such a bad idea if one could 
> prove how it would help the community. GO is an attempt for function, 
> and HUGO for gene names ... no reason not to do it for namespaces 
> (databasenamespaces ;) ).
> 
> Peter
> 
> p.s. perhaps a big pair of billy boots is good enough to wade through it 
> all.
> 
> 
> 
> 
> 
> At 09:01 PM 23/10/2003 +0100, michael wrote:
> 
> 
>>         Is there any code out there that can make an educated guess to 
>> the
>> origin of any given (biological) ID/accession number?
>>
>>         X93993 AJ010957 are both valid EMBL accession numbers, P47202
>> looks similar but is from swissprot (a bit of digging reveals the
>> swissprot patten as /[OPQ]\d[A-Z\d][A-Z\d][A-Z\d]\d/ ).  Failing code is
>> there a biological name space document out there?
>>
>>         I'm writing a public gene symbol submission form and want it 
>> to do
>> the right thing regardless of where the data is pasted in.
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Michael John Lush PhD                   Tel:44-20-7679-5027
>> Nomenclature Bioinformatics Support     Fax:44-20-7387-3496
>> HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
>> The Galton Laboratory
>> University College London, UK
>> URL: http://www.gene.ucl.ac.uk/nomenclature/
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 
> -------------------------------------
> Peter Wilkinson
> Bioinformatics Consultant
> 
> ------------------------------------- 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 


-- 
------------------------------------------------------------------
Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Pfotenhauerstr. 108
01307 Dresden, Germany
Tel. +49(351)210-2699
Fax  +49(351)210-1309

public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg
------------------------------------------------------------------


From markw at illuminae.com  Fri Oct 24 10:26:26 2003
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri Oct 24 10:23:41 2003
Subject: [BioPerl] Re: [Bioperl-l] What's that number?
In-Reply-To: <5.2.0.9.0.20031023213506.00b242b8@pop.videotron.ca>
References: <200309241917.h8OJGoMj031893@portal.open-bio.org>
	<5.2.0.9.0.20031023213506.00b242b8@pop.videotron.ca>
Message-ID: <1067005586.2036.24.camel@localhost.localdomain>

There are at least two "initiatives" looking at exactly this problem,
but they wont solve the precise problem that you raise (i.e. determining
the namespace of an in-hand ID number post facto):

1)  The LSID proposal from the I3C makes ID numbers "resolvable" so that
you can always determine the namespace of an ID by querying a resolver
service with your in-hand data.  In this system the ID number must take
the form of a LSID-type URI, and someone (the authority, or someone
else) must have set up a resolver service for URI's of that type.

2)  The BioMOBY project, in which ID numbers are always passed together
with a second identifier indicating the namespace under which that ID is
to be interpreted.  Although, unlike LSIDs, we in the BioMOBY project
use the existing ID numbers _verbatim_, this still wont help you in this
case since the person who gave you that ID is obligated by the BioMOBY
API to give you the namespace identifier at the same time.  We do have a
public registry of namespaces, however, largely based on the GO Xref
Abbreviations List.

in any case, once you get an ID number without namespace information you
are throwing your life on the mercy of regular expression searches of
loosely defined conventions...  bad luck for you!

All the more reason we should start using these two technologies as
quickly as possible!! (though call me biased ;-) )

Mark


On Thu, 2003-10-23 at 19:41, Peter Wilkinson wrote:
> Well it would be nice if there existed some type of global namespace 
> management for that sort of thing, however there is none.
> 
> I am afraid that we will have to put up with the mountainous clutter of 
> sequences and annotations.
> 
> Now if someone wants to start some type of public registry for defining 
> theses namespaces .... which would not be such a bad idea if one could 
> prove how it would help the community. GO is an attempt for function, and 
> HUGO for gene names ... no reason not to do it for namespaces 
> (databasenamespaces ;) ).
> 
> Peter
> 
> p.s. perhaps a big pair of billy boots is good enough to wade through it all.
> 
> 
> 
> 
> 
> At 09:01 PM 23/10/2003 +0100, michael wrote:
> 
> 
> >         Is there any code out there that can make an educated guess to the
> >origin of any given (biological) ID/accession number?
> >
> >         X93993 AJ010957 are both valid EMBL accession numbers, P47202
> >looks similar but is from swissprot (a bit of digging reveals the
> >swissprot patten as /[OPQ]\d[A-Z\d][A-Z\d][A-Z\d]\d/ ).  Failing code is
> >there a biological name space document out there?
> >
> >         I'm writing a public gene symbol submission form and want it to do
> >the right thing regardless of where the data is pasted in.
> >
> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >Michael John Lush PhD                   Tel:44-20-7679-5027
> >Nomenclature Bioinformatics Support     Fax:44-20-7387-3496
> >HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
> >The Galton Laboratory
> >University College London, UK
> >URL: http://www.gene.ucl.ac.uk/nomenclature/
> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l@portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> -------------------------------------
> Peter Wilkinson
> Bioinformatics Consultant
> 
> -------------------------------------  
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
Mark Wilkinson 
Illuminae

From chenn at cshl.edu  Fri Oct 24 15:15:36 2003
From: chenn at cshl.edu (Jack Chen)
Date: Fri Oct 24 15:13:07 2003
Subject: [Bioperl-l] Bio::Graphics::Pictogram
Message-ID: 

A nice and useful module. Is there a plan to make it work with proteins?
Also, it currently does not recognize lower case sequences.

Jack

++++++++++++++++++++++++++++++++++++++++++++
    o-o     Jack Chen, Stein Laboratory      
    o---o   Cold Spring Harbor Laboratory    
  o----o    #5 Williams, 1 Bungtown Road           
 O----O     Cold Spring Harbor, NY, 11724   
 0--o       Tel: 1 516 367 8394              
   O        e-mail: chenn@cshl.org  	    
  o-o       Website: http://www.wormbase.org
+++++++++++++++++++++++++++++++++++++++++++++
        


From shawnh at stanford.edu  Fri Oct 24 15:59:09 2003
From: shawnh at stanford.edu (Shawn Hoon)
Date: Fri Oct 24 15:52:02 2003
Subject: [Bioperl-l] Bio::Graphics::Pictogram
In-Reply-To: 
References: 
Message-ID: <87CD5708-065C-11D8-A8A6-000A95783436@stanford.edu>


On Friday, October 24, 2003, at 12:15PM, Jack Chen wrote:

> A nice and useful module. Is there a plan to make it work with 
> proteins?
> Also, it currently does not recognize lower case sequences.
>
Thanks, just committed a fix for the lowercase.

I was supposed to work on a project with Allen Day moving the module to 
a SVG
package he was writing for cpan. This would make Pictogram a generic 
module that
should handle aa as well since the current module will need some work 
to get it to extend.
  However 1st year of grad school is keeping me busy right now
and its not going very far. If you would like to look at contributing, 
you might want to talk to Allen more on
this

cheers,

shawn


> Jack
>
> ++++++++++++++++++++++++++++++++++++++++++++
>     o-o     Jack Chen, Stein Laboratory
>     o---o   Cold Spring Harbor Laboratory
>   o----o    #5 Williams, 1 Bungtown Road
>  O----O     Cold Spring Harbor, NY, 11724
>  0--o       Tel: 1 516 367 8394
>    O        e-mail: chenn@cshl.org  	
>   o-o       Website: http://www.wormbase.org
> +++++++++++++++++++++++++++++++++++++++++++++
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From heikki at nildram.co.uk  Sat Oct 25 10:44:14 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Sat Oct 25 10:41:37 2003
Subject: [Bioperl-l] Codon Table
In-Reply-To: <1066398681.7861.47.camel@localhost>
References: <20B7EB075F2D4542AFFAF813E98ACD9301C00BEB@cl-exsrv1.irad.bbsrc.ac.uk>
	<1066398681.7861.47.camel@localhost>
Message-ID: <1067093053.8427.59.camel@localhost>

Mick,

The PrimarySeq::translate interface is a mess, so adding one more
attribute the the end of the long list is not going to make much a
difference. I added the code into CVS.

	-Heikki


On Fri, 2003-10-17 at 14:51, Heikki Lehvaslaiho wrote:
> Mick,
> 
> I really have not thought about this possibility. CodonTable can easily
> be modified, but there is no way of passing the modified codontable
> object to sequence::translate. The translate function has really complex
> argument list already, so there is no way we can add anything in there. 
> 
> Depending what you want to do, it might be enough to modify the
> codontable object and use its translate function. Compare it to
> Bio::PrimarySeqI::translate to see what I mean. If you need full
> seq::translate functionality, Bio::SeqUtils is the place to put the
> code, e.g. $polypept = Bio::SeqUtils::translate($seq, $codontable);
> 
> I wrote the following method to be added into Bio::Tools::CodonTable. If
> you think it is useful, I can commit it.
> 
> Yours,
> 	-Heikki
> 
> 
> =head2 add_table
> 
>  Title   : add_table
>  Usage   : $newid = $ct->add_table($name, $table, $starts)
>  Function: Add a custom Codon Table into the object.
>            Know what you are doing, only the length of
>            the argument strings is checked!
>  Returns : the id of the new codon table
>  Args    : name, a string, optional (can be empty)
>            table, a string of 64 characters
>            startcodons, a string of 64 characters, defaults to standard
> 
> =cut
> 
> sub add_table {
>     my ($self, $name, $table, $starts) = @_;
> 
>     $name ||= 'Custom'. scalar @NAMES + 1;
>     $starts ||= $STARTS[0]; 
>     $self->throw('Suspect input!')
>         unless length($table) == 64 and length($starts) == 64;
> 
>     push @NAMES, $name;
>     push @TABLES, $table;
>     push @STARTS, $starts;
> 
>     return scalar @NAMES;
> 
> }
> 
> usage:
> 
> $ct_id = $ct->add_table(@custom_table);
> $ct->id($ct_id);
> $string = $ct->translate($nt_string);
> 
> 
>  
> 
> 
> 
> On Tue, 2003-10-14 at 17:03, michael watson (IAH-C) wrote:
> > Hi
> > 
> > I want to use a different codon table than any that are present in CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I have to hack CodonTable.pm?
> > 
> > Thanks
> > Mick
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From heikki at nildram.co.uk  Sat Oct 25 11:06:27 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Sat Oct 25 11:03:39 2003
Subject: [Bioperl-l] tests
Message-ID: <1067094387.8433.68.camel@localhost>


I went to a really boring meeting and there was no network connection,
so I ended up fixing bioperl tests to better skip individual tests when
network is down. 

The only remaining test files with failures (under linux and perl 5.8.1)
are BioGraphics.t and Registry.t. Brian is working on the latter and
Lincoln has previously hinted that there might be a better way of
testing png file generation. Would be nice to see it in place.

	-Heikki


From hcuong at ibt.ac.vn  Fri Oct 24 23:19:35 2003
From: hcuong at ibt.ac.vn (hcuong)
Date: Sat Oct 25 12:52:52 2003
Subject: [Bioperl-l] Help me to deal with "MSG: blastall call crashed: -1
	blastall ..."
Message-ID: <002f01c39aa6$d0e71680$12010b0a@nhc>

Hi, Please help me. I try to make BLAST search for the first time by the test script:
> #----------------
>
> #!/usr/bin/perl
>
>  use strict;
>
> use Bio::Tools::Run::StandAloneBlast;
>
>  my @params = (program => 'blastn',
>
>                             database => 'ecoli1.nt');
>
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>
> my $input = Bio::Seq->new(-id => "test query",
>
>                                              -seq => "ACTAAGTGGGGG");
>
> my $blast_report = $factory->blastall ($input);
>
>  print "$blast_report\n";
>
> #----------------

But I always get the following error only:

>  ------------- EXCEPTION  -------------
>
> MSG: blastall call crashed: -1 blastall -p  blastn  -d  /ecoli1.nt  -i  /tmp/bSh3ZAfK7n  -o  /tmp/gv9wpcMj8g
>
>  STACK Bio::Tools::Run::StandAloneBlast::_runblast /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:633
>
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:602
>
> STACK Bio::Tools::Run::StandAloneBlast::blastall /usr/local/ActivePerl-5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:489
>
> TACK toplevel blast_local.pl:15


---
Nguyen Huu Cuong
Plant Cell Biotechnology Department
Institute of Biotechnology, NCST
18 Hoang Quoc Viet, Cau Giay, Ha Noi
Tel: 84 - 4 - 7562368
Email: hcuong@ibt.ac.vn
From rpraca5 at yahoo.com  Sat Oct 25 10:45:36 2003
From: rpraca5 at yahoo.com (Richard's    Resume)
Date: Sat Oct 25 13:45:21 2003
Subject: [Bioperl-l] Mechanical   &   Design     E n g i n e e r
Message-ID: <200310251745.h9PHjBdb008499@portal.open-bio.org>




Richard's


Resume	 for Job, 	Consulting or Service

OBJECTIVE: 	

			

	Sr.  MECHANICAL  &  DESIGN    ENGINEER

Project Mgr, Electro-Mechanical Design, Mfg, Product Development, R&D, CADD

Tel: ( 408)  309-7006 	rpraca3@yahoo.com


EXPERIENCE:
08/93-present          Sr. MECHANICAL & DESIGN ENGINEER, CADD Mgr "Mech-Tronic" 
                   
Engineering, Design & Product Development Service; Project Management, Mfg, Tooling, Product Improvement; Developing Working Product, Design and Prototype Production;  Controlling & Managing testing,  redesign, manufacturing documentation preparation;  
and full realization of Task using technical approach, schedules,  and budget to 
achieve Final Product.  

Selecting vendors and specialist to supply performance  satisfying customers expectation and to create a new, modern product with advanced properties, quality and market desirable working abilities and sellable values.


Preparing propositions & presentations, Review Manufacturing Process and Quality 
Control, Inspecting standards, Engineering Computations and Technical Improvements,  
Supplying and Production Automation. Project Management & Development. Preparing technical documentation, calculations, engineering, design, layouts, drawings, 
3D and Solid Modeling, development & propositions. Hard Drive Design, testing, 
balancing, recalculating and redesign. 

Manufacturing and Assembly Equipment design and build.  Systems Integration.
Tooling and Operations Development, Implementation & Automation for mass production.  Energy, Electric Vehicles and Computerized Transportation System Design & Implement. Solar Panels. Solid Works, Pro-E, CAD Management and Operations, Analyzing, Micro Station, ACAD 10-2002 & LT, Win 3x & 2000', Net, Internet, Softdesk, Structural Design. Network, Security, Electrical Design & Installations; Commercial, Industrial, Residential, Fire Alarms, Smoke Detectors, Lights, Plugs, Panels, Power Supply,  Electro - Solar Installations, CADD automation. Dynamics, Kinematics, thermodynamics / heat transfer & FEA analyzing.

Manufacturing hydraulic & pneumatic equipment, machinery and control systems, mechanisms, robotics device, precision machine elements.  Inspecting and control manufacturing standards, analyzing stresses and tolerances, selecting materials, engineering computations and technical improvements, documentation, projects development, supplying.  Automation, Conveyors, Spiral Elevator, Fast Cannery Transportation, Electronic and Electrical Components, Master Control Center, Sheet Metal Oven Rebuilding Project. Power Systems, UPS.


Automation equipment and machine control using for machines and robotics precision mechanisms motion programming, fluid mechanics, pneumatics systems, mounting and positioning devices, electro-mechanical and vacuum mechanisms, design and analysis of structures, castings, welded frames, mechanical detailing. 


Computers: 

DOS, SUN UNIX, MAC, WP, dB, Lotus, Network, Windows & Applications; MS Project, Excel, Access, Word, PFS, Graphics, CAD / CAM, Excel, Basic, C, Fortran, Analyzes. 
CADD systems, Algor, VAX, Net.  MCAD, Acad's 2002 & Softdesk, Script, Nastran, Infusoft, LAN, Tektronix, Cadkey,  Lisp, Personal Designer, ACAD / Computer Instructor, Machine Design, Robotics & Automation, WIND, SOLAR, METRIC.



EDUCATION:

Institute for Business & Technology, California
CADD Engineer,  Programming,  Design,  Management

Electro - Mechanical  College
Mechanical Engineering - BSME,   ASEE,  MBA


Open for Travel  *  Salary open *  Permanent  preferred  or Consulting



.
From rpraca5 at yahoo.com  Sat Oct 25 10:45:36 2003
From: rpraca5 at yahoo.com (Richard's    Resume)
Date: Sat Oct 25 13:45:30 2003
Subject: [Bioperl-l] Mechanical   &   Design     E n g i n e e r
Message-ID: <200310251745.h9PHjEdb008506@portal.open-bio.org>




Richard's


Resume	 for Job, 	Consulting or Service

OBJECTIVE: 	

			

	Sr.  MECHANICAL  &  DESIGN    ENGINEER

Project Mgr, Electro-Mechanical Design, Mfg, Product Development, R&D, CADD

Tel: ( 408)  309-7006 	rpraca3@yahoo.com


EXPERIENCE:
08/93-present          Sr. MECHANICAL & DESIGN ENGINEER, CADD Mgr "Mech-Tronic" 
                   
Engineering, Design & Product Development Service; Project Management, Mfg, Tooling, Product Improvement; Developing Working Product, Design and Prototype Production;  Controlling & Managing testing,  redesign, manufacturing documentation preparation;  
and full realization of Task using technical approach, schedules,  and budget to 
achieve Final Product.  

Selecting vendors and specialist to supply performance  satisfying customers expectation and to create a new, modern product with advanced properties, quality and market desirable working abilities and sellable values.


Preparing propositions & presentations, Review Manufacturing Process and Quality 
Control, Inspecting standards, Engineering Computations and Technical Improvements,  
Supplying and Production Automation. Project Management & Development. Preparing technical documentation, calculations, engineering, design, layouts, drawings, 
3D and Solid Modeling, development & propositions. Hard Drive Design, testing, 
balancing, recalculating and redesign. 

Manufacturing and Assembly Equipment design and build.  Systems Integration.
Tooling and Operations Development, Implementation & Automation for mass production.  Energy, Electric Vehicles and Computerized Transportation System Design & Implement. Solar Panels. Solid Works, Pro-E, CAD Management and Operations, Analyzing, Micro Station, ACAD 10-2002 & LT, Win 3x & 2000', Net, Internet, Softdesk, Structural Design. Network, Security, Electrical Design & Installations; Commercial, Industrial, Residential, Fire Alarms, Smoke Detectors, Lights, Plugs, Panels, Power Supply,  Electro - Solar Installations, CADD automation. Dynamics, Kinematics, thermodynamics / heat transfer & FEA analyzing.

Manufacturing hydraulic & pneumatic equipment, machinery and control systems, mechanisms, robotics device, precision machine elements.  Inspecting and control manufacturing standards, analyzing stresses and tolerances, selecting materials, engineering computations and technical improvements, documentation, projects development, supplying.  Automation, Conveyors, Spiral Elevator, Fast Cannery Transportation, Electronic and Electrical Components, Master Control Center, Sheet Metal Oven Rebuilding Project. Power Systems, UPS.


Automation equipment and machine control using for machines and robotics precision mechanisms motion programming, fluid mechanics, pneumatics systems, mounting and positioning devices, electro-mechanical and vacuum mechanisms, design and analysis of structures, castings, welded frames, mechanical detailing. 


Computers: 

DOS, SUN UNIX, MAC, WP, dB, Lotus, Network, Windows & Applications; MS Project, Excel, Access, Word, PFS, Graphics, CAD / CAM, Excel, Basic, C, Fortran, Analyzes. 
CADD systems, Algor, VAX, Net.  MCAD, Acad's 2002 & Softdesk, Script, Nastran, Infusoft, LAN, Tektronix, Cadkey,  Lisp, Personal Designer, ACAD / Computer Instructor, Machine Design, Robotics & Automation, WIND, SOLAR, METRIC.



EDUCATION:

Institute for Business & Technology, California
CADD Engineer,  Programming,  Design,  Management

Electro - Mechanical  College
Mechanical Engineering - BSME,   ASEE,  MBA


Open for Travel  *  Salary open *  Permanent  preferred  or Consulting



.
From lstein at cshl.edu  Sat Oct 25 16:25:50 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat Oct 25 16:23:44 2003
Subject: [Bioperl-l] tests
In-Reply-To: <1067094387.8433.68.camel@localhost>
References: <1067094387.8433.68.camel@localhost>
Message-ID: <200310251625.50445.lstein@cshl.edu>

Hi Heikki,

Option 1:

Run BioGraphics.t with the --write switch:

	perl t/BioGraphics.t --write

This will create a set of pngs in t/data/biographics named 
t1.png, t2.png and t3.png.  Look at them visually and 
confirm that they are similar to the variants located in 
t/data/biographics/version*.  If so, move the new versions 
into the appropriate version directory.

Option 2:

I will disable the PNG tests completely.  Every different 
combination of libpng and libgd generates files that are 
visually identical but incompatible at the binary level.  
These tests aren't scaling.

The SVG version of Bio::Graphics is almost finished, and 
when done I will replace the PNG tests with SVG tests.  
Since SVG is a text-only XML format, it won't suffer these 
problems.

Lincoln

On Saturday 25 October 2003 11:06 am, Heikki Lehvaslaiho 
wrote:
> I went to a really boring meeting and there was no
> network connection, so I ended up fixing bioperl tests to
> better skip individual tests when network is down.
>
> The only remaining test files with failures (under linux
> and perl 5.8.1) are BioGraphics.t and Registry.t. Brian
> is working on the latter and Lincoln has previously
> hinted that there might be a better way of testing png
> file generation. Would be nice to see it in place.
>
> 	-Heikki
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
From heikki at nildram.co.uk  Sat Oct 25 18:07:32 2003
From: heikki at nildram.co.uk (Heikki Lehvaslaiho)
Date: Sat Oct 25 18:04:35 2003
Subject: [Bioperl-l] tests
In-Reply-To: <200310251625.50445.lstein@cshl.edu>
References: <1067094387.8433.68.camel@localhost>
	<200310251625.50445.lstein@cshl.edu>
Message-ID: <1067119651.8428.73.camel@localhost>

I'd prefer option 2: disabling the png tests and replacing them later
with SVG tests.

Thanks,
	-Heikki

On Sat, 2003-10-25 at 21:25, Lincoln Stein wrote:
> Hi Heikki,
> 
> Option 1:
> 
> Run BioGraphics.t with the --write switch:
> 
> 	perl t/BioGraphics.t --write
> 
> This will create a set of pngs in t/data/biographics named 
> t1.png, t2.png and t3.png.  Look at them visually and 
> confirm that they are similar to the variants located in 
> t/data/biographics/version*.  If so, move the new versions 
> into the appropriate version directory.
> 
> Option 2:
> 
> I will disable the PNG tests completely.  Every different 
> combination of libpng and libgd generates files that are 
> visually identical but incompatible at the binary level.  
> These tests aren't scaling.
> 
> The SVG version of Bio::Graphics is almost finished, and 
> when done I will replace the PNG tests with SVG tests.  
> Since SVG is a text-only XML format, it won't suffer these 
> problems.
> 
> Lincoln
> 
> On Saturday 25 October 2003 11:06 am, Heikki Lehvaslaiho 
> wrote:
> > I went to a really boring meeting and there was no
> > network connection, so I ended up fixing bioperl tests to
> > better skip individual tests when network is down.
> >
> > The only remaining test files with failures (under linux
> > and perl 5.8.1) are BioGraphics.t and Registry.t. Brian
> > is working on the latter and Lincoln has previously
> > hinted that there might be a better way of testing png
> > file generation. Would be nice to see it in place.
> >
> > 	-Heikki
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From lstein at cshl.edu  Sat Oct 25 21:33:47 2003
From: lstein at cshl.edu (Lincoln Stein)
Date: Sat Oct 25 21:31:00 2003
Subject: [Bioperl-l] tests
In-Reply-To: <1067119651.8428.73.camel@localhost>
References: <1067094387.8433.68.camel@localhost>
	<200310251625.50445.lstein@cshl.edu>
	<1067119651.8428.73.camel@localhost>
Message-ID: <200310252133.47115.lstein@cshl.edu>

Done.

Lincoln

On Saturday 25 October 2003 06:07 pm, Heikki Lehvaslaiho wrote:
> I'd prefer option 2: disabling the png tests and replacing them later
> with SVG tests.
>
> Thanks,
> 	-Heikki
>
> On Sat, 2003-10-25 at 21:25, Lincoln Stein wrote:
> > Hi Heikki,
> >
> > Option 1:
> >
> > Run BioGraphics.t with the --write switch:
> >
> > 	perl t/BioGraphics.t --write
> >
> > This will create a set of pngs in t/data/biographics named
> > t1.png, t2.png and t3.png.  Look at them visually and
> > confirm that they are similar to the variants located in
> > t/data/biographics/version*.  If so, move the new versions
> > into the appropriate version directory.
> >
> > Option 2:
> >
> > I will disable the PNG tests completely.  Every different
> > combination of libpng and libgd generates files that are
> > visually identical but incompatible at the binary level.
> > These tests aren't scaling.
> >
> > The SVG version of Bio::Graphics is almost finished, and
> > when done I will replace the PNG tests with SVG tests.
> > Since SVG is a text-only XML format, it won't suffer these
> > problems.
> >
> > Lincoln
> >
> > On Saturday 25 October 2003 11:06 am, Heikki Lehvaslaiho
> >
> > wrote:
> > > I went to a really boring meeting and there was no
> > > network connection, so I ended up fixing bioperl tests to
> > > better skip individual tests when network is down.
> > >
> > > The only remaining test files with failures (under linux
> > > and perl 5.8.1) are BioGraphics.t and Registry.t. Brian
> > > is working on the latter and Lincoln has previously
> > > hinted that there might be a better way of testing png
> > > file generation. Would be nice to see it in place.
> > >
> > > 	-Heikki
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein@cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
From jbedell at oriongenomics.com  Sun Oct 26 01:51:51 2003
From: jbedell at oriongenomics.com (Joseph Bedell)
Date: Sun Oct 26 01:51:03 2003
Subject: [Bioperl-l] Help me to deal with "MSG: blastall call crashed:
	-1blastall ..."
Message-ID: <434AF352F9D03C4C896782B8CC78BC761A3CF4@vader.oriongenomics.com>


Hi-

This is only a guess, but by the looks of the error statement (the -d
/ecoli1.nt), I think you need to set an environment variable to point to
the location of your ecoli1.nt database. I believe that you can set
either $BLASTDATADIR or $BLASTDB to the correct directory and it should
work.

Joey


>-----Original Message-----
>From: bioperl-l-bounces@portal.open-bio.org [mailto:bioperl-l-
>bounces@portal.open-bio.org] On Behalf Of hcuong
>Sent: Friday, October 24, 2003 10:20 PM
>To: bioperl-l@bioperl.org
>Subject: [Bioperl-l] Help me to deal with "MSG: blastall call crashed:
-
>1blastall ..."
>
>Hi, Please help me. I try to make BLAST search for the first time by
the
>test script:
>> #----------------
>>
>> #!/usr/bin/perl
>>
>>  use strict;
>>
>> use Bio::Tools::Run::StandAloneBlast;
>>
>>  my @params = (program => 'blastn',
>>
>>                             database => 'ecoli1.nt');
>>
>> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>>
>> my $input = Bio::Seq->new(-id => "test query",
>>
>>                                              -seq => "ACTAAGTGGGGG");
>>
>> my $blast_report = $factory->blastall ($input);
>>
>>  print "$blast_report\n";
>>
>> #----------------
>
>But I always get the following error only:
>
>>  ------------- EXCEPTION  -------------
>>
>> MSG: blastall call crashed: -1 blastall -p  blastn  -d  /ecoli1.nt
-i
>/tmp/bSh3ZAfK7n  -o  /tmp/gv9wpcMj8g
>>
>>  STACK Bio::Tools::Run::StandAloneBlast::_runblast
/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:633
>>
>> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
>/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:602
>>
>> STACK Bio::Tools::Run::StandAloneBlast::blastall
/usr/local/ActivePerl-
>5.6/lib/site_perl/5.6.1/Bio/Tools/Run/StandAloneBlast.pm:489
>>
>> TACK toplevel blast_local.pl:15
>
>
>---
>Nguyen Huu Cuong
>Plant Cell Biotechnology Department
>Institute of Biotechnology, NCST
>18 Hoang Quoc Viet, Cau Giay, Ha Noi
>Tel: 84 - 4 - 7562368
>Email: hcuong@ibt.ac.vn

From michael.watson at bbsrc.ac.uk  Mon Oct 27 04:14:06 2003
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Mon Oct 27 04:12:30 2003
Subject: [Bioperl-l] Codon Table
Message-ID: <20B7EB075F2D4542AFFAF813E98ACD930282236E@cl-exsrv1.irad.bbsrc.ac.uk>

Thanks Heidi, your efforts are appreciated :-)

-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki@nildram.co.uk]
Sent: 25 October 2003 15:44
To: michael watson (IAH-C)
Cc: 'bioperl-l@bioperl.org'
Subject: Re: [Bioperl-l] Codon Table


Mick,

The PrimarySeq::translate interface is a mess, so adding one more
attribute the the end of the long list is not going to make much a
difference. I added the code into CVS.

	-Heikki


On Fri, 2003-10-17 at 14:51, Heikki Lehvaslaiho wrote:
> Mick,
> 
> I really have not thought about this possibility. CodonTable can easily
> be modified, but there is no way of passing the modified codontable
> object to sequence::translate. The translate function has really complex
> argument list already, so there is no way we can add anything in there. 
> 
> Depending what you want to do, it might be enough to modify the
> codontable object and use its translate function. Compare it to
> Bio::PrimarySeqI::translate to see what I mean. If you need full
> seq::translate functionality, Bio::SeqUtils is the place to put the
> code, e.g. $polypept = Bio::SeqUtils::translate($seq, $codontable);
> 
> I wrote the following method to be added into Bio::Tools::CodonTable. If
> you think it is useful, I can commit it.
> 
> Yours,
> 	-Heikki
> 
> 
> =head2 add_table
> 
>  Title   : add_table
>  Usage   : $newid = $ct->add_table($name, $table, $starts)
>  Function: Add a custom Codon Table into the object.
>            Know what you are doing, only the length of
>            the argument strings is checked!
>  Returns : the id of the new codon table
>  Args    : name, a string, optional (can be empty)
>            table, a string of 64 characters
>            startcodons, a string of 64 characters, defaults to standard
> 
> =cut
> 
> sub add_table {
>     my ($self, $name, $table, $starts) = @_;
> 
>     $name ||= 'Custom'. scalar @NAMES + 1;
>     $starts ||= $STARTS[0]; 
>     $self->throw('Suspect input!')
>         unless length($table) == 64 and length($starts) == 64;
> 
>     push @NAMES, $name;
>     push @TABLES, $table;
>     push @STARTS, $starts;
> 
>     return scalar @NAMES;
> 
> }
> 
> usage:
> 
> $ct_id = $ct->add_table(@custom_table);
> $ct->id($ct_id);
> $string = $ct->translate($nt_string);
> 
> 
>  
> 
> 
> 
> On Tue, 2003-10-14 at 17:03, michael watson (IAH-C) wrote:
> > Hi
> > 
> > I want to use a different codon table than any that are present in CodonTable.pm.  Does Bioperl have a way to implement this?  Or will I have to hack CodonTable.pm?
> > 
> > Thanks
> > Mick
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________
From birney at ebi.ac.uk  Mon Oct 27 05:15:41 2003
From: birney at ebi.ac.uk (Ewan Birney)
Date: Mon Oct 27 05:13:14 2003
Subject: [Bioperl-l] Codon Table
In-Reply-To: <20B7EB075F2D4542AFFAF813E98ACD930282236E@cl-exsrv1.irad.bbsrc.ac.uk>
Message-ID: 

On Mon, 27 Oct 2003, michael watson (IAH-C) wrote:

> Thanks Heidi, your efforts are appreciated :-)
> 


Heidi? Who's Heidi? (Heikki - time to get your hair extensions and 
pig-tails out!)


From Marc.Logghe at devgen.com  Mon Oct 27 05:20:53 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Mon Oct 27 05:23:31 2003
Subject: [Bioperl-l] Codon Table
Message-ID: 


> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Monday, October 27, 2003 11:16 AM
> To: michael watson (IAH-C)
> Cc: 'bioperl-l@bioperl.org'; 'heikki@ebi.ac.uk'
> Subject: RE: [Bioperl-l] Codon Table
> 
> 
> On Mon, 27 Oct 2003, michael watson (IAH-C) wrote:
> 
> > Thanks Heidi, your efforts are appreciated :-)
> > 
> 
> 
> Heidi? Who's Heidi? (Heikki - time to get your hair extensions and 
> pig-tails out!)
He already did, apparently. Don't know what was better though ;-)
http://www.ebi.ac.uk/Information/Staff/person_maint.php?person_id=305

From michael.watson at bbsrc.ac.uk  Mon Oct 27 05:36:07 2003
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Mon Oct 27 05:37:19 2003
Subject: [Bioperl-l] Codon Table
Message-ID: <20B7EB075F2D4542AFFAF813E98ACD9302822373@cl-exsrv1.irad.bbsrc.ac.uk>

It'S MONDAY MORNING!! ;-)

-----Original Message-----
From: Marc Logghe [mailto:Marc.Logghe@devgen.com]
Sent: 27 October 2003 10:21
To: Ewan Birney; michael watson (IAH-C)
Cc: bioperl-l@bioperl.org; heikki@ebi.ac.uk
Subject: RE: [Bioperl-l] Codon Table



> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Monday, October 27, 2003 11:16 AM
> To: michael watson (IAH-C)
> Cc: 'bioperl-l@bioperl.org'; 'heikki@ebi.ac.uk'
> Subject: RE: [Bioperl-l] Codon Table
> 
> 
> On Mon, 27 Oct 2003, michael watson (IAH-C) wrote:
> 
> > Thanks Heidi, your efforts are appreciated :-)
> > 
> 
> 
> Heidi? Who's Heidi? (Heikki - time to get your hair extensions and 
> pig-tails out!)
He already did, apparently. Don't know what was better though ;-)
http://www.ebi.ac.uk/Information/Staff/person_maint.php?person_id=305
From ssacrich at yahoo.com  Mon Oct 27 04:58:26 2003
From: ssacrich at yahoo.com (Civil & Structural Designer )
Date: Mon Oct 27 07:58:00 2003
Subject: [Bioperl-l] Resume from  CAD  Specialist / Operator / Drafter
Message-ID: <200310271257.h9RCvrdb011310@portal.open-bio.org>








RIC  SIE

Tel   (408)    482-2840    rzbig@yahoo.com



OBJECTIVE:		STRUCTURAL &  MECHANICAL  DESIGNER

CIVIL, ARCHITECTURAL, TRANSPORTATION,  CAD Operator 

EXPERIENCE:

89 - present
DESIGNER, ENGINEER,  CAD MANAGER; 

Engineering & Design Service, Project Management & Development.
Preparing technical documentation, calculations, layouts drawings &
propositions. CAD Management and Operations, drafting & redesigning.
Intergraph, MicroStation,  Autodesk, ACAD, Win, Net, Softdesk Mgmt
Civil, Bridges and Structural Design, Plans, Mapping, Detail Freeway
& Roadway, data translation & inserting. Script & CAD automation.
Geological Structures, Viaducts, Freeways, Highways, Shopping Center. 
Architectural and Environmental Projects and cooperation; military
facilities and plans, Cities, Airports, remediation drawings upgrade,
correcting and redesign. Traffic design & problem analyzes-reorganize.
Freeway Design & Drafting Support, Site analyzing for Caltrans,
Architectural, Archeotype & Electrical drawings, "as is" and initial design;          
Develop remediation procedure and equipment for lead painted buildings.
Construction management, Job site inspection, civil & structural support
Mechanical Evaluations - Design - Service and Maintenance; R&D.

EDUCATION:


 College -  BS  Degree - CAD, Engineering

DOS, UNIX, MAC, SUN computers;  WP, dBase, Lotus, Network, Lisp,
Windows & Applications:  Excel, Words, Access, Power Point & more
METRIC,  SOLAR,  AutoCAD/Computer Instructor. Transportation Spec.
Personal Designer, MS Project, C, Script, File Management, File transfer. 
Learn quickly, work independly, shift, overtime.



From ssacrich at yahoo.com  Mon Oct 27 04:58:26 2003
From: ssacrich at yahoo.com (Civil & Structural Designer )
Date: Mon Oct 27 07:58:21 2003
Subject: [Bioperl-l] Resume from  CAD  Specialist / Operator / Drafter
Message-ID: <200310271257.h9RCvrdb011311@portal.open-bio.org>








RIC  SIE

Tel   (408)    482-2840    rzbig@yahoo.com



OBJECTIVE:		STRUCTURAL &  MECHANICAL  DESIGNER

CIVIL, ARCHITECTURAL, TRANSPORTATION,  CAD Operator 

EXPERIENCE:

89 - present
DESIGNER, ENGINEER,  CAD MANAGER; 

Engineering & Design Service, Project Management & Development.
Preparing technical documentation, calculations, layouts drawings &
propositions. CAD Management and Operations, drafting & redesigning.
Intergraph, MicroStation,  Autodesk, ACAD, Win, Net, Softdesk Mgmt
Civil, Bridges and Structural Design, Plans, Mapping, Detail Freeway
& Roadway, data translation & inserting. Script & CAD automation.
Geological Structures, Viaducts, Freeways, Highways, Shopping Center. 
Architectural and Environmental Projects and cooperation; military
facilities and plans, Cities, Airports, remediation drawings upgrade,
correcting and redesign. Traffic design & problem analyzes-reorganize.
Freeway Design & Drafting Support, Site analyzing for Caltrans,
Architectural, Archeotype & Electrical drawings, "as is" and initial design;          
Develop remediation procedure and equipment for lead painted buildings.
Construction management, Job site inspection, civil & structural support
Mechanical Evaluations - Design - Service and Maintenance; R&D.

EDUCATION:


 College -  BS  Degree - CAD, Engineering

DOS, UNIX, MAC, SUN computers;  WP, dBase, Lotus, Network, Lisp,
Windows & Applications:  Excel, Words, Access, Power Point & more
METRIC,  SOLAR,  AutoCAD/Computer Instructor. Transportation Spec.
Personal Designer, MS Project, C, Script, File Management, File transfer. 
Learn quickly, work independly, shift, overtime.



From brian_osborne at cognia.com  Mon Oct 27 09:56:13 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Mon Oct 27 09:55:13 2003
Subject: [Bioperl-l] RE: :DB::Registry
In-Reply-To: <1067260843.2296.37.camel@localhost>
Message-ID: 

Heikki,

Yes, with your modified Registry.t I see a problem. With my version,
everything was OK. The problem is that I can only work on this after-hours.
If you're trying to stay on schedule you have some choices: we can remove
Registry.t, and the code stays broken. We can solicit help from bioperl-l,
whoever's interested, or you can wait while I take a closer look.

Here's what I've done. No index method was being passed to Flat, that won't
work since it's required. Also, config.dat wasn't being read. That wouldn't
work since these databases are created before Registry is called, and the
only way Flat knows whether something is bdb or binarysearch (flat) is by
reading config.dat, then it knows which child class to call. Also, Registry
was reading only the first file in OBDA_SEARCH_PATH, that was also not
desirable. I think I see where the problem is now. If you take a look at the
$db passed to Failover using your test you'll see that there's a file path
missing:

db: Bio::DB::Flat::BDB::fasta=HASH(0x105b7d28)
key: flat_directory t/tmp
key: flat_flat_file_no HASH(0x105b7e6c)
key: flat_format fasta
key: flat_primary_namespace ACC
key: flat_indexing BerkeleyDB/1
key: flat_flat_file_path HASH(0x105b7e48)
Use of uninitialized value in print at
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Failover.pm line 113.
key: flat_verbose
key: flat_dbname testbdb
key: flat_secondary_namespaces ARRAY(0x105b7d7c)
key: flat_alphabet protein
key: bdb_maxopen 32

So the proper child class is involved, Flat::BDB, the correct flat_indexing
is there, the name is right. So that's what I'll be looking at next. I could
be wrong, of course, this is just my suspicion. You decide whether you want
someone who can work faster than me!

Brian O.




-----Original Message-----
From: Heikki Lehvaslaiho [mailto:heikki@ebi.ac.uk]
Sent: Monday, October 27, 2003 8:21 AM
To: Brian Osborne
Subject: RE: :DB::Registry

Brian,

I hope my mail yesterday made sense. I had to send it off in a hurry.

I think there is a fundamental problem in processing multiple registry
files. I know that you have take on this area, but I if you get stuck, I
recommend contacting Lincoln directly. I would. Now.

        -Heikki

On Sun, 2003-10-26 at 03:26, Brian Osborne wrote:
> Heikki,
>
> I have a guesss. Since you're running 11 tests that means you have DB_File
> installed. Here are the 9th and 10th tests:
>
> $db = $registry->get_database('testbdb');
>  ok defined($db);
>  $seq = $db->get_Seq_by_id("ALEU_HORVU");
>  ok defined($seq);
>
> So, apparently the flat database testdbd is getting made. One way to
confirm
> this is to comment out the END block in Registry.t and run the test. You
> should see t/tmp/testbdb, t/tmp/testbdb/config.dat, and the index file
> t/tmp/testbdb/key_ACC. Now, if you see those files the database has been
> made, so the question is why can't you retrieve the sequence?
>
> I've noticed this note in DB/Flat.pm:
>
> -index is one of "bdb" or "binarysearch" and indicates the type of
> index to generate.  "bdb" corresponds to Berkeley DB.  You *must* be
> using BerkeleyDB version 2 or higher, and have the Perl BerkeleyDB
> extension installed (DB_File will *not* work).
>
> Do you have this recent version of BerkeleyDB? I'll add this check to
> Registry.t.
>
>
> Brian O.
>
> -----Original Message-----
> From: Heikki Lehvaslaiho [mailto:heikki@nildram.co.uk]
> Sent: Saturday, October 25, 2003 10:41 AM
> To: Brian Osborne
> Subject: Bio::DB::Registry
>
> Brian,
>
> Your recent changes broke Registry.t for me. Can you give a hint what
> might be going on?
>
>         -Heikki
>
> localhost ~/src/bioperl/core> perl -w t/Registry.t
> 1..11
> ok 1
> ok 2
>
> -------------------- WARNING ---------------------
> MSG: Couldn't call new_from_registry on [Bio::DB::Flat]
>
> ------------- EXCEPTION  -------------
> MSG: First line not compatible with flat file index.  Should be
> something like
>
> index   flat/1
> STACK Bio::DB::Flat::BinarySearch::read_config_file
> /home/heikki/src/bioperl/core/Bio/DB/Flat/BinarySearch.pm:1192
> STACK Bio::DB::Flat::BinarySearch::new
> /home/heikki/src/bioperl/core/Bio/DB/Flat/BinarySearch.pm:270
> STACK Bio::DB::Flat::new
> /home/heikki/src/bioperl/core/Bio/DB/Flat.pm:178
> STACK Bio::DB::Flat::new_from_registry
> /home/heikki/src/bioperl/core/Bio/DB/Flat.pm:254
> STACK (eval) /home/heikki/src/bioperl/core/Bio/DB/Registry.pm:182
> STACK Bio::DB::Registry::_load_registry
> /home/heikki/src/bioperl/core/Bio/DB/Registry.pm:181
> STACK Bio::DB::Registry::new
> /home/heikki/src/bioperl/core/Bio/DB/Registry.pm:97
> STACK toplevel t/Registry.t:56
>
> --------------------------------------
>
> ---------------------------------------------------
> ok 3
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> not ok 10
> # Failed test 10 in t/Registry.t at line 75
> Use of uninitialized value in scalar assignment at t/Registry.t line 85.
--
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________


From heikki at ebi.ac.uk  Mon Oct 27 11:24:52 2003
From: heikki at ebi.ac.uk (Heikki Lehvaslaiho)
Date: Mon Oct 27 11:29:33 2003
Subject: [Bioperl-l] Re: Question on the scf file format
In-Reply-To: 
References: <001001c39c9a$fbb2c6c0$0201a8c0@distance>
	
Message-ID: <1067271892.2301.52.camel@localhost>

Guillaume,

In other words: Tony's fixes are only in the CVS head and in developer
releases in our website. They never made it out into the 1.2 release
series. It was an oversight  which I apologise profusely.

Please install the 1.3.02 from 
http://bioperl.org/DIST/current_core_unstable.tar.gz
and try again.

Yours,
	-Heikki




On Mon, 2003-10-27 at 15:38, Tony Cox wrote:
> On Mon, 27 Oct 2003, Guillaume Giraudon wrote:
> 
> Hi Guillaume,
> 
> This looks like this may be the "cast" you have to apply if you are using
> 8bit/16bit data values. Check the code I added to the Bioperl SCF.pm module to
> make this work properly for all SCF files.
> 
> Tony
> 
> 
> 
> +>Hi Jason, Hi Tony, Hi Heikki
> +>
> +>I'm sorry to bother you with this simple question but I saw one of your source files (scf.pm) on the web and though you might be able to help me out on this matter : I am trying to write a web based scf file viewer (in php). I came across a lot of documents that seem to all be based on the RFC I found at
> +>http://www.mrc-lmb.cam.ac.uk/pubseq/scf-rfc.html
> +>
> +>I have attached a zip file of the files I'm working with so that you might take a look at them. I'm comparing the results I get from my program with what Chromas (v1.45) gives me. So far, I believe I'm parsing the header correctly. What I get makes sense :
> +>
> +>scf_header Object
> +>(
> +>    [magic_number] => 779314022
> +>    [samples] => 10934
> +>    [samples_offset] => 128
> +>    [bases] => 899
> +>    [bases_left_clip] => 0
> +>    [bases_right_clip] => 0
> +>    [bases_offset] => 87600
> +>    [comments_size] => 364
> +>    [comments_offset] => 98388
> +>    [version] => 3.00
> +>    [sample_size] => 2
> +>    [code_set] => 0
> +>    [private_size] => 0
> +>    [private_offset] => 0
> +>    [spare] =>
> +>)
> +>
> +>Now when I start parsing the Samples section, I get confused. From what I can gather, Its composed of delta differences between each sample (and not the values themselves as I originally thought).
> +>
> +>Strangely, I believe I'm calculating my offsets fine because the very first vales of all A,C,G and T match what I have in the raw_data.txt file (exported with chromas). But I cant seem to read the rest of the samples correctly.
> +>
> +>Here is a little HEX extract from the scf file :
> +>
> +>00000000h: 2E 73 63 66 00 00 2A B6 00 00 00 80 00 00 03 83 ; .scf..*?...?...?
> +>00000010h: 00 00 00 00 00 00 00 00 00 01 56 30 00 00 01 6C ; ..........V0...l
> +>00000020h: 00 01 80 54 33 2E 30 30 00 00 00 02 00 00 00 00 ; ..?T3.00........
> +>00000030h: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>00000040h: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>00000050h: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>00000060h: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>00000070h: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>00000080h: 00 A0 FF 60 00 00 00 10 00 03 FF FE FF FD FF FB ; . ?`......??????
> +>00000090h: FF FE FF FA FF FB FF FD FF FB FF FF FF FF 00 00 ; ??????????????..
> +>000000a0h: FF FF 00 01 00 00 FF FD 00 01 FF FD 00 03 00 00 ; ??....??..??....
> +>000000b0h: 00 04 00 01 00 03 00 01 00 03 00 00 00 02 FF FF ; ..............??
> +>000000c0h: 00 02 00 01 00 00 00 00 00 00 00 00 00 00 00 00 ; ................
> +>
> +>The first 128 bytes are the header and I seem to read the part fine. My samples_offset is 128 (80h) and my sample_size is 2. At that location (80h), the first value is '00 A0' witch is 160 in decimal. That?s exactly my first value so that look about right. But then I have FF 60. Is this supposed to be a delta ?
> +>I though it could be but then, if its an unsigned value, it?s a bit huge.
> +>I tried to consider it as a signed value but then again, I cant seem to get the same thing as Chromas.
> +>
> +>Here is a short extract of what I get :
> +>
> +>A	C	G	T
> +>160	0	72	6
> +>-160	0	-84	-8
> +>0	0	-5	-1
> +>16	0	2	2
> +>3	0	3	1
> +>-2	0	2	0
> +>-3	0	5	0
> +>-5	0	4	0
> +>-2	0	1	0
> +>-6	0	0	0
> +>-5	0	0	0
> +>-3	0	0	0
> +>-5	0	0	0
> +>-1	0	0	0
> +>
> +>Any idea of what I might be doing wrong ?
> +>
> +>Thank you in advance,
> +>
> +>G.Giraudon
> +>
> +>
> +>
> 
> ******************************************************
> Tony Cox			Email:avc@sanger.ac.uk
> Sanger Institute		WWW:www.sanger.ac.uk
> Wellcome Trust Genome Campus	Head,Software Services
> Hinxton				Tel: +44 1223 834244
> Cambs. CB10 1SA			Fax: +44 1223 494919
> ******************************************************
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________

From Tony.LeGall at bichat.inserm.fr  Mon Oct 27 15:48:07 2003
From: Tony.LeGall at bichat.inserm.fr (LE GALL Tony)
Date: Mon Oct 27 18:47:12 2003
Subject: [Bioperl-l] running T_coffee with bioperl on a windows system
Message-ID: <000801c39ccb$a01e99c0$129f39c2@INSERMY7LJC34Q>

Hello,
Can I run T_coffee with bioperl on a windows system. If it is possible, how can I do ? 
Thanks,
LE GALL
From Luc.Gauthier at aventis.com  Tue Oct 28 05:13:54 2003
From: Luc.Gauthier at aventis.com (Luc.Gauthier@aventis.com)
Date: Tue Oct 28 05:10:55 2003
Subject: [Bioperl-l] RangeI.pm warnings
Message-ID: <6FA8B454A1DF1E4A97F0A48DCC324EAB819CB3@crbsmxsusr05.pharma.aventis.com>

Hi everyone,

I use the SearchIO mechanism to parse BLASTN 2.1.3 reports.

I yesterday downloaded an upgrade to the bioperl-live library I currently use
for my developments.
The problem is that since then, I get the following warning messages from
RangeI.pm :

-----
Argument "start" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 505.
Argument "end" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 506.
Argument "strand" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 507.
-----

Here is how it happens...

First, I get a raw blastall report from a wrapper tool I wrote :
     my $result = $self->_run_ReadWrite($toolpath, $toolparams,
$params{query});
     my $raw_report = join "\n", @{$results->{OUTPUT}};

Then I instantiate an IO::String (v1.03) object from the obtained string :
     my $pseudoFH = IO::String->new( $raw_report );

Finally, I want to obtain a Bio::SearchIO report from that :
     my $searchIO = Bio::SearchIO->new( -format => 'blast' , -fh => $pseudoFH
);


And this is that command that brings the warnings messages from RangeI.pm.

One interesting thing is that when I parse blast reports in a loop, only the
first Bio::SearchIO
report creation will bring the warning messages...

Has anyone else seen that problem ?

Thank you for reading, and have a good day !
Luc Gauthier


From Richard.Adams at ed.ac.uk  Tue Oct 28 06:57:06 2003
From: Richard.Adams at ed.ac.uk (Richard Adams)
Date: Tue Oct 28 06:54:05 2003
Subject: [Bioperl-l] Bio::SimpleAlign methods
Message-ID: <3F9E5992.1539CAD5@ed.ac.uk>

Hello,
    I'm writing a wrapper for the SIFT program which predicts functional
effects of SNPs using protein sequence
alignments and have written 3 methods for formatting alignments
necessary for input into this program and maybe useful for others as
well.

    1. $aln->get_ungapped_slices($seq_id);
        returns an array of alignment slices corresponding to ungapped
sequence blocks of the specified  sequence.

    2. $aln->merge_slices();
        concatenates alignment slices into 1 big alignment.

    3. $aln->set_pos($seq_id, pos);
        changes the position of a sequence in the alignment

    If these are of any potential use should I CVS them into
Bio::SimpleAlign (or given they're rather esoteric) into
Bio::Align::Utilities?

Richard

--
Dr Richard Adams
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams@ed.ac.uk



From brian_osborne at cognia.com  Tue Oct 28 10:19:55 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Tue Oct 28 10:19:00 2003
Subject: [Bioperl-l] running T_coffee with bioperl on a windows system
In-Reply-To: <000801c39ccb$a01e99c0$129f39c2@INSERMY7LJC34Q>
Message-ID: 

Tony,

Certainly. There are a few different ways of installing Bioperl on Windows.
Take a look at the INSTALL.WIN file.

Brian O.


-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of LE GALL Tony
Sent: Monday, October 27, 2003 3:48 PM
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] running T_coffee with bioperl on a windows system

Hello,
Can I run T_coffee with bioperl on a windows system. If it is possible, how
can I do ?
Thanks,
LE GALL


From jason at cgt.duhs.duke.edu  Tue Oct 28 15:43:19 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Tue Oct 28 15:41:09 2003
Subject: [Bioperl-l] bug #1546 and BPlite/BPpsilite
In-Reply-To: <3F9EBF99.3010306@chem.ucsd.edu>
References: <3F9EBF99.3010306@chem.ucsd.edu>
Message-ID: 

WRT buggy code - Do you mean the parser or the running of BLAST from
withing Bioperl?

If in regard to StandAloneBlast, I totally agree.  I frequently ask for
someone to propose a new rewrite of this module which is more robust,
scalable to WU-BLAST, but so far have had no takers.  I don't personally
run BLAST that way so I've not had an itching desire to rewrite it.

As for buggy parsing, you're using BPpsilite which has been superceeded by
new code in Bio::SearchIO::blast on the main trunk (but not necessarily in
1.2.3).  I do not have any plans to personally maintain any of the
BPlite/BPpsilite/BPbl2seq modules as all of my own development effort is
focused on Bio::SearchIO.  Others are welcome to maintain these - we'll
get you an account to do this if someone volunteers.


As for the problems you are specifically reporting, hopefully someone will
have a chance to look at it soon.

-jason

On Tue, 28 Oct 2003, Michael Prentiss wrote:

> Jason,
> I did not think about the attachment.  I included the inputs, stderr,
> the code, and an example of the problem.
> I found this part of BioPerl really buggy, and the errors were transient
> !?!?.   Is this some sort of memory problem
> because perl is not careful enough with memory allocation?
> Thanks for you help, I am rather confused.
> Michael Prentiss
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From hawkins at scharp.org  Tue Oct 28 21:34:56 2003
From: hawkins at scharp.org (Natalie Hawkins)
Date: Tue Oct 28 21:31:54 2003
Subject: [Bioperl-l] bioperl-db schema
Message-ID: <3F9F2750.4010502@scharp.org>



Hello,

I was looking for a diagram of the bioperl-db schema.

I found a file in the /bioperl-db/model CVS dir called:

bioperl-maps.dia

I am not sure what to do w/that.  How do I use it?

thanks,
Natalie

From fangl at genomics.org.cn  Wed Oct 29 00:53:50 2003
From: fangl at genomics.org.cn (Magic Fang)
Date: Wed Oct 29 00:51:03 2003
Subject: [Bioperl-l] how to align the description to glyph
Message-ID: <3F9F55EE.6010805@genomics.org.cn>

Hi,
sometime, the description of a glyph will out of range of the panel, so 
if i can set the alignment to right, i will avoid this problem, how can i?

Magic

From Marc.Logghe at devgen.com  Wed Oct 29 03:12:36 2003
From: Marc.Logghe at devgen.com (Marc Logghe)
Date: Wed Oct 29 03:10:03 2003
Subject: [Bioperl-l] bioperl-db schema
Message-ID: 



> -----Original Message-----
> From: Natalie Hawkins [mailto:hawkins@scharp.org]
> Sent: Wednesday, October 29, 2003 3:35 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] bioperl-db schema
> 
> 
> 
> 
> Hello,
> 
> I was looking for a diagram of the bioperl-db schema.
> 
> I found a file in the /bioperl-db/model CVS dir called:
> 
> bioperl-maps.dia
> 
> I am not sure what to do w/that.  How do I use it?
You have to install dia (http://www.lysator.liu.se/~alla/dia/) in order to load the file.
There is also a pdf version available at the biodas cvs site
http://cvs.biodas.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biosql-schema/doc/biosql-ERD.pdf?rev=1.5&cvsroot=biosql
HTH,
Marc 

From amackey at pcbi.upenn.edu  Wed Oct 29 07:15:48 2003
From: amackey at pcbi.upenn.edu (Aaron J Mackey)
Date: Wed Oct 29 07:12:42 2003
Subject: [Bioperl-l] Re: [Bioperl-guts-l] bioperl commit
In-Reply-To: <200310291030.h9TAUiJu017418@pub.open-bio.org>
Message-ID: 


Note that DSN's can also have "db=foo", "dbname=foo", "port=1234", etc.  
etc.  Additionally, one can pass DBI parameters (RaiseError, AutoCommit,
etc) via the DSN.  To make your day even worse, these parameters can
legitimately come in any order.

Why do you have to mangle the DSN?

On Wed, 29 Oct 2003, Chuah Aaron wrote:

> 
> baaron
> Wed Oct 29 05:30:44 EST 2003
> Update of /home/repository/bioperl/bioperl-live/scripts/Bio-DB-GFF
> In directory pub.open-bio.org:/tmp/cvs-serv17394
> 
> Modified Files:
> 	bulk_load_gff.PLS 
> Log Message:
> added support for dsn strings in the form of "dbi:mysql:database=xxx;host=xxx"
> 
> bioperl-live/scripts/Bio-DB-GFF bulk_load_gff.PLS,1.13,1.14
> ===================================================================
> RCS file: /home/repository/bioperl/bioperl-live/scripts/Bio-DB-GFF/bulk_load_gff.PLS,v
> retrieving revision 1.13
> retrieving revision 1.14
> diff -u -r1.13 -r1.14
> --- /home/repository/bioperl/bioperl-live/scripts/Bio-DB-GFF/bulk_load_gff.PLS	2003/10/28 06:32:40	1.13
> +++ /home/repository/bioperl/bioperl-live/scripts/Bio-DB-GFF/bulk_load_gff.PLS	2003/10/29 10:30:44	1.14
> @@ -155,14 +155,17 @@
>    $AUTH .= " -p$PASSWORD";
>  }
>  
> +$DSN=~s/database=//i;
> +$DSN=~s/;host=/:/i; #cater for dsn in the form of "dbi:mysql:database=$dbname;host=$host"
> +
>  my($DBI,$DBD,$DBNAME,$HOST)=split /:/,$DSN;
>  if (defined $HOST) {
>    $AUTH .= " -h$HOST";  
>  }
> +$DBNAME=$DSN unless $DSN=~/:/;
>  if (defined $DBNAME) {
>    $AUTH .= " -D$DBNAME";
>  }
> -
>  if (defined $LOCAL) {
>    $LOCAL='local';
>    $AUTH.=' --local-infile=1';
> @@ -170,6 +173,7 @@
>    $LOCAL='';
>  }
>  
> +
>  my $db = Bio::DB::GFF->new(-adaptor=>'faux',-dsn => $DSN,@auth)
>    or die "Can't open database: ",Bio::DB::GFF->error,"\n";
>  
> 
> _______________________________________________
> Bioperl-guts-l mailing list
> Bioperl-guts-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-guts-l
> 


From Alexandre.Irrthum at icr.ac.uk  Wed Oct 29 08:02:11 2003
From: Alexandre.Irrthum at icr.ac.uk (Alexandre Irrthum)
Date: Wed Oct 29 07:59:35 2003
Subject: [Bioperl-l] rpsblast from bioperl
Message-ID: 

Hi everybody,

I have to call the NCBI rpsblast program from within a Perl script. I
wonder if there is a "bioperl" way to do that, similar to what the
StandAloneBlast object can do for blastall or blastpgp. I also wonder if
the Blast or BPlite parser objects support parsing of rpsblast reports.

Thanks a lot for your help,

alex


P.S. please cc your answer to my email address if possible 
From jason at cgt.duhs.duke.edu  Wed Oct 29 08:08:34 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 29 08:06:07 2003
Subject: [Bioperl-l] bioperl-db schema
In-Reply-To: <3F9F2750.4010502@scharp.org>
References: <3F9F2750.4010502@scharp.org>
Message-ID: 

I think the dia diagram is for an OLD marker/map db schema I was writing.

If you want an ER diagram of the biosql schema check-out the docs
directory in biosql/schema

cvs -d:pserver:cvs@cvs.open-bio.org:/home/repository/biosql co schema

look in docs/biosql-ERD.pdf is the diagram.

Or just click here:
http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/*checkout*/biosql-schema/doc/biosql-ERD.pdf?rev=1.5&cvsroot=biosql&content-type=application/pdf

-jason
On Tue, 28 Oct 2003, Natalie Hawkins wrote:

>
>
> Hello,
>
> I was looking for a diagram of the bioperl-db schema.
>
> I found a file in the /bioperl-db/model CVS dir called:
>
> bioperl-maps.dia
>
> I am not sure what to do w/that.  How do I use it?
>
> thanks,
> Natalie
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jason at cgt.duhs.duke.edu  Wed Oct 29 08:09:43 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 29 08:06:34 2003
Subject: [Bioperl-l] rpsblast from bioperl
In-Reply-To: 
References: 
Message-ID: 

Yes we support parsing it (use Bio::SearchIO format 'blast').

No we don't have a StandAloneBlast way of doing it, but you're welcome to
add that one method and we'll add it back into the toolkit.

-jason
On Wed, 29 Oct 2003, Alexandre Irrthum wrote:

> Hi everybody,
>
> I have to call the NCBI rpsblast program from within a Perl script. I
> wonder if there is a "bioperl" way to do that, similar to what the
> StandAloneBlast object can do for blastall or blastpgp. I also wonder if
> the Blast or BPlite parser objects support parsing of rpsblast reports.
>
> Thanks a lot for your help,
>
> alex
>
>
> P.S. please cc your answer to my email address if possible
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From skirov at utk.edu  Wed Oct 29 11:54:55 2003
From: skirov at utk.edu (Stefan Kirov)
Date: Wed Oct 29 11:51:58 2003
Subject: [Bioperl-l] LargeSeq performance
Message-ID: <3F9FF0DF.6020302@utk.edu>

I have a problem with the performance of  LargeSeq. I am working with 
whole chromosomes (mouse, human) and next_seq takes forever.
I do not know if it is worth, since any portion can be read with random 
access, but I am still curious to know id pepople think it might be a 
good idea to create an object, that hadles extremely large sequences- 
whole chromosomes for example without impact on the performance?
If you think it's worth I can try to do it. What I have in mind is use 
grep to map the record separators ">" (in case you are mad enogh to put 
more than one chromosome in a single file). Thus next_seq will know 
where to look for the next sequence and, parse the id line and calc the 
length. And I doubt anyone will use this under Windows (anyway, OS can 
be checked to avoid problems). Also the object will use random 
accessinstead of  Bio::Root::IO to get sequence data.
Let me know what you think...
Stefan Kirov

From jason at cgt.duhs.duke.edu  Wed Oct 29 12:32:30 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 29 12:29:29 2003
Subject: [Bioperl-l] LargeSeq performance
In-Reply-To: <3F9FF0DF.6020302@utk.edu>
References: <3F9FF0DF.6020302@utk.edu>
Message-ID: 

Yeah I think it is pretty much not a good solution in the end.
My strategy would be separate annotation from the actual sequence.
Put the sequence in fasta files and use Lincoln's Bio::DB::Fasta which
allows random access and subsequence retrieval quite nicely for large
files or lots of sequences.  Perhaps we should just think about abandoning
LargeSeq for the Indexed approach that Lincoln uses.

In addition to parse large chromosome files with annotations would need to
fix-up/check that SeqIO::genbank/embl can still parse a file which is a
CONTIG file or a genbank record which doesn't have any sequence (all you
want is the annotations/features anyways).  This might need a little more
tweaking to make sure it works.  I feel like the SeqIO parsing right now
is pretty fragile to certain types of changes so I can't say that it would
right now out of the box.

That's the way I'd go, personally but may be a more proper engineering
solution.

-jason

On Wed, 29 Oct 2003, Stefan Kirov wrote:

> I have a problem with the performance of  LargeSeq. I am working with
> whole chromosomes (mouse, human) and next_seq takes forever.
> I do not know if it is worth, since any portion can be read with random
> access, but I am still curious to know id pepople think it might be a
> good idea to create an object, that hadles extremely large sequences-
> whole chromosomes for example without impact on the performance?
> If you think it's worth I can try to do it. What I have in mind is use
> grep to map the record separators ">" (in case you are mad enogh to put
> more than one chromosome in a single file). Thus next_seq will know
> where to look for the next sequence and, parse the id line and calc the
> length. And I doubt anyone will use this under Windows (anyway, OS can
> be checked to avoid problems). Also the object will use random
> accessinstead of  Bio::Root::IO to get sequence data.
> Let me know what you think...
> Stefan Kirov
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From John.Gray at stjude.org  Wed Oct 29 11:39:09 2003
From: John.Gray at stjude.org (Gray, John)
Date: Wed Oct 29 18:39:58 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
Message-ID: <1E0CC447E59C974CA5C7160D2A2854ECC51A71@SJMEMXMB04.stjude.sjcrh.local>

I am trying to find documentation for the Bio::Restriction module, to see if it can properly predict restriction fragment sizes for circular plasmids.

 

I'm sorry to have to ask.  The tutorial at http://www.bioperl.org/Core/Latest/bptutorial.html says that Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I have used.  I can't find any documentation for this method at http://doc.bioperl.org/releases/bioperl-1.2.3/.  

 

The Seq documentation does not provide any description of the 'is_circular' method, and I was hoping that I could set the Seq object to be circular, and then just run something like $enyme_object->cut_seq($seq_object) to get my list of strings containing the resulting fragments.

 

Thank you for your help.

 

PS.  When I try and search the Bioperl-l archive, it doesn't return any matches, even when I try to match the word 'bioperl'.  Should I tell someone about this?

 

-------------------------------------------------------------------------------------
John T. Gray, Ph.D.
Director, Vector Development & Production
Experimental Hematology Division
Hematology-Oncology
St. Jude Children's Research Hospital
D2038A, Mail Stop 341
332 N. Lauderdale Street
Memphis, TN 38105 

(901) 495-4729 phone
(901) 495-2176 fax

John.Gray@stjude.org  

 

From murmanmadi at yahoo.com  Wed Oct 29 12:03:53 2003
From: murmanmadi at yahoo.com (M V)
Date: Wed Oct 29 18:40:22 2003
Subject: [Bioperl-l] perl script to retrieve accession numbers
Message-ID: <20031029170353.14118.qmail@web14612.mail.yahoo.com>

Hi there,
 
Is there a perl script that retrieves the genbank accession numbers if I have a list of gene names? Thanks in advance.
 
Murmanmadi


---------------------------------
Do you Yahoo!?
Exclusive Video Premiere - Britney Spears
From redwards at utmem.edu  Wed Oct 29 19:31:04 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Wed Oct 29 19:27:56 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <1E0CC447E59C974CA5C7160D2A2854ECC51A71@SJMEMXMB04.stjude.sjcrh.local>
Message-ID: <5850FFBC-0A70-11D8-A107-000A959E1622@utmem.edu>

The new Bio::Restriction modules should tell you the correct sizes of  
circular plasmids. This will do exactly what you want. The old  
Bio::Tools::RestrictionEnzyme does not have this ability, though you  
can just merge the first and last fragments of a sequence.

The newer Bio::Restriction are (I believe) only available in BioPerl  
1.3 and later. This is the upcoming release and the first RC seems  
quite stable.

You should probably tell someone about the searches not working, but I  
guess you just have :)

Rob



On Wednesday, October 29, 2003, at 10:39  AM, Gray, John wrote:

> I am trying to find documentation for the Bio::Restriction module, to  
> see if it can properly predict restriction fragment sizes for circular  
> plasmids.
>
>
>
> I'm sorry to have to ask.  The tutorial at  
> http://www.bioperl.org/Core/Latest/bptutorial.html says that  
> Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I  
> have used.  I can't find any documentation for this method at  
> http://doc.bioperl.org/releases/bioperl-1.2.3/.
>
>
>
> The Seq documentation does not provide any description of the  
> 'is_circular' method, and I was hoping that I could set the Seq object  
> to be circular, and then just run something like  
> $enyme_object->cut_seq($seq_object) to get my list of strings  
> containing the resulting fragments.
>
>
>
> Thank you for your help.
>
>
>
> PS.  When I try and search the Bioperl-l archive, it doesn't return  
> any matches, even when I try to match the word 'bioperl'.  Should I  
> tell someone about this?
>
>
>
> ----------------------------------------------------------------------- 
> --------------
> John T. Gray, Ph.D.
> Director, Vector Development & Production
> Experimental Hematology Division
> Hematology-Oncology
> St. Jude Children's Research Hospital
> D2038A, Mail Stop 341
> 332 N. Lauderdale Street
> Memphis, TN 38105
>
> (901) 495-4729 phone
> (901) 495-2176 fax
>
> John.Gray@stjude.org 
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

From jason at cgt.duhs.duke.edu  Wed Oct 29 21:21:06 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Wed Oct 29 21:17:44 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <1E0CC447E59C974CA5C7160D2A2854ECC51A71@SJMEMXMB04.stjude.sjcrh.local>
References: <1E0CC447E59C974CA5C7160D2A2854ECC51A71@SJMEMXMB04.stjude.sjcrh.local>
Message-ID: 

On Wed, 29 Oct 2003, Gray, John wrote:

> I am trying to find documentation for the Bio::Restriction module, to
> see if it can properly predict restriction fragment sizes for circular
> plasmids.
>
See http://doc.bioperl.org/bioperl-live for docs for code on the latest
CVS not the stable 1.2.x release series.

>
>
> I'm sorry to have to ask.  The tutorial at
> http://www.bioperl.org/Core/Latest/bptutorial.html says that
> Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I have
> used.  I can't find any documentation for this method at
> http://doc.bioperl.org/releases/bioperl-1.2.3/.
>

As Rob has said - it's new - not sure why the tutorial has been updated to
preceede the not-yet released code though.

>
>
> The Seq documentation does not provide any description of the
> 'is_circular' method, and I was hoping that I could set the Seq object
> to be circular, and then just run something like
> $enyme_object->cut_seq($seq_object) to get my list of strings containing
> the resulting fragments.
>

Bio::Seq is a Bio::PrimarySeq
http://doc.bioperl.org/releases/bioperl-1.2.3/Bio/PrimarySeqI.html#POD14

>
>
> Thank you for your help.
>
>
>
> PS.  When I try and search the Bioperl-l archive, it doesn't return any
> matches, even when I try to match the word 'bioperl'.  Should I tell
> someone about this?

http://search.open-bio.org/   ?  Seems to work just fine for me.  Putting
in 'Restriction' finds lots of hits and restricting that with 'Enzyme'
finds more hits too.

-jason
>
>
>
> -------------------------------------------------------------------------------------
> John T. Gray, Ph.D.
> Director, Vector Development & Production
> Experimental Hematology Division
> Hematology-Oncology
> St. Jude Children's Research Hospital
> D2038A, Mail Stop 341
> 332 N. Lauderdale Street
> Memphis, TN 38105
>
> (901) 495-4729 phone
> (901) 495-2176 fax
>
> John.Gray@stjude.org 
>
>
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From redwards at utmem.edu  Wed Oct 29 22:21:38 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Wed Oct 29 22:18:29 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: 
Message-ID: <2C8DDD99-0A88-11D8-A107-000A959E1622@utmem.edu>


>
> As Rob has said - it's new - not sure why the tutorial has been 
> updated to
> preceede the not-yet released code though.

Because it's so cool?


> http://search.open-bio.org/   ?  Seems to work just fine for me.  
> Putting
> in 'Restriction' finds lots of hits and restricting that with 'Enzyme'
>

Searching the web archive at http://bioperl.org/pipermail/bioperl-l/ 
doesn't work. The main difference seems to be these two lines:

http://search.open-bio.org/ : (works)



and

http://bioperl.org/pipermail/bioperl-l : (doesn't work)




(procrastination means always having something to do tomorrow).

Rob

From Richard.Adams at ed.ac.uk  Thu Oct 30 04:16:39 2003
From: Richard.Adams at ed.ac.uk (Richard Adams)
Date: Thu Oct 30 04:13:32 2003
Subject: [Bioperl-l] RemoteBlast
Message-ID: <3FA0D6F7.906983D4@ed.ac.uk>

I'd be willing to volunteer for maintaining RemoteBlast if there are no
other takers, I've used it quite a bit so I guess should try and put
something back .

Just from first thoughts I'd plan to

- incorporate Megablast / Blast2seqs /rpsblast functionality
-separate out the form submission bits of code from the Blast specific
code in the module, perhaps by inheriting
    from Bio::WebAgent.

Other than making sure that the output is parseable by Bio::SearchIO,
are there any strong feelings for  how new features should be
implemented?

If anyone has requests/ideas fornew functionality please say so!

Richard



--
Dr Richard Adams

Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams@ed.ac.uk



From brian_osborne at cognia.com  Thu Oct 30 07:30:23 2003
From: brian_osborne at cognia.com (Brian Osborne)
Date: Thu Oct 30 07:29:07 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <2C8DDD99-0A88-11D8-A107-000A959E1622@utmem.edu>
Message-ID: 

John and Rob,

News of the release of these new classes appeared at the Bioperl Web site on
July 15, in the News section. I updated bptutorial shortly thereafter.

Brian O.

-----Original Message-----
From: bioperl-l-bounces@portal.open-bio.org
[mailto:bioperl-l-bounces@portal.open-bio.org]On Behalf Of Rob Edwards
Sent: Wednesday, October 29, 2003 10:22 PM
To: Gray, John
Cc: bioperl-l@portal.open-bio.org
Subject: Re: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids


>
> As Rob has said - it's new - not sure why the tutorial has been
> updated to
> preceede the not-yet released code though.

Because it's so cool?


> http://search.open-bio.org/   ?  Seems to work just fine for me.
> Putting
> in 'Restriction' finds lots of hits and restricting that with 'Enzyme'
>

Searching the web archive at http://bioperl.org/pipermail/bioperl-l/
doesn't work. The main difference seems to be these two lines:

http://search.open-bio.org/ : (works)



and

http://bioperl.org/pipermail/bioperl-l : (doesn't work)




(procrastination means always having something to do tomorrow).

Rob

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


From walsh at cenix-bioscience.com  Thu Oct 30 02:08:17 2003
From: walsh at cenix-bioscience.com (Andrew Walsh)
Date: Thu Oct 30 08:32:21 2003
Subject: [Bioperl-l] perl script to retrieve accession numbers
In-Reply-To: <20031029170353.14118.qmail@web14612.mail.yahoo.com>
References: <20031029170353.14118.qmail@web14612.mail.yahoo.com>
Message-ID: <3FA0B8E1.4090808@cenix-bioscience.com>

You should read the Bioperl tutorial section on this:

http://www.bioperl.org/Core/Latest/bptutorial.html

http://www.bioperl.org/Core/Latest/bptutorial.html#iii.1.1_accessing_remote_databases_(bio::db::genbank,_etc)

Also read the PODs for Bio::DB::GenBank (i.e. use perldoc).

If you are retrieving lots of sequences, try using Batch Entrez on the 
NCBI website to get local copies of the sequences, then use 
Bio::Index::GenBank and Bio::SeqIO.  Check out those POD and you should 
go through the tutorial.

Andrew


M V wrote:
> Hi there,
>  
> Is there a perl script that retrieves the genbank accession numbers if I have a list of gene names? Thanks in advance.
>  
> Murmanmadi
> 
> 
> ---------------------------------
> Do you Yahoo!?
> Exclusive Video Premiere - Britney Spears
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l


-- 
------------------------------------------------------------------
Andrew Walsh, M.Sc.
Bioinformatics Software Engineer
IT Unit
Cenix BioScience GmbH
Pfotenhauerstr. 108
01307 Dresden, Germany
Tel. +49(351)210-2699
Fax  +49(351)210-1309

public key: http://www.cenix-bioscience.com/public_keys/walsh.gpg
------------------------------------------------------------------


From John.Gray at stjude.org  Thu Oct 30 09:37:34 2003
From: John.Gray at stjude.org (Gray, John)
Date: Thu Oct 30 09:34:27 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
Message-ID: <1E0CC447E59C974CA5C7160D2A2854ECC51A72@SJMEMXMB04.stjude.sjcrh.local>

Thank you all for the help.

The broken archive search is at http://bioperl.org/pipermail/bioperl-l/.  I will use http://search.open-bio.org in the future.

Cutting circular DNAs is not as simple as concatenating the first and last fragments, as frequently the recognition sequence will span the origin of the plasmid, and in that case the site gets missed.  I have made a work-around within Bio::RestrictionEnzyme by appending the sequence with a short duplication of the beginning:

## Make circularity function properly AGAIN!!
## $concat is set to the length of the recognition sequence -1
$concat = 5;
$sequence = uc ($& . (substr $sequence, 0, $concat-1));

The additional sequence must then be later removed from the appropriate fragment.  (Here I am only after the length of the fragments):

## Cut the sequence with the restriction enzyme object.
@fragments = eval{ $re->cut_seq($seq); };
$@ && die "\n*** TROUBLE CUTTING:\n$@\n"; 

## pull lengths from array of sequences
my @fraglen;
my $i = 0;
foreach (@fragments) {
        $fraglen[$i] = length $_;
        $i++;
        }
## Sum first and last fragment lengths due to circularity, remove last
$fraglen[0] = $fraglen[0] + $fraglen[@fraglen-1] - $concat;
pop @fraglen;


This works well so far, but it is cumbersome because I must modify the sequence in a specific way for each enzyme recognition site length.

Reading the documentation for the new Bio::Restriction module I see that it has many improvements which would have made my code much easier, but it is not clear that the methods address the problem that I raised above.  Anyone have any idea?

Thanks again-

John Gray


 

-----Original Message-----
From: Rob Edwards [mailto:redwards@utmem.edu] 
Sent: Wednesday, October 29, 2003 6:31 PM
To: Gray, John
Cc: bioperl-l@portal.open-bio.org
Subject: Re: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids

The new Bio::Restriction modules should tell you the correct sizes of  
circular plasmids. This will do exactly what you want. The old  
Bio::Tools::RestrictionEnzyme does not have this ability, though you  
can just merge the first and last fragments of a sequence.

The newer Bio::Restriction are (I believe) only available in BioPerl  
1.3 and later. This is the upcoming release and the first RC seems  
quite stable.

You should probably tell someone about the searches not working, but I  
guess you just have :)

Rob



On Wednesday, October 29, 2003, at 10:39  AM, Gray, John wrote:

> I am trying to find documentation for the Bio::Restriction module, to  
> see if it can properly predict restriction fragment sizes for circular  
> plasmids.
>
>
>
> I'm sorry to have to ask.  The tutorial at  
> http://www.bioperl.org/Core/Latest/bptutorial.html says that  
> Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I  
> have used.  I can't find any documentation for this method at  
> http://doc.bioperl.org/releases/bioperl-1.2.3/.
>
>
>
> The Seq documentation does not provide any description of the  
> 'is_circular' method, and I was hoping that I could set the Seq object  
> to be circular, and then just run something like  
> $enyme_object->cut_seq($seq_object) to get my list of strings  
> containing the resulting fragments.
>
>
>
> Thank you for your help.
>
>
>
> PS.  When I try and search the Bioperl-l archive, it doesn't return  
> any matches, even when I try to match the word 'bioperl'.  Should I  
> tell someone about this?
>
>
>
> ----------------------------------------------------------------------- 
> --------------
> John T. Gray, Ph.D.
> Director, Vector Development & Production
> Experimental Hematology Division
> Hematology-Oncology
> St. Jude Children's Research Hospital
> D2038A, Mail Stop 341
> 332 N. Lauderdale Street
> Memphis, TN 38105
>
> (901) 495-4729 phone
> (901) 495-2176 fax
>
> John.Gray@stjude.org 
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l




From John.Gray at stjude.org  Thu Oct 30 09:48:59 2003
From: John.Gray at stjude.org (Gray, John)
Date: Thu Oct 30 09:45:53 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
Message-ID: <1E0CC447E59C974CA5C7160D2A2854ECC520A3@SJMEMXMB04.stjude.sjcrh.local>

Sorry, the code I pasted in my last email was missing some hard returns.  It should have looked like this:

## Make circularity function properly AGAIN!!
## $concat is set to the length of the recognition sequence -1 
$concat = 5; 
$sequence = uc ($& . (substr $sequence, 0, $concat-1));

The additional sequence must then be later removed from the appropriate fragment.  (Here I am only after the length of the fragments):

## Cut the sequence with the restriction enzyme object. 
@fragments = eval{ $re->cut_seq($seq); }; 
$@ && die "\n*** TROUBLE CUTTING:\n$@\n"; 

## pull lengths from array of sequences
my @fraglen;
my $i = 0;
foreach (@fragments) {
        $fraglen[$i] = length $_;
        $i++;
        }
## Sum first and last fragment lengths due to circularity, remove last 
$fraglen[0] = $fraglen[0] + $fraglen[@fraglen-1] - $concat; 
pop @fraglen;



-------------------------------------------------------------------------------------
John T. Gray, Ph.D.
Director, Vector Development & Production
Experimental Hematology Division
Hematology-Oncology
St. Jude Children's Research Hospital
D2038A, Mail Stop 341
332 N. Lauderdale Street
Memphis, TN 38105?
(901) 495-4729 phone
(901) 495-2176 fax
John.Gray@stjude.org



From redwards at utmem.edu  Thu Oct 30 10:37:44 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Thu Oct 30 10:34:35 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <1E0CC447E59C974CA5C7160D2A2854ECC51A72@SJMEMXMB04.stjude.sjcrh.local>
Message-ID: <0141582E-0AEF-11D8-A107-000A959E1622@utmem.edu>

The best way to do it is to probably cut the sequences, join the first  
and last sequence as is done now, and then see if the enzyme cuts that  
fragment and if so sort out where the fragment should be. I think it is  
reasonably trivial and I can take a look at it soon.

Rob


On Thursday, October 30, 2003, at 08:37  AM, Gray, John wrote:

> Thank you all for the help.
>
> The broken archive search is at  
> http://bioperl.org/pipermail/bioperl-l/.  I will use  
> http://search.open-bio.org in the future.
>
> Cutting circular DNAs is not as simple as concatenating the first and  
> last fragments, as frequently the recognition sequence will span the  
> origin of the plasmid, and in that case the site gets missed.  I have  
> made a work-around within Bio::RestrictionEnzyme by appending the  
> sequence with a short duplication of the beginning:
>
> ## Make circularity function properly AGAIN!!
> ## $concat is set to the length of the recognition sequence -1
> $concat = 5;
> $sequence = uc ($& . (substr $sequence, 0, $concat-1));
>
> The additional sequence must then be later removed from the  
> appropriate fragment.  (Here I am only after the length of the  
> fragments):
>
> ## Cut the sequence with the restriction enzyme object.
> @fragments = eval{ $re->cut_seq($seq); };
> $@ && die "\n*** TROUBLE CUTTING:\n$@\n";
>
> ## pull lengths from array of sequences
> my @fraglen;
> my $i = 0;
> foreach (@fragments) {
>         $fraglen[$i] = length $_;
>         $i++;
>         }
> ## Sum first and last fragment lengths due to circularity, remove last
> $fraglen[0] = $fraglen[0] + $fraglen[@fraglen-1] - $concat;
> pop @fraglen;
>
>
> This works well so far, but it is cumbersome because I must modify the  
> sequence in a specific way for each enzyme recognition site length.
>
> Reading the documentation for the new Bio::Restriction module I see  
> that it has many improvements which would have made my code much  
> easier, but it is not clear that the methods address the problem that  
> I raised above.  Anyone have any idea?
>
> Thanks again-
>
> John Gray
>
>
>
>
> -----Original Message-----
> From: Rob Edwards [mailto:redwards@utmem.edu]
> Sent: Wednesday, October 29, 2003 6:31 PM
> To: Gray, John
> Cc: bioperl-l@portal.open-bio.org
> Subject: Re: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
>
> The new Bio::Restriction modules should tell you the correct sizes of
> circular plasmids. This will do exactly what you want. The old
> Bio::Tools::RestrictionEnzyme does not have this ability, though you
> can just merge the first and last fragments of a sequence.
>
> The newer Bio::Restriction are (I believe) only available in BioPerl
> 1.3 and later. This is the upcoming release and the first RC seems
> quite stable.
>
> You should probably tell someone about the searches not working, but I
> guess you just have :)
>
> Rob
>
>
>
> On Wednesday, October 29, 2003, at 10:39  AM, Gray, John wrote:
>
>> I am trying to find documentation for the Bio::Restriction module, to
>> see if it can properly predict restriction fragment sizes for circular
>> plasmids.
>>
>>
>>
>> I'm sorry to have to ask.  The tutorial at
>> http://www.bioperl.org/Core/Latest/bptutorial.html says that
>> Bio::Restriction replaces the older Bio::RestrictionEnzyme, which I
>> have used.  I can't find any documentation for this method at
>> http://doc.bioperl.org/releases/bioperl-1.2.3/.
>>
>>
>>
>> The Seq documentation does not provide any description of the
>> 'is_circular' method, and I was hoping that I could set the Seq object
>> to be circular, and then just run something like
>> $enyme_object->cut_seq($seq_object) to get my list of strings
>> containing the resulting fragments.
>>
>>
>>
>> Thank you for your help.
>>
>>
>>
>> PS.  When I try and search the Bioperl-l archive, it doesn't return
>> any matches, even when I try to match the word 'bioperl'.  Should I
>> tell someone about this?
>>
>>
>>
>> ---------------------------------------------------------------------- 
>> -
>> --------------
>> John T. Gray, Ph.D.
>> Director, Vector Development & Production
>> Experimental Hematology Division
>> Hematology-Oncology
>> St. Jude Children's Research Hospital
>> D2038A, Mail Stop 341
>> 332 N. Lauderdale Street
>> Memphis, TN 38105
>>
>> (901) 495-4729 phone
>> (901) 495-2176 fax
>>
>> John.Gray@stjude.org 
>>
>>
>>
>> _______________________________________________
>> 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 redwards at utmem.edu  Thu Oct 30 20:52:41 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Thu Oct 30 20:49:31 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <1E0CC447E59C974CA5C7160D2A2854ECC520A3@SJMEMXMB04.stjude.sjcrh.local>
Message-ID: 

The following is a quick patch for Bio/Restriction/Analysis.pm so that 
it handles circular sequences correctly if there is another cut site in 
the region that has been linearized. At the moment it won't handle a 
single cut site at that point (e.g. pBR322 has a single EcoRI site at 
the point it is circularized). I am not sure how to deal with this and 
need to think about it (the fragments are right but the cut sites are 
not).

Can someone submit it for me?

I have submitted a Bugzilla report as #1548

120c120,121
< for further analysis. However, this will change the start of the
---
 > for further analysis. This fragment will also be checked for cuts
 > by the enzyme(s). However, this will change the start of the
737c738,749
<                 unshift (@re_frags, $last.$first);
---
 >               my $newfrag=$last.$first;
 >               my @cuts = split /($beforeseq)($afterseq)/i, $newfrag;
 >               my @newfrags;
 >               if ($#cuts) {
 >                # there is another cut
 >                for (my $i=0; $i<=$#cuts; $i+=2) {push (@newfrags, 
$cuts[$i].$cuts[$i+1])}
 >               }
 >               else {
 >                # there isn't another cut
 >                push (@newfrags, $newfrag);
 >               }
 >               push @re_frags, @newfrags;


Thanks

Rob

From wes.barris at csiro.au  Fri Oct 31 00:58:43 2003
From: wes.barris at csiro.au (Wes Barris)
Date: Fri Oct 31 00:55:51 2003
Subject: [Bioperl-l] How do you create a Bio::Align::AlignI object?
Message-ID: <3FA1FA13.8070806@csiro.au>

Hi,

I need to convert the contents of an ACE file into a series of MSF files
(one for each contig).  Since BioPerl does not offer a straight-forward
conversion process for this task, I have to manually read each contig
section of the ACE file and manually create the structures for an
AlignI object.  The only way I have found to create an AlignI object
was by opening an input stream to an existing file.  As a result, I
had to write the consensus to a file just so that I could open it again
and gain access to an AlignI object.

Here is my code.  Is there a slicker way to do this?

acetomsf.pl:

#!/usr/local/bin/perl -w
#
#
use strict;
use Bio::Assembly::IO;
use Bio::AlignIO;
use Bio::SeqIO;
#
my $usage = "Usage: $0 \n";
my $infile = shift or die $usage;
my $prefix = 'btcn';
my $io = new Bio::Assembly::IO(-file=>$infile, -format=>'ace');
my $assembly = $io->next_assembly;

foreach my $contig ($assembly->all_contigs()) {
    my $contigName = $prefix.$contig->id;
#  $contig->match();    # not yet implemented
#
# Write the consensus to a file.
#
    my $consensusSeq = new Bio::Seq(
                         -seq=>$contig->get_consensus_sequence->seq,
                         -id=>$prefix.$contig->id);
    my $seqout = new Bio::SeqIO(-file=>">$contigName.fa", -format=>'fasta');
    $seqout->write_seq($consensusSeq);
#
# Snarf the consensus back in so that we can create a Bio::Align::AlignI object.
#
    my $instream  = new Bio::AlignIO(-format=>'fasta', -file=>"$contigName.fa");
    my $outstream = new Bio::AlignIO(-format=>'msf', -file=>">$contigName.msf");
    my $aln = $instream->next_aln();
#
# Loop through each sequence in the contig adding it to the new alignment.
#
    foreach my $seq ($contig->each_seq) {
#
# Some of the ACE starting locations are negative.
#
       if ($contig->get_seq_coord($seq)->start <= 0) {
          my $offset = -$contig->get_seq_coord($seq)->start + 2;
          $seq->seq($seq->subseq($offset,$seq->length));
          print($seq->primary_id," was clipped at the beginning by $offset\n");
          }
#
# Pad each sequence so it aligns with the consensus.
#
       my $before = $contig->get_seq_coord($seq)->start - 1;
       my $after = $contig->get_consensus_length - $contig->get_seq_coord($seq)->end;
       my $alignedSequence = '-' x $before . $seq->seq . '-' x $after;
#
# Some of the ACE ending locations go beyond the consensus.
#
       if (length($alignedSequence) > $contig->get_consensus_length) {
          $alignedSequence = substr($alignedSequence, 1 ,$contig->get_consensus_length);
          print($seq->primary_id," was clipped at the end\n");
          }
       $seq->seq($alignedSequence);
       $aln->add_seq($seq);
       }
    $aln->set_displayname_flat;
    $outstream->write_aln($aln);
    undef $outstream;
    }


-- 
Wes Barris
E-Mail: Wes.Barris@csiro.au


From Daniel.Lang at biologie.uni-freiburg.de  Fri Oct 31 05:30:48 2003
From: Daniel.Lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Fri Oct 31 05:27:46 2003
Subject: [Bioperl-l] SearchIO::Writer::HTMLResultWriter question
Message-ID: <3FA239D8.4040609@biologie.uni-freiburg.de>

Hi,
Is it possible, that currently the search function on the Archives page 
doesn?t work...I don?t get any search results at all, no matter what 
search term I use:(
So mabye this has already been asked...

Is there a "No Hits found" function in HTMLResultWriter?
Or can I make the results-filter do something like this?

Thanks in advance,
Daniel


From d.gatherer at vir.gla.ac.uk  Fri Oct 31 07:13:21 2003
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Fri Oct 31 07:09:45 2003
Subject: [Bioperl-l] gcg.pm
In-Reply-To: <200310311034.h9VAWjde004507@portal.open-bio.org>
Message-ID: <5.2.1.1.1.20031031120319.00af7328@udcf.gla.ac.uk>

Hi

Please excuse if this is an already known bug.

Seq.pm says you can do this:


# make from strings in script
     $seqobj = Bio::Seq->new( -display_id => 'my_id',
                              -seq => $sequence_as_string);

and then you can do:

     $seq_out->write_seq($seqobj);

which is fine, except if you previously defined a GCG-format IO, eg:

my $seq_out = Bio::SeqIO->new('-file' => ">$outfile", '-format' => "GCG");

in which case you have to do

$seqobj = Bio::Seq->new( -display_id => 'my_id',
                              -seq => $sequence_as_string,
                              -desc => "a description");

Otherwise, you get:

Use of uninitialized value in concatenation (.) or string at 
/usr/local/lib/site_perl/5.8.0//Bio/SeqIO/gcg.pm line 197,

The offending line in gcg.pm is:

197 push(@out,"$comment\n");

which causes offence since:

178     my $comment     = $seq->desc;

If the IO format is FASTA, none of this happens and the output is clean.

I suggest that a default $comment should be used in gcg.pm, which is 
"!!AA_SEQUENCE" or "!!NA_SEQUENCE" depending on sequence type, as that is 
the normal first line in most CGC files.

Cheers
Derek

From Richard.Adams at ed.ac.uk  Fri Oct 31 07:24:28 2003
From: Richard.Adams at ed.ac.uk (Richard Adams)
Date: Fri Oct 31 07:21:24 2003
Subject: [Bioperl-l] Re: default RemoteBlast user agent
References: 
Message-ID: <3FA2547C.9030202@ed.ac.uk>


Hi Jason,
    Do you think it's worthwhile including error checking for sensible 
blast parameters or  is it acceptable to just let people figure out the 
blast failed submsiion html for themselves?

Richard
Jason Stajich wrote:

> Richard -
>
> Grateful that you are willing to take on RemoteBlast.  Not my cup of tea
> any more.  I think SearchIO should be able to handle bl2seq, megablast,
> and rpsblast outputs just fine now.  May have to cleanup any 
 
> tags if
> NCBI throws them in there.
>
> Here is some correspondance I've had with someone at NCBI - presumably 
> the
> simple script he sent is probably what you already knew - but I'm sending
> it along at any rate.
>
> Let me know if you have any questions, etc.
>
> Best,
> -jason
>
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
> ---------- Forwarded message ----------
> Date: Wed, 22 Oct 2003 11:57:51 -0400
> From: George Coulouris 
> Cc: jason@bioperl.org
> Subject: Re: default RemoteBlast user agent?
>
> George Coulouris wrote:
>
>> Jason-
>>
>> On an unrelated note, are there plans to support multiple queries /
>> megablast nucleotide searches?
>>
>> -George
>
>
> Jason,
>
> I've attached some perl code that demonstrates how to do batch
> submission of multiple nucleotide sequences with megablast. Usage is:
>
> ./remote_megablastp.pl file1 file2..
>
> Input files should be in fasta format.
>
> It will emit the CGI output from which the RID can be obtained. Polling
> for results / obtaining results / formatting results can proceed as usual.
>
>------------------------------------------------------------------------
>
>#!/opt/local/bin/perl
>
>use URI::Escape;
>use LWP::UserAgent;
>use HTTP::Request::Common qw(POST);
>
>$ua = LWP::UserAgent->new;
>
># read and encode the queries
>foreach $query (@ARGV)
>{
>open(QUERY,$query);
>while()
>{
>$encoded_query = $encoded_query . uri_escape($_);
>}
>}
>
>$args = 'CMD=Put&PROGRAM=blastn&DATABASE=nt&MEGABLAST=on&QUERY=' . $encoded_query;
>
>$req = new HTTP::Request POST => 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi';
>$req->content_type('application/x-www-form-urlencoded');
>$req->content($args);
>
>#print $req->as_string();
>
>$response = $ua->request($req);
>
>if ($response->is_success)
>{
>print $response->content;
>}
>else
>{
>print $response->error_as_HTML;
>}
>  
>

-- 
Dr Richard Adams
Bioinformatician,
Psychiatric Genetics Group,
Medical Genetics,
Molecular Medicine Centre,
Western General Hospital,
Crewe Rd West,
Edinburgh UK
EH4 2XU

Tel: 44 131 651 1084
richard.adams@ed.ac.uk



From jason at cgt.duhs.duke.edu  Fri Oct 31 08:15:03 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 31 08:12:24 2003
Subject: [Bioperl-l] SearchIO::Writer::HTMLResultWriter question
In-Reply-To: <3FA239D8.4040609@biologie.uni-freiburg.de>
References: <3FA239D8.4040609@biologie.uni-freiburg.de>
Message-ID: 

On Fri, 31 Oct 2003, Daniel Lang wrote:

> Hi,
> Is it possible, that currently the search function on the Archives page
> doesn´t work...I don´t get any search results at all, no matter what
> search term I use:(
> So mabye this has already been asked...

Use http://search.open-bio.org/ which works just fine for me  -- will get
Chris to look at the other page to see what is going on.
>

> Is there a "No Hits found" function in HTMLResultWriter?
> Or can I make the results-filter do something like this?
>
You mean, print out 'No Hits found' in the report?  Not currently - should
be an easy extension though.  You'd need edit HTMLResultWriter though as
there is currently no hook for this particular part - if there are no Hits
the hit_filter won't be called of course.

-jason

> Thanks in advance,
> Daniel
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From jason at cgt.duhs.duke.edu  Fri Oct 31 08:24:48 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 31 08:21:49 2003
Subject: [Bioperl-l] gcg.pm
In-Reply-To: <5.2.1.1.1.20031031120319.00af7328@udcf.gla.ac.uk>
References: <5.2.1.1.1.20031031120319.00af7328@udcf.gla.ac.uk>
Message-ID: 

Go ahead and submit it as a bug at http://bugzilla.open-bio.org/ so that
we have a record of this and someone who wants to jump in and fix simple
bugs can do so.

You can also just change the line
 my $comment     = $seq->desc;
to
 $comment = '' unless defined $comment;
To get rid of the warning.

Note that the GCG output is still clean and usuable, you're just getting
warnings to STDERR.

The more sophisticated soln you propose would be a pretty simple
if / elsif based on $seq->alphabet

I would love to see people submitting code patches too when it
something pretty straight forward like this...

-jason
On Fri, 31 Oct 2003, Derek Gatherer wrote:

> Hi
>
> Please excuse if this is an already known bug.
>
> Seq.pm says you can do this:
>
>
> # make from strings in script
>      $seqobj = Bio::Seq->new( -display_id => 'my_id',
>                               -seq => $sequence_as_string);
>
> and then you can do:
>
>      $seq_out->write_seq($seqobj);
>
> which is fine, except if you previously defined a GCG-format IO, eg:
>
> my $seq_out = Bio::SeqIO->new('-file' => ">$outfile", '-format' => "GCG");
>
> in which case you have to do
>
> $seqobj = Bio::Seq->new( -display_id => 'my_id',
>                               -seq => $sequence_as_string,
>                               -desc => "a description");
>
> Otherwise, you get:
>
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/lib/site_perl/5.8.0//Bio/SeqIO/gcg.pm line 197,
>
> The offending line in gcg.pm is:
>
> 197 push(@out,"$comment\n");
>
> which causes offence since:
>
> 178     my $comment     = $seq->desc;
>
> If the IO format is FASTA, none of this happens and the output is clean.
>
> I suggest that a default $comment should be used in gcg.pm, which is
> "!!AA_SEQUENCE" or "!!NA_SEQUENCE" depending on sequence type, as that is
> the normal first line in most CGC files.
>
> Cheers
> Derek
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From Daniel.Lang at biologie.uni-freiburg.de  Fri Oct 31 08:54:24 2003
From: Daniel.Lang at biologie.uni-freiburg.de (Daniel Lang)
Date: Fri Oct 31 08:51:16 2003
Subject: [Bioperl-l] allowgaps parameter in Bio::SearchIO
Message-ID: <3FA26990.5030909@biologie.uni-freiburg.de>

Hi,
I?m getting wrong values for the "allowgaps" parameter while parsing
NCBI-like BLAST results:
The parser does not detect if a the report was generated with -g F
switch(ungapped) and the allowgaps values is "yes", when it should be
"no"...
I guess the parameter is based on the occurence of "Gapped" after the
"Lambda"-part, right?

Here is an example BLAST output snipplet(-g F):

Searching..................................................done

  ***** No hits found ******

   Database: ppp_orfpep
     Posted date:  Sep 18, 2003  6:31 AM
   Number of letters in database: 2,367,445
   Number of sequences in database:  14,583

Lambda     K      H
    0.318    0.135    0.401


Matrix: BLOSUM62
Number of Hits to DB: 378,425

Or did I missinterpret the parameter?
Thanks ind advance,
Daniel:)


From John.Gray at stjude.org  Fri Oct 31 09:36:04 2003
From: John.Gray at stjude.org (Gray, John)
Date: Fri Oct 31 09:32:56 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
Message-ID: <1E0CC447E59C974CA5C7160D2A2854ECC51A76@SJMEMXMB04.stjude.sjcrh.local>

After reading some of your comments about how the site recognition is functioning, I am concerned that there may be another problem.  It commonly occurs that restriction enzyme recognition sites will overlap, and I think this may cause your method to miss some sites.  I am wondering whether it may be necessary to separate the process of site mapping and cleavage. 

For example, BssH II cuts at G^CGCGC, and the sequence of GCGCGCGC theoretically has two cut sites within it.  Of course, your algorithm is similar to reality in that once the enzyme cuts the sequence once, it probably won't be able to recognize the other site.  However, in the test tube what you will actually get is a random distribution of cutting at the two sites.  Traditionally (at least in the software I have used), the site mapping algorithms have returned all possible cut sites.

I am thinking the only way around this would be to first map the sites into an array, and then use that array to either calculate fragment sizes or sequences.  With the possibility of overlapping sites in mind, I still can't think of any way to circumvent the problem of the origin on circular sequences without concatenating the sequence to simulate circularity.

John

-----Original Message-----
From: Rob Edwards [mailto:redwards@utmem.edu] 
Sent: Thursday, October 30, 2003 7:53 PM
To: bioperl-l@portal.open-bio.org
Subject: Re: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids

The following is a quick patch for Bio/Restriction/Analysis.pm so that 
it handles circular sequences correctly if there is another cut site in 
the region that has been linearized. At the moment it won't handle a 
single cut site at that point (e.g. pBR322 has a single EcoRI site at 
the point it is circularized). I am not sure how to deal with this and 
need to think about it (the fragments are right but the cut sites are 
not).

Can someone submit it for me?

I have submitted a Bugzilla report as #1548

120c120,121
< for further analysis. However, this will change the start of the
---
 > for further analysis. This fragment will also be checked for cuts
 > by the enzyme(s). However, this will change the start of the
737c738,749
<                 unshift (@re_frags, $last.$first);
---
 >               my $newfrag=$last.$first;
 >               my @cuts = split /($beforeseq)($afterseq)/i, $newfrag;
 >               my @newfrags;
 >               if ($#cuts) {
 >                # there is another cut
 >                for (my $i=0; $i<=$#cuts; $i+=2) {push (@newfrags, 
$cuts[$i].$cuts[$i+1])}
 >               }
 >               else {
 >                # there isn't another cut
 >                push (@newfrags, $newfrag);
 >               }
 >               push @re_frags, @newfrags;


Thanks

Rob

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



From redwards at utmem.edu  Fri Oct 31 09:48:10 2003
From: redwards at utmem.edu (Rob Edwards)
Date: Fri Oct 31 09:45:00 2003
Subject: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
In-Reply-To: <1E0CC447E59C974CA5C7160D2A2854ECC51A76@SJMEMXMB04.stjude.sjcrh.local>
Message-ID: <3F2E5F98-0BB1-11D8-94D7-000A959E1622@utmem.edu>

Yes, you are quite right. Probably in the test tube one of the sites 
will be cut randomly - behavior we could mimic but that would be very 
confusing. I agree it may be better to map the sites rather than cut 
the sequences, and this may be the best way to do it (and actually 
could be faster).

Perhaps a better way to do it is to add a new function that returns 
mapped cut sites. I need to look more at the docs, but isn't there a 
bioperl feature already to look for occurrences of a single sequence in 
a sequence? This could actually be a lot faster for non-ambiguous 
sequences by using index rather than split, and use less memory.

At the moment the module actually calculates cut sites by fragmenting 
the sequence and then calculating the length of each of the sequences 
returned by the split. This is probably not optimal.

Maybe this should be a bugzilla bug report....

Rob






On Friday, October 31, 2003, at 08:36  AM, Gray, John wrote:

> After reading some of your comments about how the site recognition is 
> functioning, I am concerned that there may be another problem.  It 
> commonly occurs that restriction enzyme recognition sites will 
> overlap, and I think this may cause your method to miss some sites.  I 
> am wondering whether it may be necessary to separate the process of 
> site mapping and cleavage.
>
> For example, BssH II cuts at G^CGCGC, and the sequence of GCGCGCGC 
> theoretically has two cut sites within it.  Of course, your algorithm 
> is similar to reality in that once the enzyme cuts the sequence once, 
> it probably won't be able to recognize the other site.  However, in 
> the test tube what you will actually get is a random distribution of 
> cutting at the two sites.  Traditionally (at least in the software I 
> have used), the site mapping algorithms have returned all possible cut 
> sites.
>
> I am thinking the only way around this would be to first map the sites 
> into an array, and then use that array to either calculate fragment 
> sizes or sequences.  With the possibility of overlapping sites in 
> mind, I still can't think of any way to circumvent the problem of the 
> origin on circular sequences without concatenating the sequence to 
> simulate circularity.
>
> John
>
> -----Original Message-----
> From: Rob Edwards [mailto:redwards@utmem.edu]
> Sent: Thursday, October 30, 2003 7:53 PM
> To: bioperl-l@portal.open-bio.org
> Subject: Re: [Bioperl-l] Restriction Enzyme cuts on Circular plasmids
>
> The following is a quick patch for Bio/Restriction/Analysis.pm so that
> it handles circular sequences correctly if there is another cut site in
> the region that has been linearized. At the moment it won't handle a
> single cut site at that point (e.g. pBR322 has a single EcoRI site at
> the point it is circularized). I am not sure how to deal with this and
> need to think about it (the fragments are right but the cut sites are
> not).
>
> Can someone submit it for me?
>
> I have submitted a Bugzilla report as #1548
>
> 120c120,121
> < for further analysis. However, this will change the start of the
> ---
>> for further analysis. This fragment will also be checked for cuts
>> by the enzyme(s). However, this will change the start of the
> 737c738,749
> <                 unshift (@re_frags, $last.$first);
> ---
>>               my $newfrag=$last.$first;
>>               my @cuts = split /($beforeseq)($afterseq)/i, $newfrag;
>>               my @newfrags;
>>               if ($#cuts) {
>>                # there is another cut
>>                for (my $i=0; $i<=$#cuts; $i+=2) {push (@newfrags,
> $cuts[$i].$cuts[$i+1])}
>>               }
>>               else {
>>                # there isn't another cut
>>                push (@newfrags, $newfrag);
>>               }
>>               push @re_frags, @newfrags;
>
>
> Thanks
>
> Rob
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>

From jason at cgt.duhs.duke.edu  Fri Oct 31 10:11:13 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 31 10:08:27 2003
Subject: [Bioperl-l] allowgaps parameter in Bio::SearchIO
In-Reply-To: <3FA26990.5030909@biologie.uni-freiburg.de>
References: <3FA26990.5030909@biologie.uni-freiburg.de>
Message-ID: 

It's not parsed separately probably.  What you're seeing is a default
parameter which is reset to no when parsing WU-BLAST output (which
conviently has a line which says 'nogaps' to make this determination
easily).

The logic of the parsing will have to be reconsidered to try and add this
sort of information in I guess.  Unfortunately NCBI-BLAST doesn't do a
particularly nice job of reporting what were all the input parameters to
the BLAST run so it a bit of work to try and infer all of them from the
output based on what is present/absent.

A bit more work and attention needs to be paid to the stats and param
parsing, as we are not really capturing all of them.  Something I'd love
for someone to try and help with, or I will try and get to it towards the
end of November when my schedule frees up a little bit.

-jason

On Fri, 31 Oct 2003, Daniel Lang wrote:

> Hi,
> I?m getting wrong values for the "allowgaps" parameter while parsing
> NCBI-like BLAST results:
> The parser does not detect if a the report was generated with -g F
> switch(ungapped) and the allowgaps values is "yes", when it should be
> "no"...
> I guess the parameter is based on the occurence of "Gapped" after the
> "Lambda"-part, right?
>
> Here is an example BLAST output snipplet(-g F):
>
> Searching..................................................done
>
>   ***** No hits found ******
>
>    Database: ppp_orfpep
>      Posted date:  Sep 18, 2003  6:31 AM
>    Number of letters in database: 2,367,445
>    Number of sequences in database:  14,583
>
> Lambda     K      H
>     0.318    0.135    0.401
>
>
> Matrix: BLOSUM62
> Number of Hits to DB: 378,425
>
> Or did I missinterpret the parameter?
> Thanks ind advance,
> Daniel:)
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From d.gatherer at vir.gla.ac.uk  Fri Oct 31 10:40:25 2003
From: d.gatherer at vir.gla.ac.uk (Derek Gatherer)
Date: Fri Oct 31 10:36:16 2003
Subject: [Bioperl-l] gcg.pm, another one
In-Reply-To: <200310311034.h9VAWjde004507@portal.open-bio.org>
Message-ID: <5.2.1.1.1.20031031153144.00b1f160@udcf.gla.ac.uk>

Hello again

Last bug submitted to bugzilla.  The following may be a bug, but I wonder 
if there is a problem with my GCG format.

Try this script:

#!/usr/bin/perl -w

use lib "/usr/local/lib/site_perl/5.8.0/";
use strict;
use Bio::Seq;
use Bio::SeqIO;

my $dnain = Bio::SeqIO->new( '-format' => 'GCG' , -file => "cds.gcg");

while((my $seqobj = $dnain->next_seq()))
{
     $seqobj->display_id;
}

on the file cds.gcg below.

to get:

------------- EXCEPTION  -------------
MSG: Looks like start of another sequence. See documentation.
STACK Bio::SeqIO::gcg::next_seq 
/usr/local/lib/site_perl/5.8.0//Bio/SeqIO/gcg.pm:124
STACK toplevel gcgtest.pl:10

The problem, I think, is that the SeqIO stream doesn't seem to recognise 
the change over from one sequence to another.  Or do I need some record 
separator between my sequences???  If this really is also a bug, I'll 
submit it too.

Offending line in gcg.pm is:

  124      if( /\.\.$/ ) {
         $self->throw("Looks like start of another sequence. See 
documentation. ");
        }

and here's the file cds.gcg, containing two sequences in GCG format

!!NA_SEQUENCE 1.0
  ASSEMBLE    October 27, 2003 15:32

Symbols:     1 to: 1269  from: merlin.seq /rev   ck: 8363, 55186 to: 56454

LOCUS       MERLIN                235645 bp    DNA     linear   VRL 14-AUG-2003
DEFINITION  Human herpesvirus 5 strain Merlin, complete genome.
ACCESSION   MERLIN
VERSION
KEYWORDS    .
SOURCE      Human herpesvirus 5 . . .

merlin_ul43.cds  Length: 1269  October 27, 2003 15:32  Type: N  Check: 9039  ..

        1  ATGGAGAAAA CGCCGGCGGA GACGACGGCG GTTTCAGCTG GCAACGTGCC

       51  ACGTGACTCA ATTCCGTGTA TAACTAACGT GTCCGCGGAC ACCCGCGGCC

      101  GTACCCGCCC CAGCAGACCA GCCACCGTCC CTCAGCGACG TCCCGCGCGG

      151  ATCGGACACT TTAGGCGGCG CAGCGCCAGC CTTAGCTTTC TTGACTGGCC

      201  GGACGACAGC GTCACAGAGG GCGTTCGGAC GACCTCCGCG TCGGTCGCCG

      251  CCTCCGCGGC CCGTTTCGAC GAAATCCGGC GGCGCCGCCA GAGCATCAAC

      301  GACGAGATGA AGGAACGCAC GCTGGAGGAC GCGCTGGCTG TCGAGCTGGT

      351  CAACGAGACC TTCCGCTGCT CTGTCACCTC CGACGCCCGC AAGGACTTGC

      401  AGAAGCTGGT TCGTCGCGTC AGCGGCACGG TGCTGCGTCT CAGCTGGCCA

      451  AACGGTTGGT TCTTCACCTA CTGCGACCTG TTACGCGTCG GCTACTTTGG

      501  ACATCTCAAT ATTAAAGGTT TGGAGAAGAC CTTCCTGTGC TGCGACAAGT

      551  TCTTGCTGCC GGTGGGCACT GTGAGTCGTT GCGAAGCCAT CGGCCGCCCA

      601  CCGCTACCCG TACTCATCGG CGAGGGCGGT CGCGTCTACG TCTACTCGCC

      651  TGTGGTGGAA TCGCTGTACC TGGTGTCGCG GTCCGGTTTC CGCGGCTTCG

      701  TGCAGGAGGG CCTGCGCAAC TACGCGCCGC TGCGCGAAGA ACTGGGCTAT

      751  GTCCGCTTCG AGACCGGCGG CGACGTGGGT CGCGAGTTCA TGTTGGCGCG

      801  CGACCTGCTG GCCCTGTGGC GCCTGTGCAT GAAGCGCGAG GGTTCTATCT

      851  TCAGCTGGCG AGACGGTAAC GAGGCGCTGA CGACGGTCGT CTTGAACGGG

      901  AGCCAGACTT ACGAGGATCC GGCCCACGGC AACTGGTTAA AAGAGACGTG

      951  CTCGCTGAAC GTGCTGCAGG TATTTGTGGT GCGGGCCGTG CCGGTGGAGT

     1001  CGCAGCAGCG CCTGGACATC TCCATACTGG TGAACGAGAG CGGCGCCGTC

     1051  TTCGGCGTGC ATCCCGATAC GCGGCAGGCG CACTTTCTGG CGCGCGGACT

     1101  CCTGGGCTTC TTTCGCGTCG GGTTCTTGCG GTTCTGCAAC AACTACTGCT

     1151  TCGCCCGCGA CTGTTTTACC CACCCTGAAA GCGTGGCACC CGCTTACCGC

     1201  GCCACCGGCT GTCCCAGAGA ACTGTTTTGT CGTCGTTTGC GCAAAAAGAA

     1251  GGGGCTCTTT GCTCGAAGG

!!NA_SEQUENCE 1.0
  ASSEMBLE    October 27, 2003 15:32

Symbols:     1 to: 2718  from: merlin.seq /rev   ck: 8363, 57946 to: 60663

LOCUS       MERLIN                235645 bp    DNA     linear   VRL 14-AUG-2003
DEFINITION  Human herpesvirus 5 strain Merlin, complete genome.
ACCESSION   MERLIN
VERSION
KEYWORDS    .
SOURCE      Human herpesvirus 5 . . .

merlin_ul45.cds  Length: 2718  October 27, 2003 15:32  Type: N  Check: 4998  ..

        1  ATGAATCCGG CTGACGCGGA CGAGGAACAG CGGGTGTCCT CGGTGCCCGC

       51  ACATCGGTGC CGGCCAGGTA GGATTCCAAG CCGCAGCGCG GAAACCGAGA

      101  CGGAGGAATC GTCGGCAGAG GTCGCCGCTG ATACTATCGG GGGAGATGAC

      151  AGCGAGCTCG AGGAGGGGCC GCTGCCCGGG GGTGACAAGG AAGCGTCCGC

      201  TGGAAATACC AACGTATCGA GCGGTGTAGC ATGTGTAGCG GGTTTTACGA

      251  GTGGTGGCGG CGTCGTCAGT TGGCGTCCCG AGTCGCCGTC TCCCGACGGC

      301  ACGCCGTCTG TGCTGTCGTT GACGCGTGAC AGCGGTCCCG CCGTGCCCAG

      351  TCGCGGTGGA CGCGTGAGTA GCGGTCTGAG CACCTTTAAT CCGGCCGGCG

      401  CGACCAGGAT GGAGCTGGAC AGTGTCGAGG AGGAGGACGA TTTCGGGGCT

      451  TCGCTCTGCA AAGTATCGCC GCCGATACAA GCTATGCGCA TGTTGATGGG

      501  CAAAAAGTGT CATTGTCACG GCTACTGGGG CAAGTTTCGC TTTTGCGGCG

      551  TACAGGAGCC GGCGCGGGAG CTGCCGTCCG ACAGGAACGC GCTGTGGCGC

      601  GAGATGGACA CCGTGTCGCG GCACAGTGCC GGTTTGGGCA GTTTCAGGCT

      651  ATTTCAGCTC ATTATGCGCC ACGGTCCCTG TCTGATTCGT CACTCGCCGC

      701  GTTGCGACCT GCTGTTGGGT CGCTTTTATT TCAAAGCCAA CTGGGCGCGT

      751  GAAAGCCGCA CGCCACTGTG TTACGCTTCG GAGCTGTGCG ATGAGTCGGT

      801  GCGCCGTTTT GTGCTGCGTC ACATGGAGGA TCTACCCAAG CTGGCCGAGG

      851  AGACGGCGCG TTTTGTGGAA TTGGCCGGTT GCTGGGGCTT GTACGCGGCC

      901  ATTTTGTGTT TGGATAAGGT GTGTCGCCAA CTGCACGGAC AGGACGAGAG

      951  CCCGGGCGGC GTGTTTTTGC GCATCGCCGT GGCGTTGACG GCCGCTATCG

     1001  AGAACAGTAG GCACTCGCGC ATCTATCGTT TCCATCTGGA TGCGCGTTTC

     1051  GAGGGCGAGG TGTTGGAATC GGTGTTGAAG CGCTGTCGCG ATGGGCAGCT

     1101  GTCGCTGTCC ACCTTCACCA TGTCTACCGT GGGTTTCGAT CGCGTGCCGC

     1151  AGTACGACTT TCTGATCTCG GCCGACCCTT TCTCGCGTGA CGCCAGTTGG

     1201  GCGGCCATGT GCAAGTGGAT GAGTACCTTG AGTTGCGGCG TTTCTGTGTC

     1251  GGTGAACGTA ACGCGACTTA ACGCCGATGT GAACAGCGTG ATTCGTTGCC

     1301  TGGGGGGATA CTGCGATTTG ATACGCGAGA AGGAGGTGCA TCGACCCGTG

     1351  GTACGTGTGT TTGTGGACAT GTGGGACGTG GCCGCTATCC GCGTGATTAA

     1401  CTTTATTCTC AAAGAAAGCA CGTCGGAGTT GACGGGGGTT TGCTACGCTT

     1451  TCAACGTGCC TAGCGTGTTA ATGAAGCGCT ACCGTGCGCG TGAGCAGCGC

     1501  TACTCGCTGT TTGGGCGGCC TGTCTCCCGG CGGCTCTCGG ACCTGGGTCA

     1551  GGAGTCGGCT TTCGAGAAAG AGTATTCGCG CTGCGAGCAA TCGTGCCCCA

     1601  AGGTGGTCGT GAACACGGAC GATTTTCTGA AAAAGATGTT GCTGTGCGCG

     1651  CTCAAGGGCC GTGCCTCGGT GGTCTTTGTC CATCACGTAG TCAAGTACTC

     1701  GATTATGGCC GACAGCGTGT GCCTGCCGCC GTGCTTGAGT CCCGATATGG

     1751  CGTCGTGCCA CTTTGGCGAG TGTGACATGC CGGTGCAGCG GCTGACGGTG

     1801  AACGTGGCTC GCTGCGTGTT TGCGCGTAGC GACGAGCAGA AGCTGCATCT

     1851  ACCCGACGTG GTTTTGGGGA ACACGCGACG TTACTTTGAT TTGAGCGTGC

     1901  TGCGCGAGTT GGTGACCGAG GCGGTGGTTT GGGGCAACGC GCGCTTGGAC

     1951  GCGCTAATGT CGGCGTCCGA ATGGTGGGTA GAGAGCGCGC TGGAAAAACT

     2001  GCGTCCGCTG CACATCGGCG TGGCTGGCTT GCACACGGCG CTCATGCGGT

     2051  TAGGGTTCAC GTACTTTGCC TCTTGGGACT TGATCGAGCG CATCTTTGAG

     2101  CACATGTACT TTGCCGCGGT GCGCGCTAGC GTCGATTTGT GCAAGTCGGG

     2151  TTTGCCGCGC TGCGAGTGGT TCGAACGCAC CATCTATCAA GAGGGCAAAT

     2201  TCATTTTCGA ATTGTATCGG TTGCCGCGGC TCTCCATCGC CAGCGCGCGC

     2251  TGGGAAGCGC TGCGCGCCGA CATGCTCGAG TTCGGATTGC GCAACTGTCA

     2301  GTTTCTGGCG GTGGGTCCCG ACGACGAGGT GGCGCATCTG TGGGGCGTGA

     2351  CGCCGTCAGT GTGGGCTTCG CGCGGCACCG TGTTCGAGGA GGAGACGGTG

     2401  TGGTCATTGT GCCCGCCCAA CCGTGAGTGT TACTTCCCCA CCGTGGTGCG

     2451  GAGGCCGCTG CGCGTGCCCG TGGTGAATTA CGCGTGGTTG GAGCAGCACC

     2501  AGGAGGAGGG CAAGGCGACG CAGTGTCTGT TCCAGGCGGC ACCGGCGATC

     2551  CAAAACGACG TGGAAATGGC GGCCGTGAAC CTGAGCGTGT TTGTGGACCA

     2601  GTGCGTGGCC CTGGTTTTCT ACTATGACTC GGGGATGACG CCCGACGTGC

     2651  TTCTGGCCAG GATGCTCAAG TGGTACCACT GGCGCTTTAA GGTCGGAGTA

     2701  TATAAGTACT GTGCCTCT

From michael.watson at bbsrc.ac.uk  Fri Oct 31 11:54:09 2003
From: michael.watson at bbsrc.ac.uk (michael watson (IAH-C))
Date: Fri Oct 31 11:53:08 2003
Subject: [Bioperl-l] Glimmer
Message-ID: <20B7EB075F2D4542AFFAF813E98ACD9302822399@cl-exsrv1.irad.bbsrc.ac.uk>

Hi

Does anyone have, or does there exist, any perl modules to parse and handle the output from glimmer?

Thanks

Michael Watson
From laurichj at bioinfo.ucr.edu  Fri Oct 31 12:15:19 2003
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Fri Oct 31 12:12:10 2003
Subject: [Bioperl-l] How do you create a Bio::Align::AlignI object?
In-Reply-To: <3FA1FA13.8070806@csiro.au>
References: <3FA1FA13.8070806@csiro.au>
Message-ID: <20031031171519.GA18009@bioinfo.ucr.edu>

On Fri 10/31/03 15:58, Wes Barris wrote:
> Hi,
> 
> I need to convert the contents of an ACE file into a series of MSF files
> (one for each contig).  Since BioPerl does not offer a straight-forward
> conversion process for this task, I have to manually read each contig
> section of the ACE file and manually create the structures for an
> AlignI object.  The only way I have found to create an AlignI object
> was by opening an input stream to an existing file.  As a result, I
> had to write the consensus to a file just so that I could open it again
> and gain access to an AlignI object.
> 
> Here is my code.  Is there a slicker way to do this?

Without reading through your code, the way to create and AlignI
implementing object is useing Bio::SimpleAlign.

> 
> acetomsf.pl:
> 
> #!/usr/local/bin/perl -w
> #
> #
> use strict;
> use Bio::Assembly::IO;
> use Bio::AlignIO;
> use Bio::SeqIO;
> #
> my $usage = "Usage: $0 \n";
> my $infile = shift or die $usage;
> my $prefix = 'btcn';
> my $io = new Bio::Assembly::IO(-file=>$infile, -format=>'ace');
> my $assembly = $io->next_assembly;
> 
> foreach my $contig ($assembly->all_contigs()) {
>    my $contigName = $prefix.$contig->id;
> #  $contig->match();    # not yet implemented
> #
> # Write the consensus to a file.
> #
>    my $consensusSeq = new Bio::Seq(
>                         -seq=>$contig->get_consensus_sequence->seq,
>                         -id=>$prefix.$contig->id);
>    my $seqout = new Bio::SeqIO(-file=>">$contigName.fa", -format=>'fasta');
>    $seqout->write_seq($consensusSeq);
> #
> # Snarf the consensus back in so that we can create a Bio::Align::AlignI 
> object.
> #
>    my $instream  = new Bio::AlignIO(-format=>'fasta', 
>    -file=>"$contigName.fa");
>    my $outstream = new Bio::AlignIO(-format=>'msf', 
>    -file=>">$contigName.msf");
>    my $aln = $instream->next_aln();
> #
> # Loop through each sequence in the contig adding it to the new alignment.
> #
>    foreach my $seq ($contig->each_seq) {
> #
> # Some of the ACE starting locations are negative.
> #
>       if ($contig->get_seq_coord($seq)->start <= 0) {
>          my $offset = -$contig->get_seq_coord($seq)->start + 2;
>          $seq->seq($seq->subseq($offset,$seq->length));
>          print($seq->primary_id," was clipped at the beginning by 
>          $offset\n");
>          }
> #
> # Pad each sequence so it aligns with the consensus.
> #
>       my $before = $contig->get_seq_coord($seq)->start - 1;
>       my $after = $contig->get_consensus_length - 
>       $contig->get_seq_coord($seq)->end;
>       my $alignedSequence = '-' x $before . $seq->seq . '-' x $after;
> #
> # Some of the ACE ending locations go beyond the consensus.
> #
>       if (length($alignedSequence) > $contig->get_consensus_length) {
>          $alignedSequence = substr($alignedSequence, 1 
>          ,$contig->get_consensus_length);
>          print($seq->primary_id," was clipped at the end\n");
>          }
>       $seq->seq($alignedSequence);
>       $aln->add_seq($seq);
>       }
>    $aln->set_displayname_flat;
>    $outstream->write_aln($aln);
>    undef $outstream;
>    }
> 
> 
> -- 
> Wes Barris
> E-Mail: Wes.Barris@csiro.au
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 

-- 

----------------------------
| Josh Lauricha            |
| laurichj@bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|
From laurichj at bioinfo.ucr.edu  Fri Oct 31 12:54:11 2003
From: laurichj at bioinfo.ucr.edu (Josh Lauricha)
Date: Fri Oct 31 12:51:01 2003
Subject: [Bioperl-l] Bio::SeqIO::tigr
Message-ID: <20031031175411.GB18009@bioinfo.ucr.edu>

I've written a SeqIO parser for the tigr xml data format, and would like
to contribute it to BioPerl. However, there are a couple things I don't
really like about it but don't have the time to fix right now. Could I
get some feedback from the list regaurding each?

First, some background. Since each XML file is roughly 60MB, using the
XML parsers provided by TIGR (using XML::Simple and XML::Sax, IIRC)
takes around 7-10 minutes to parse (no including BioPerl object
creation) and occationally used more than ~2.5GB of memory, which an x86
can't handle.

To get around this, I took advantage of the fact that these are machine
generated and parsed the entire file using regexp, only storing what is
"relavent" to retrieve a sequence. This means, the ~75 lines of code
TIGR used is around 1280. However, it uses around 250MB of memory and
(converting from TIGR to GenBank) runs in around two to three and a half
minutes, 30-60% slower than GenBank -> GenBank convertion.

1) The code is pretty ugly. It was one of my first "large" perl projects
   and reflects that. The uglyness is partially due to my inexperiance
   at the time, and partially do to the ugliness of the problem.

2) Its not very well commented, ok its not commented. This isn't too big
   a problem, as everything acts basically the same way, and once
   someone understands that the rest is easy. (Its really just the same
   thing over and over). Its just fairly bad form.

3) The memory usage (and runtime) could be improved by one or more of:
   a) Storing everything directly into objects rather than a tree 
   b) Using arrays to store everything rather than hashes
   c) Ignoring any tags that aren't actually used.

4) The coding style is nothing like the rest of BioPerl's. Mainly
   because, I prefer this style (PERSONAL preference, no flames,
   everyone gets their own oppinion). This is bad for a project,
   but in all honesty if I need to drastically change my coding
   style I will probably never get around to fixing up this code.

5) There is quite a long delay before anything is actually accessible
   because the nucleotide data is given at the end of the files
   (actually, at the end of an ASSEMBLY tag) so everything before it
   needs to be parsed. This leads to the first ->next_seq() call taking
   a significant time.

Since I can't show you what the object looks like, I'll show you what
the GenBank file looks like. An example of the genbank file is at:

http://bioinfo.ucr.edu/cgi-bin/seqfetch.pl?database=all&accession=At1g03870

Thanks for your time,

-- 

----------------------------
| Josh Lauricha            |
| laurichj@bioinfo.ucr.edu |
| Bioinformatics, UCR      |
|--------------------------|
From jason at cgt.duhs.duke.edu  Fri Oct 31 13:41:08 2003
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Fri Oct 31 13:37:48 2003
Subject: [Bioperl-l] Glimmer
In-Reply-To: <20B7EB075F2D4542AFFAF813E98ACD9302822399@cl-exsrv1.irad.bbsrc.ac.uk>
References: <20B7EB075F2D4542AFFAF813E98ACD9302822399@cl-exsrv1.irad.bbsrc.ac.uk>
Message-ID: 

Bio::Tools::Glimmer

Only in CVS or or 1.3.x releases NOT in 1.2.x series.

-jason

On Fri, 31 Oct 2003, michael watson (IAH-C) wrote:

> Hi
>
> Does anyone have, or does there exist, any perl modules to parse and handle the output from glimmer?
>
> Thanks
>
> Michael Watson
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From hlapp at gnf.org  Fri Oct 31 14:10:08 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Fri Oct 31 14:06:58 2003
Subject: [Bioperl-l] gcg.pm, another one
In-Reply-To: <5.2.1.1.1.20031031153144.00b1f160@udcf.gla.ac.uk>
Message-ID: 

The SeqIO gcg parser was written for single-sequence gcg files.

In fact, the parser I think doesn't currently have a maintainer, so anyone
who is willing to become that is welcome. Since GCG has been commercialized
since many years, you'll not easily find people among the core who actively
use GCG, just to explain why there is no maintainer.

    -hilmar

On 10/31/03 7:40 AM, "Derek Gatherer"  wrote:

> Hello again
> 
> Last bug submitted to bugzilla.  The following may be a bug, but I wonder
> if there is a problem with my GCG format.
> 
> Try this script:
> 
> #!/usr/bin/perl -w
> 
> use lib "/usr/local/lib/site_perl/5.8.0/";
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> 
> my $dnain = Bio::SeqIO->new( '-format' => 'GCG' , -file => "cds.gcg");
> 
> while((my $seqobj = $dnain->next_seq()))
> {
>    $seqobj->display_id;
> }
> 
> on the file cds.gcg below.
> 
> to get:
> 
> ------------- EXCEPTION  -------------
> MSG: Looks like start of another sequence. See documentation.
> STACK Bio::SeqIO::gcg::next_seq
> /usr/local/lib/site_perl/5.8.0//Bio/SeqIO/gcg.pm:124
> STACK toplevel gcgtest.pl:10
> 
> The problem, I think, is that the SeqIO stream doesn't seem to recognise
> the change over from one sequence to another.  Or do I need some record
> separator between my sequences???  If this really is also a bug, I'll
> submit it too.
> 
> Offending line in gcg.pm is:
> 
> 124      if( /\.\.$/ ) {
>        $self->throw("Looks like start of another sequence. See
> documentation. ");
>       }
> 
> and here's the file cds.gcg, containing two sequences in GCG format
> 
> !!NA_SEQUENCE 1.0
> ASSEMBLE    October 27, 2003 15:32
> 
> Symbols:     1 to: 1269  from: merlin.seq /rev   ck: 8363, 55186 to: 56454
> 
> LOCUS       MERLIN                235645 bp    DNA     linear   VRL
> 14-AUG-2003
> DEFINITION  Human herpesvirus 5 strain Merlin, complete genome.
> ACCESSION   MERLIN
> VERSION
> KEYWORDS    .
> SOURCE      Human herpesvirus 5 . . .
> 
> merlin_ul43.cds  Length: 1269  October 27, 2003 15:32  Type: N  Check: 9039
> ..
> 
>       1  ATGGAGAAAA CGCCGGCGGA GACGACGGCG GTTTCAGCTG GCAACGTGCC
> 
>      51  ACGTGACTCA ATTCCGTGTA TAACTAACGT GTCCGCGGAC ACCCGCGGCC
> 
>     101  GTACCCGCCC CAGCAGACCA GCCACCGTCC CTCAGCGACG TCCCGCGCGG
> 
>     151  ATCGGACACT TTAGGCGGCG CAGCGCCAGC CTTAGCTTTC TTGACTGGCC
> 
>     201  GGACGACAGC GTCACAGAGG GCGTTCGGAC GACCTCCGCG TCGGTCGCCG
> 
>     251  CCTCCGCGGC CCGTTTCGAC GAAATCCGGC GGCGCCGCCA GAGCATCAAC
> 
>     301  GACGAGATGA AGGAACGCAC GCTGGAGGAC GCGCTGGCTG TCGAGCTGGT
> 
>     351  CAACGAGACC TTCCGCTGCT CTGTCACCTC CGACGCCCGC AAGGACTTGC
> 
>     401  AGAAGCTGGT TCGTCGCGTC AGCGGCACGG TGCTGCGTCT CAGCTGGCCA
> 
>     451  AACGGTTGGT TCTTCACCTA CTGCGACCTG TTACGCGTCG GCTACTTTGG
> 
>     501  ACATCTCAAT ATTAAAGGTT TGGAGAAGAC CTTCCTGTGC TGCGACAAGT
> 
>     551  TCTTGCTGCC GGTGGGCACT GTGAGTCGTT GCGAAGCCAT CGGCCGCCCA
> 
>     601  CCGCTACCCG TACTCATCGG CGAGGGCGGT CGCGTCTACG TCTACTCGCC
> 
>     651  TGTGGTGGAA TCGCTGTACC TGGTGTCGCG GTCCGGTTTC CGCGGCTTCG
> 
>     701  TGCAGGAGGG CCTGCGCAAC TACGCGCCGC TGCGCGAAGA ACTGGGCTAT
> 
>     751  GTCCGCTTCG AGACCGGCGG CGACGTGGGT CGCGAGTTCA TGTTGGCGCG
> 
>     801  CGACCTGCTG GCCCTGTGGC GCCTGTGCAT GAAGCGCGAG GGTTCTATCT
> 
>     851  TCAGCTGGCG AGACGGTAAC GAGGCGCTGA CGACGGTCGT CTTGAACGGG
> 
>     901  AGCCAGACTT ACGAGGATCC GGCCCACGGC AACTGGTTAA AAGAGACGTG
> 
>     951  CTCGCTGAAC GTGCTGCAGG TATTTGTGGT GCGGGCCGTG CCGGTGGAGT
> 
>    1001  CGCAGCAGCG CCTGGACATC TCCATACTGG TGAACGAGAG CGGCGCCGTC
> 
>    1051  TTCGGCGTGC ATCCCGATAC GCGGCAGGCG CACTTTCTGG CGCGCGGACT
> 
>    1101  CCTGGGCTTC TTTCGCGTCG GGTTCTTGCG GTTCTGCAAC AACTACTGCT
> 
>    1151  TCGCCCGCGA CTGTTTTACC CACCCTGAAA GCGTGGCACC CGCTTACCGC
> 
>    1201  GCCACCGGCT GTCCCAGAGA ACTGTTTTGT CGTCGTTTGC GCAAAAAGAA
> 
>    1251  GGGGCTCTTT GCTCGAAGG
> 
> !!NA_SEQUENCE 1.0
> ASSEMBLE    October 27, 2003 15:32
> 
> Symbols:     1 to: 2718  from: merlin.seq /rev   ck: 8363, 57946 to: 60663
> 
> LOCUS       MERLIN                235645 bp    DNA     linear   VRL
> 14-AUG-2003
> DEFINITION  Human herpesvirus 5 strain Merlin, complete genome.
> ACCESSION   MERLIN
> VERSION
> KEYWORDS    .
> SOURCE      Human herpesvirus 5 . . .
> 
> merlin_ul45.cds  Length: 2718  October 27, 2003 15:32  Type: N  Check: 4998
> ..
> 
>       1  ATGAATCCGG CTGACGCGGA CGAGGAACAG CGGGTGTCCT CGGTGCCCGC
> 
>      51  ACATCGGTGC CGGCCAGGTA GGATTCCAAG CCGCAGCGCG GAAACCGAGA
> 
>     101  CGGAGGAATC GTCGGCAGAG GTCGCCGCTG ATACTATCGG GGGAGATGAC
> 
>     151  AGCGAGCTCG AGGAGGGGCC GCTGCCCGGG GGTGACAAGG AAGCGTCCGC
> 
>     201  TGGAAATACC AACGTATCGA GCGGTGTAGC ATGTGTAGCG GGTTTTACGA
> 
>     251  GTGGTGGCGG CGTCGTCAGT TGGCGTCCCG AGTCGCCGTC TCCCGACGGC
> 
>     301  ACGCCGTCTG TGCTGTCGTT GACGCGTGAC AGCGGTCCCG CCGTGCCCAG
> 
>     351  TCGCGGTGGA CGCGTGAGTA GCGGTCTGAG CACCTTTAAT CCGGCCGGCG
> 
>     401  CGACCAGGAT GGAGCTGGAC AGTGTCGAGG AGGAGGACGA TTTCGGGGCT
> 
>     451  TCGCTCTGCA AAGTATCGCC GCCGATACAA GCTATGCGCA TGTTGATGGG
> 
>     501  CAAAAAGTGT CATTGTCACG GCTACTGGGG CAAGTTTCGC TTTTGCGGCG
> 
>     551  TACAGGAGCC GGCGCGGGAG CTGCCGTCCG ACAGGAACGC GCTGTGGCGC
> 
>     601  GAGATGGACA CCGTGTCGCG GCACAGTGCC GGTTTGGGCA GTTTCAGGCT
> 
>     651  ATTTCAGCTC ATTATGCGCC ACGGTCCCTG TCTGATTCGT CACTCGCCGC
> 
>     701  GTTGCGACCT GCTGTTGGGT CGCTTTTATT TCAAAGCCAA CTGGGCGCGT
> 
>     751  GAAAGCCGCA CGCCACTGTG TTACGCTTCG GAGCTGTGCG ATGAGTCGGT
> 
>     801  GCGCCGTTTT GTGCTGCGTC ACATGGAGGA TCTACCCAAG CTGGCCGAGG
> 
>     851  AGACGGCGCG TTTTGTGGAA TTGGCCGGTT GCTGGGGCTT GTACGCGGCC
> 
>     901  ATTTTGTGTT TGGATAAGGT GTGTCGCCAA CTGCACGGAC AGGACGAGAG
> 
>     951  CCCGGGCGGC GTGTTTTTGC GCATCGCCGT GGCGTTGACG GCCGCTATCG
> 
>    1001  AGAACAGTAG GCACTCGCGC ATCTATCGTT TCCATCTGGA TGCGCGTTTC
> 
>    1051  GAGGGCGAGG TGTTGGAATC GGTGTTGAAG CGCTGTCGCG ATGGGCAGCT
> 
>    1101  GTCGCTGTCC ACCTTCACCA TGTCTACCGT GGGTTTCGAT CGCGTGCCGC
> 
>    1151  AGTACGACTT TCTGATCTCG GCCGACCCTT TCTCGCGTGA CGCCAGTTGG
> 
>    1201  GCGGCCATGT GCAAGTGGAT GAGTACCTTG AGTTGCGGCG TTTCTGTGTC
> 
>    1251  GGTGAACGTA ACGCGACTTA ACGCCGATGT GAACAGCGTG ATTCGTTGCC
> 
>    1301  TGGGGGGATA CTGCGATTTG ATACGCGAGA AGGAGGTGCA TCGACCCGTG
> 
>    1351  GTACGTGTGT TTGTGGACAT GTGGGACGTG GCCGCTATCC GCGTGATTAA
> 
>    1401  CTTTATTCTC AAAGAAAGCA CGTCGGAGTT GACGGGGGTT TGCTACGCTT
> 
>    1451  TCAACGTGCC TAGCGTGTTA ATGAAGCGCT ACCGTGCGCG TGAGCAGCGC
> 
>    1501  TACTCGCTGT TTGGGCGGCC TGTCTCCCGG CGGCTCTCGG ACCTGGGTCA
> 
>    1551  GGAGTCGGCT TTCGAGAAAG AGTATTCGCG CTGCGAGCAA TCGTGCCCCA
> 
>    1601  AGGTGGTCGT GAACACGGAC GATTTTCTGA AAAAGATGTT GCTGTGCGCG
> 
>    1651  CTCAAGGGCC GTGCCTCGGT GGTCTTTGTC CATCACGTAG TCAAGTACTC
> 
>    1701  GATTATGGCC GACAGCGTGT GCCTGCCGCC GTGCTTGAGT CCCGATATGG
> 
>    1751  CGTCGTGCCA CTTTGGCGAG TGTGACATGC CGGTGCAGCG GCTGACGGTG
> 
>    1801  AACGTGGCTC GCTGCGTGTT TGCGCGTAGC GACGAGCAGA AGCTGCATCT
> 
>    1851  ACCCGACGTG GTTTTGGGGA ACACGCGACG TTACTTTGAT TTGAGCGTGC
> 
>    1901  TGCGCGAGTT GGTGACCGAG GCGGTGGTTT GGGGCAACGC GCGCTTGGAC
> 
>    1951  GCGCTAATGT CGGCGTCCGA ATGGTGGGTA GAGAGCGCGC TGGAAAAACT
> 
>    2001  GCGTCCGCTG CACATCGGCG TGGCTGGCTT GCACACGGCG CTCATGCGGT
> 
>    2051  TAGGGTTCAC GTACTTTGCC TCTTGGGACT TGATCGAGCG CATCTTTGAG
> 
>    2101  CACATGTACT TTGCCGCGGT GCGCGCTAGC GTCGATTTGT GCAAGTCGGG
> 
>    2151  TTTGCCGCGC TGCGAGTGGT TCGAACGCAC CATCTATCAA GAGGGCAAAT
> 
>    2201  TCATTTTCGA ATTGTATCGG TTGCCGCGGC TCTCCATCGC CAGCGCGCGC
> 
>    2251  TGGGAAGCGC TGCGCGCCGA CATGCTCGAG TTCGGATTGC GCAACTGTCA
> 
>    2301  GTTTCTGGCG GTGGGTCCCG ACGACGAGGT GGCGCATCTG TGGGGCGTGA
> 
>    2351  CGCCGTCAGT GTGGGCTTCG CGCGGCACCG TGTTCGAGGA GGAGACGGTG
> 
>    2401  TGGTCATTGT GCCCGCCCAA CCGTGAGTGT TACTTCCCCA CCGTGGTGCG
> 
>    2451  GAGGCCGCTG CGCGTGCCCG TGGTGAATTA CGCGTGGTTG GAGCAGCACC
> 
>    2501  AGGAGGAGGG CAAGGCGACG CAGTGTCTGT TCCAGGCGGC ACCGGCGATC
> 
>    2551  CAAAACGACG TGGAAATGGC GGCCGTGAAC CTGAGCGTGT TTGTGGACCA
> 
>    2601  GTGCGTGGCC CTGGTTTTCT ACTATGACTC GGGGATGACG CCCGACGTGC
> 
>    2651  TTCTGGCCAG GATGCTCAAG TGGTACCACT GGCGCTTTAA GGTCGGAGTA
> 
>    2701  TATAAGTACT GTGCCTCT
> 
> _______________________________________________
> 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 gnf.org  Fri Oct 31 14:11:38 2003
From: hlapp at gnf.org (Hilmar Lapp)
Date: Fri Oct 31 14:08:26 2003
Subject: [Bioperl-l] gcg.pm
In-Reply-To: <5.2.1.1.1.20031031120319.00af7328@udcf.gla.ac.uk>
Message-ID: 

On 10/31/03 4:13 AM, "Derek Gatherer"  wrote:

> Otherwise, you get:
> 
> Use of uninitialized value in concatenation (.) or string at
> /usr/local/lib/site_perl/5.8.0//Bio/SeqIO/gcg.pm line 197,
> 
> The offending line in gcg.pm is:

This is just a warning, and the line has no detrimental effects. So as for
your code, you can safely ignore it.

I still agree with Jason to file a bug report. Or better yet, submit a patch
along with it if you have one ...

    -hilmar
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------



From paul.boutros at utoronto.ca  Fri Oct 31 15:59:00 2003
From: paul.boutros at utoronto.ca (paul.boutros@utoronto.ca)
Date: Fri Oct 31 15:57:07 2003
Subject: [Bioperl-l] Re: RemoteBlast
Message-ID: <1067633940.3fa2cd147b189@webmail.utoronto.ca>

>I'd be willing to volunteer for maintaining RemoteBlast if there are no
>other takers, I've used it quite a bit so I guess should try and put
>something back .
>
>Just from first thoughts I'd plan to
>
>- incorporate Megablast / Blast2seqs /rpsblast functionality
>-separate out the form submission bits of code from the Blast specific
>code in the module, perhaps by inheriting
>    from Bio::WebAgent.
>
>Other than making sure that the output is parseable by Bio::SearchIO,
>are there any strong feelings for  how new features should be
>implemented?
>
>If anyone has requests/ideas fornew functionality please say so!
>

Hi,

I started doing some modifications myself, and I'd be happy to help you if I 
can.  I have a version with Megablast enabled, as well as with additional 
set/get functions for parameters.

One thing that would be really nice: to have a standardized interface for both 
StandAloneBlast and RemoteBlast.  Perhaps that could be done with a new class, 
BlastInterfaceI?  Not sure.  I'm attaching my version below.  I've meant to 
post this here, but I've been procrastinating on adding to the test suite....

Paul

###Begin Code
# $Id: RemoteBlast.pm,v 1.14.2.1 2003/03/25 12:32:17 heikki Exp $
#
# BioPerl module for Bio::Tools::Run::RemoteBlast
#
# Cared for by Jason Stajich, Mat Wiepert
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast
via HTTP

=head1 SYNOPSIS

  #Remote-blast "factory object" creation and blast-parameter initialization

  use Bio::Tools::Run::RemoteBlast;
  use strict;
  my $prog   = 'blastp';
  my $db     = 'swissprot';
  my $e_val  = '1e-10';
  my $matrix = 'BLOSUM62';

  my @params = (
         '-prog'       => $prog,
         '-data'       => $db,
         '-expect'     => $e_val,
         '-readmethod' => 'SearchIO',
         '-matrix'     => $matrix
         );

  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

  # Methods exist to change many parameters.  A full listing of 
  # available parameters is at:
  # http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

  # For example, one interesting feature of QBlast is that allows filtering
  # of results by expectation value.  For instance:
  $factory->expect_low(1e-30);
  $factory->expect_high(1e-10);
  # retrieves only results where the expected number of hits by chance
  # in the database would be between 1 and 10.  Note that this filtering
  # is done after the BLAST is run, but before results are returned.

  # One can also limit the number of alignments returned:
  $factory->alignments(20);

  # Some CGI parameters can only be changed directly, for instance
  $Bio::Tools::Run::RemoteBlast::HEADER{'PERC_IDENT'} = 97;

  # Parameters can also be removed in this way:
  delete $Bio::Tools::Run::RemoteBlast::HEADER{'PERC_IDENT'};

  my $v = 1;
  #$v is just to turn on and off the messages

  my $str = Bio::SeqIO->new(-file=>'amino.fa' , '-format' => 'fasta' );

  while (my $input = $str->next_seq()){
    #Blast a sequence against a database:

    #Alternatively, you could  pass in a file with many
    #sequences rather than loop through sequence one at a time
    #Remove the loop starting 'while (my $input = $str->next_seq())'
    #and swap the two lines below for an example of that.
    my $r = $factory->submit_blast($input);
    #my $r = $factory->submit_blast('amino.fa');

    print STDERR "waiting..." if( $v > 0 );
    while ( my @rids = $factory->each_rid ) {
      foreach my $rid ( @rids ) {
        my $rc = $factory->retrieve_blast($rid);
        if( !ref($rc) ) {
          if( $rc < 0 ) {
            $factory->remove_rid($rid);
          }
          print STDERR "." if ( $v > 0 );
          sleep 5;
        } else {
          my $result = $rc->next_result();
          #save the output
          my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
          $factory->remove_rid($rid);
          print "\nQuery Name: ", $result->query_name(), "\n";
          while ( my $hit = $result->next_hit ) {
            next unless ( $v > 0);
            print "\thit name is ", $hit->name, "\n";
            while( my $hsp = $hit->next_hsp ) {
              print "\t\tscore is ", $hsp->score, "\n";
            }
          }
        }
      }
    }
  }



=head1 DESCRIPTION

Class for remote execution of the NCBI Blast via HTTP.

For a description of the many CGI parameters see:
http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html

Various additional options and input formats are available.

=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://bio.perl.org/MailList.html   - 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:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

=head1 AUTHOR -  Jason Stajich

Email jason@bioperl.org

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut

package Bio::Tools::Run::RemoteBlast;

use vars qw($AUTOLOAD @ISA $URLBASE %HEADER %RETRIEVALHEADER $RIDLINE);
use strict;

use Bio::Root::Root;
use Bio::Root::IO;
use Bio::SeqIO;
use IO::String;
use Bio::Tools::BPlite;
use Bio::SearchIO;
use LWP;
use HTTP::Request::Common;
BEGIN {
    $URLBASE = 'http://www.ncbi.nlm.nih.gov/blast/Blast.cgi';
    %HEADER = (
               'CMD'                          => 'Put',
	       'PROGRAM'                      => 'blastp',
	       'DATABASE'                     => 'nr',
	       'FILTER'                       => 'L',
	       'EXPECT'                       => '1e-3',
	       'QUERY'                        =>  '',
	       'CDD_SEARCH'                   => 'off',
	       'COMPOSITION_BASED_STATISTICS' => 'no',
	       'SERVICE'                      => 'plain',
	       );

    %RETRIEVALHEADER = (
                 'CMD'            => 'Get',
		 'RID'            => '',
		 'ALIGNMENT_VIEW' => 'Pairwise',
		 'DESCRIPTIONS'   => 500,
		 'ALIGNMENTS'     => 500,
		 'FORMAT_TYPE'    => 'Text',
                 'FORMAT_OBJECT'  => 'Alignment',
                 'SERVICE'        => 'plain',
                  );

    $RIDLINE = 'RID\s+=\s+(\S+)';

}

@ISA = qw(Bio::Root::Root Bio::Root::IO);

sub new {
    my ($caller, @args) = @_;
    # chained new
    my $self = $caller->SUPER::new(@args);
    # so that tempfiles are cleaned up
    $self->_initialize_io();
    my ($prog, $program, $data, $database, $expect, $alignments, $service, 
$format_object, 
	$hitlist_size, $word_size, $auto_format, $matrix_name, $megablast, 
$filter,
        $descriptions, $expect_low, $expect_high, $entrez_query, $gapcosts, 
$nucl_penalty,
        $nucl_reward, $readmethod) =
            $self->_rearrange([
                               qw(PROG
                                  PROGRAM
                                  DATA
                                  DATABASE
				  EXPECT
                                  ALIGNMENTS
                                  SERVICE
                                  FORMAT_OBJECT
                                  HITLIST_SIZE
                                  WORD_SIZE
                                  AUTO_FORMAT
                                  MATRIX_NAME
                                  MEGABLAST
                                  FILTER
                                  DESCRIPTIONS
                                  EXPECT_LOW
                                  EXPECT_HIGH
                                  ENTREZ_QUERY
                                  GAPCOSTS
                                  NUCL_PENALTY
                                  NUCL_REWARD
				  READMETHOD)
                              ], @args);
	
    $readmethod = 'SearchIO' unless defined $readmethod;
    $self->readmethod($readmethod);
    $self->program($prog);
    $self->program($program);	# allow -program as alias for -prog
    $self->database($data);
    $self->database($database);	# allow -database as alias for -data
    $self->expect($expect);
    $self->alignments($alignments);
    $self->service($service);
    $self->format_object($format_object);
    $self->hitlist_size($hitlist_size);
    $self->word_size($word_size);
    $self->auto_format($auto_format);
    $self->matrix_name($matrix_name);
    $self->megablast($megablast);
    $self->filter($filter);
    $self->descriptions($descriptions);
    $self->expect_low($expect_low);
    $self->expect_high($expect_high);
    $self->entrez_query($entrez_query);
    $self->gapcosts($gapcosts);
    $self->nucl_penalty($nucl_penalty);
    $self->nucl_reward($nucl_reward);

    return $self;
}


=head2 header

 Title   : header
 Usage   : my $header = $self->header
 Function: Get/Set HTTP header for blast query
 Returns : string
 Args    : none

=cut

sub header {
    my ($self) = @_;
    my %h = %HEADER;
    $h{'PROGRAM'} = $self->program;
    $h{'DATABASE'} = $self->database;
    $h{'EXPECT'}  = $self->expect;
    return %h;
}


=head2 readmethod

 Title   : readmethod
 Usage   : my $readmethod = $self->readmethod
 Function: Get/Set the method to read the blast report
 Returns : string
 Args    : string [ Blast, BPlite ]

=cut

sub readmethod {
    my ($self, $val) = @_;
    if( defined $val ) {
	$self->{'_readmethod'} = $val;
    }
    return $self->{'_readmethod'};
}


=head2 program

 Title   : program
 Usage   : my $prog = $self->program
 Function: Get/Set the program to run
 Returns : string
 Args    : string [ blastp, blastn, blastx, tblastn, tblastx ]

=cut

sub program {
    my ($self, $val) = @_;
    if( defined $val ) {
	$val = lc $val;
	if( $val !~ /t?blast[pnx]/ ) {
	    $self->warn("trying to set program to an invalid program name 
($val) -- defaulting to blastp");
	    $val = 'blastp';
	}
#	$self->{'_program'} = $val;
	$HEADER{'PROGRAM'} = $val;
    }
    return $HEADER{'PROGRAM'};
}


=head2 database

 Title   : database
 Usage   : my $db = $self->database
 Function: Get/Set the database to search
 Returns : string
 Args    : string [ swissprot, nr, nt, etc... ]

=cut

sub database {
    my ($self, $val) = @_;
    if( defined $val ) {
#	$self->{'_database'} = $val;
 	$HEADER{'DATABASE'} = $val;
    }
    return $HEADER{'DATABASE'};
}


=head2 expect

 Title   : expect
 Usage   : my $expect = $self->expect
 Function: Get/Set the E value cutoff
 Returns : string
 Args    : string [ '1e-4' ]

=cut

sub expect {
    my ($self, $val) = @_;
    if( defined $val ) {
#	$self->{'_expect'} = $val;
 	$HEADER{'EXPECT'} = $val;
    }
    return $HEADER{'EXPECT'};
}


=head2 format_object

 Title   : format_object
 Usage   : my $format_object = $self->format_object
           $self->format_object($value)
 Function: Get/Set the object-type to be retrieved
 Returns : string
 Args    : string [Alignment, Neighbors, PSSM, etc.]

=cut

sub format_object {
	my ($self, $val) = @_;
	if (defined($val)) {
		$RETRIEVALHEADER{'FORMAT_OBJECT'} = $val;
		}
	return $RETRIEVALHEADER{'FORMAT_OBJECT'};
	}


=head2 service

 Title   : service
 Usage   : my $service = $self->service
           $self->service($value)
 Function: Get/Set the NCBI Blast service to be used
 Returns : string
 Args    : string [plain, psi, phi, rpsblast, megablast]

=cut

sub service {
	my ($self, $val) = @_;
	if (defined($val)) {
		$HEADER{'SERVICE'} = $val;
                $RETRIEVALHEADER{'SERVICE'} = $val;
		}
	return $HEADER{'SERVICE'};
	}


=head2 alignments

 Title   : alignments
 Usage   : my $alignments = $self->alignments
           $self->alignments($value)
 Function: Get/Set the number of alignments to be returned
 Returns : integer
 Args    : integer (default: 500)

=cut

sub alignments {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^(\d+)$/) {
		$RETRIEVALHEADER{'ALIGNMENTS'} = $1;
		}
	return $RETRIEVALHEADER{'ALIGNMENTS'};
	}


=head2 hitlist_size

 Title   : hitlist_size
 Usage   : my $hitlist_size = $self->hitlist_size
 Function: Get/Set the number of hits to be returned
 Returns : integer
 Args    : integer (default: 500)

=cut

sub hitlist_size {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^(\d+)$/) {
		$HEADER{'HITLIST_SIZE'} = $1;
		}
	return $HEADER{'HITLIST_SIZE'};
	}


=head2 word_size

 Title   : word_size
 Usage   : my $word_size = $self->word_size
           $self->word_size($value)
 Function: Get/Set the BLAST word-size for HSP generation
 Returns : integer
 Args    : integer (default: protein-3; nucleotide-11; megablast-28)

=cut

sub word_size {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^(\d+)$/) {
		$HEADER{'WORD_SIZE'} = $1;
		}
	return $HEADER{'WORD_SIZE'};
	}


=head2 auto_format

 Title   : auto_format
 Usage   : my $auto_format = $self->auto_format
           $self->auto_format($value)
 Function: Get/Set the flag for automatic result formatting
 Returns : string
 Args    : string (Values: Off (default), Semiauto, Fullauto)

=cut

sub auto_format {
	my ($self, $val) = @_;
	if (defined($val)) {
		$HEADER{'AUTO_FORMAT'} = $val;
		}
	return $HEADER{'AUTO_FORMAT'};
	}


=head2 matrix_name

 Title   : matrix_name
 Usage   : my $matrix_name = $self->matrix_name
           $self->matrix_name($value)
 Function: Get/Set the name of the substitution matrix used (protein only)
 Returns : string
 Args    : string (Default: BLOSUM62)

=cut

sub matrix_name {
	my ($self, $val) = @_;
	if (defined($val)) {
		$HEADER{'MATRIX_NAME'} = $val;
		}
	return $HEADER{'MATRIX_NAME'};
	}


=head2 megablast

 Title   : megablast
 Usage   : my $megablast = $self->megablast
           $self->megablast($value)
 Function: Flag to indicate if the MegaBLAST algorithm should be used
 Returns : string
 Args    : string (Values: 'yes', 'no' (default))

=cut

sub megablast {
	my ($self, $val) = @_;
	if (defined($val)) {
		$HEADER{'MEGABLAST'} = $val;
		}
	return $HEADER{'MEGABLAST'};
	}


=head2 filter

 Title   : filter
 Usage   : my $filter = $self->filter
           $self->filter($value)
 Function: Sequence filter identifier
 Returns : string
 Args    : string
 Values  : 'L'  for low-complexity (default)
           'R'  for human repeats
           'm'  for Mask for Lookup
           'no' to turn off

=cut

sub filter {
	my ($self, $val) = @_;
	if (defined($val) && ($val eq 'L' || $val eq 'R' || $val eq 'm' || 
$val eq 'no')) {
                if ($val eq 'no') {
		      $HEADER{'FILTER'} = '';
                      }
                else {
                      $HEADER{'FILTER'} = $val;
                      }
		}
	return $HEADER{'FILTER'};
	}


=head2 descriptions

 Title   : descriptions
 Usage   : my $descriptions = $self->descriptions
           $self->descriptions($value)
 Function: Specify number of descriptions to be returned
 Returns : integer
 Args    : integer (Default: 500)

=cut

sub descriptions {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^(\d+)$/) {
	      $RETRIEVALHEADER{'DESCRIPTIONS'} = $1;
		}
	return $RETRIEVALHEADER{'DESCRIPTIONS'};
	}


=head2 expect_low

 Title   : expect_low
 Usage   : my $expect_low = $self->expect_low
           $self->expect_low($value)
 Function: Minimum expectation value returned
 Returns : double-type value
 Args    : double-type value (Default: 0)

=cut

sub expect_low {
	my ($self, $val) = @_;
	if (defined($val)) {
	      $RETRIEVALHEADER{'EXPECT_LOW'} = $val;
		}
	return $RETRIEVALHEADER{'EXPECT_LOW'};
	}


=head2 expect_high

 Title   : expect_high
 Usage   : my $expect_high = $self->expect_high
           $self->expect_high($value)
 Function: Maximum expectation value returned
 Returns : double-type value
 Args    : double-type value (Default: 0)

=cut

sub expect_high {
	my ($self, $val) = @_;
	if (defined($val)) {
	      $RETRIEVALHEADER{'EXPECT_HIGH'} = $val;
		}
	return $RETRIEVALHEADER{'EXPECT_HIGH'};
	}


=head2 entrez_query

 Title   : entrez_query
 Usage   : my $entrez_query = $self->entrez_query
           $self->entrez_query($value)
 Function: An Entrez query to use in limiting searches
 Returns : string
 Args    : string (Default: empty)

=cut

sub entrez_query {
	my ($self, $val) = @_;
	if (defined($val)) {
	      $HEADER{'ENTREZ_QUERY'} = $val;
		}
	return $HEADER{'ENTREZ_QUERY'};
	}


=head2 gapcosts

 Title   : gapcosts
 Usage   : my $gapcosts = $self->gapcosts
           $self->gapcosts($value)
 Function: Scoring cost for opening and extending gaps in alignments
 Returns : Two space-separated floats (open, extend)
 Args    : Two space-separated floats (open, extend)
 Default : nucleotide   5 + 2x
           protein     11 +  x
           megablast   non-affine

=cut

sub gapcosts {
	my ($self, $val) = @_;

	if (defined($val)) {

		my $flag = 1;

		my @costs = split(/ /, $val);

		if (scalar(@costs) != 2) { # require only two values
			$flag = 0;
			}

		foreach my $cost (@costs) {
			$cost =~ s/^\s+//;
			$cost =~ s/\s+$//;

			# require +ve integers or floats
			if (($cost !~ /^\d+$/) && ($cost !~ /^\d+\.\d+$/)) {
				$flag = 0;
				}

			}

		if ($flag == 1) {
			$HEADER{'GAPCOSTS'} = join(' ', @costs);
			}

		}

	return $HEADER{'GAPCOSTS'};

	}


=head2 nucl_penalty

 Title   : nucl_penalty
 Usage   : my $nucl_penalty = $self->nucl_penalty
           $self->nucl_penalty($value)
 Function: Negative score assigned to nucleotide mismatches (BLASTN)
 Returns : -ve integer
 Args    : -ve integer

=cut

sub nucl_penalty {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^-\d+$/) {
	      $HEADER{'NUCL_PENALTY'} = $val;
		}
	return $HEADER{'NUCL_PENALTY'};
	}


=head2 nucl_reward

 Title   : nucl_reward
 Usage   : my $nucl_reward = $self->nucl_reward
           $self->nucl_reward($value)
 Function: Positive score assigned to a nucleotide match (BLASTN)
 Returns : +ve integer
 Args    : +ve integer

=cut

sub nucl_reward {
	my ($self, $val) = @_;
	if (defined($val) && $val =~ /^(\d+)$/) {
              if ($val > 0) { $HEADER{'NUCL_REWARD'} = $val; }
              }
	return $HEADER{'NUCL_REWARD'};
	}


=head2 ua

 Title   : ua
 Usage   : my $ua = $self->ua or
           $self->ua($ua)
 Function: Get/Set a LWP::UserAgent for use
 Returns : reference to LWP::UserAgent Object
 Args    : none
 Comments: Will create a UserAgent if none has been requested before.

=cut

sub ua {
    my ($self, $value) = @_;
    if( ! defined $self->{'_ua'} ) {
	$self->{'_ua'} = new LWP::UserAgent;
    }
    return $self->{'_ua'};
}


=head2 proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy
 Returns : a string indicating the proxy
 Args    : $protocol : an array ref of the protocol(s) to set/get
           $proxyurl : url of the proxy to use for the specified protocol

=cut

sub proxy {
    my ($self,$protocol,$proxy) = @_;
    return undef if ( !defined $self->ua || !defined $protocol
		      || !defined $proxy );
    return $self->ua->proxy($protocol,$proxy);
}


sub add_rid {
    my ($self, @vals) = @_;
    foreach ( @vals ) {
	$self->{'_rids'}->{$_} = 1;
    }
    return scalar keys %{$self->{'_rids'}};
}


sub remove_rid {
    my ($self, @vals) = @_;
    foreach ( @vals ) {
	delete $self->{'_rids'}->{$_};
    }
    return scalar keys %{$self->{'_rids'}};
}


sub each_rid {
    my ($self) = @_;
    return keys %{$self->{'_rids'}};
}


=head2 submit_blast

 Title   : submit_blast
 Usage   : $self->submit_blast([$seq1,$seq2]);
 Function: Submit blast jobs to ncbi blast queue on sequence(s)
 Returns : Blast report object as defined by $self->readmethod
 Args    : input can be:
           * sequence object
           * array ref of sequence objects
           * filename of file containing fasta formatted sequences

=cut

sub submit_blast {
    my ($self, $input) = @_;
    my @seqs = $self->_load_input($input);
    return 0 unless ( @seqs );
    my $tcount = 0;
    my %header = $self->header;
    foreach my $seq ( @seqs ) {
	#If query has a fasta header, the output has the query line.
	$header{'QUERY'} = ">".(defined $seq->display_id() ? $seq->display_id
() : "").
		" ".(defined $seq->desc() ? $seq->desc() : "")."\n".$seq->seq
();
	my $request = POST $URLBASE, [%header];
	$self->warn($request->as_string) if ( $self->verbose > 0);
	my $response = $self->ua->request( $request);

	if( $response->is_success ) {
	    if( $self->verbose > 0 ) {
		my ($tempfh) = $self->tempfile();
		# Hmm, what exactly are we trying to do here?
		print $tempfh $response->content;
		close($tempfh);
		undef $tempfh;
	    }
	    my @subdata = split(/\n/, $response->content );
	    my $count = 0;
	    foreach ( @subdata ) {
		if( /$RIDLINE/ ) {
		    $count++;
		    print STDERR $_ if( $self->verbose > 0);
		    $self->add_rid($1);		
		    last;
		}	
	    }
	    if( $count == 0 ) {
		$self->warn("req was ". $request->as_string() . "\n");
		$self->warn(join('', @subdata));
	    }    	
	    $tcount += $count;
	} else {
	    # should try and be a little more verbose here
	    $self->warn("req was ". $request->as_string() . "\n" .
			$response->error_as_HTML);
	    $tcount = -1;
	}
    }
    return $tcount;
}


=head2 retrieve_blast

 Title   : retrieve_blast
 Usage   : my $blastreport = $blastfactory->retrieve_blast($rid);
 Function: Attempts to retrieve a blast report from remote blast queue
 Returns : -1 on error,
           0 on 'job not finished',
           Bio::Tools::BPlite or Bio::Tools::Blast object
           (depending on how object was initialized) on success
 Args    : Remote Blast ID (RID)

=cut

sub retrieve_blast {
    my($self, $rid) = @_;
    my (undef,$tempfile) = $self->tempfile();
    my %hdr = %RETRIEVALHEADER;
    $hdr{'RID'} = $rid;
    my $req = POST $URLBASE, [%hdr];
    if( $self->verbose > 0 ) {
	$self->warn("retrieve request is " . $req->as_string());
    }
    my $response = $self->ua->request($req, $tempfile);
    if( $self->verbose > 0 ) {
	open(TMP, $tempfile) or $self->throw("cannot open $tempfile");
	while() { print $_; }
	close TMP;
    }
    if( $response->is_success ) {	
	my $size = -s $tempfile;
	if( $size > 1000 ) {
	    my $blastobj;
	    if( $self->readmethod =~ /BPlite/ ) {
		$blastobj = new Bio::Tools::BPlite(-file => $tempfile);
	    } else {
		$blastobj = new Bio::SearchIO(-file => $tempfile,
					      -format => 'blast');
	    }
	    #save tempfile
	    $self->file($tempfile);
	    return $blastobj;
	} elsif( $size < 500 ) { # search had a problem
	    open(ERR, "<$tempfile") or $self->throw("cannot open file 
$tempfile");
	    $self->warn(join("", ));
	    close ERR;
	    return -1;
	} else { # still working
	    return 0;
	}
    } else {
	$self->warn($response->error_as_HTML);
	return -1;
    }
}


=head2 save_output

 Title   : saveoutput
 Usage   : my $saveoutput = $self->save_output($filename)
 Function: Method to save the blast report
 Returns : 1 (throws error otherwise)
 Args    : string [rid, filename]

=cut

sub save_output {
    my ($self, $filename) = @_;
    if( ! defined $filename ) {
        	$self->throw("Can't save blast output.  You must specify a filename to 
save to.");
    }
    #should be set when retrieving blast
   	my $blastfile = $self->file;
   	#open temp file and output file, have to filter out some HTML
	open(TMP, $blastfile) or $self->throw("cannot open $blastfile");
	open(SAVEOUT, ">$filename") or $self->throw("cannot open $filename");
	my $seentop=0;
	while() {
		next if (/
/);	
		if( /^(?:[T]?BLAST[NPX])\s*.+$/i ||
	   		/^RPS-BLAST\s*.+$/i ) {
	   		$seentop=1;
	   	}
	   	next if !$seentop;
	    if( $seentop ) {
			print SAVEOUT;
		}
	}
	close SAVEOUT;
	close TMP;
	return 1;	
}


sub _load_input {
    my ($self, $input) = @_;

    if( ! defined $input ) {
	$self->throw("Calling remote blast with no input");	
    }
    my @seqs;
    if( ! ref $input ) {
	if( -e $input ) {
	    my $seqio = new Bio::SeqIO(-format => 'fasta', -file => $input);
	    while( my $seq = $seqio->next_seq ) {
		push @seqs, $seq;
	    }
	} else {
	    $self->throw("Input $input was not a valid filename");
	}	
    } elsif( ref($input) =~ /ARRAY/i ) {
	foreach ( @$input ) {
	    if( ref($_) && $_->isa('Bio::PrimarySeqI') ) {
		push @seqs, $_;
	    } else {
		$self->warn("Trying to add a " . ref($_) .
			    " but expected a Bio::PrimarySeqI");
	    }
	}
	if( ! @seqs) {
	    $self->throw("Did not pass in valid input -- no sequence objects 
found");
	}
    } elsif( $input->isa('Bio::PrimarySeqI') ) {
	push @seqs, $input;
    }
    return @seqs;
}
1;
__END__

###End Code


From allenday at ucla.edu  Fri Oct 31 20:29:43 2003
From: allenday at ucla.edu (Allen Day)
Date: Fri Oct 31 20:26:33 2003
Subject: [Bioperl-l] OMIM tests failing
Message-ID: 

any idea what's going on here?  i see some recent commits (yesterday, 
first in 7 months) by juguang.  it worked two days ago...

-allen

[5:27pm]allenday@sumo:/raid5a/allenday/cvsroot/bioperl-live> make 
test_OMIMentry
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e 
'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' 
t/OMIMentry.t
t/OMIMentry....ok 5/145                                                      
------------- EXCEPTION  -------------
MSG: a hash referenced needed
STACK Bio::Phenotype::OMIM::OMIMentry::clinical_symptoms 
blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm:537
STACK toplevel t/OMIMentry.t:60

--------------------------------------
t/OMIMentry....dubious                                                       
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 17-145
        Failed 129/145 tests, 11.03% okay
Failed Test   Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/OMIMentry.t  255 65280   145  129  88.97%  17-145
Failed 1/1 test scripts, 0.00% okay. 129/145 subtests failed, 11.03% okay.
make: *** [test_OMIMentry] Error 2
[5:27pm]allenday@sumo:/raid5a/allenday/cvsroot/bioperl-live> make 
test_OMIMentryAllelicVariant
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e 
'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' 
t/OMIMentryAllelicVariant.t
t/OMIMentryAllelicVariant....ok                                              
All tests successful.
Files=1, Tests=26,  0 wallclock secs ( 0.14 cusr +  0.01 csys =  0.15 CPU)
[5:28pm]allenday@sumo:/raid5a/allenday/cvsroot/bioperl-live> make 
test_OMIMparser
PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib 
-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e 
'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' 
t/OMIMparser.t
t/OMIMparser....ok 1/173                                                     
------------- EXCEPTION  -------------
MSG: a part/organism must be assigned
STACK Bio::Phenotype::OMIM::OMIMentry::add_clinical_symptoms 
blib/lib/Bio/Phenotype/OMIM/OMIMentry.pm:567
STACK Bio::Phenotype::OMIM::OMIMparser::_finer_parse_symptoms 
blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:550
STACK Bio::Phenotype::OMIM::OMIMparser::_createOMIMentry 
blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:531
STACK Bio::Phenotype::OMIM::OMIMparser::next_phenotype 
blib/lib/Bio/Phenotype/OMIM/OMIMparser.pm:272
STACK toplevel t/OMIMparser.t:31

--------------------------------------
t/OMIMparser....dubious                                                      
        Test returned status 25 (wstat 6400, 0x1900)
DIED. FAILED tests 2-173
        Failed 172/173 tests, 0.58% okay
Failed Test    Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/OMIMparser.t   25  6400   173  172  99.42%  2-173
Failed 1/1 test scripts, 0.00% okay. 172/173 subtests failed, 0.58% okay.
make: *** [test_OMIMparser] Error 2
[5:28pm]allenday@sumo:/raid5a/allenday/cvsroot/bioperl-live>