[Bioperl-l] problem with pir sequence

[Jason Stajich]

pir support is pretty minimal - you'll have to send a copy of the original
seq file for someone to see if they can help.


On Tue, 27 Jan 2004 sebastien.frade at bayercropscience.com wrote:

>
>
>
>
> Hi,
>
> I'ma working with pir files, and i have a problem during reading file with
> bioperl.
>
> here is the code,
>
>
>
> use strict;
>
> use Bio::SeqIO;
>
> my $filename="deux.S64";
>
> print new Bio::Tools::GuessSeqFormat( -file => $filename )->guess,"\n";
>
>
> my $in  = Bio::SeqIO->new(-file => $filename , '-format' => 'pir');
> my $seq;
>
> while ($seq = $in->next_seq() ) {
>   print "Sequence ",$seq->id," first 10 bases ",$seq->subseq(1,10),"\n";
> }
>
>
> and here is the error message
>
> -------------------- WARNING ---------------------
> MSG: seq doesn't validate, mismatch is 1
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: Attempting to set the sequence to
> [N;Alternatenames:albumin2SprecursorC;Species:BertholletiaexcelsaBrazilnutC;Date:21-Nov-1993#sequence_revision26-May-1995#text_change21-Jul-2000C;Accession:S14946;S14479;S06252;S21640;B25802R;GanderES;HolmstroemKO;dePaivaGR;deCastroLAB;CarneiroM;GrossideSaMFPlantMolBiol16437-4481991A;Title:Isolationcharacterizationandexpressionofagenecodingfora2SalbuminfromBertholletiaexcelsaBrazilnutA;Referencenumber:S14946;MUID:91370890;PMID:1840683A;Accession:S14946A;Status:preliminaryA;Moleculetype:DNAA;Residues:1-146<GAN]
>  which does not look healthy
> STACK Bio::PrimarySeq::seq /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/PrimarySeq.pm:268
> STACK Bio::PrimarySeq::new /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/PrimarySeq.pm:217
> STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.8.0/Bio/Seq.pm:498
> STACK Bio::Seq::SeqFactory::create /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/Seq/SeqFactory.pm:126
> STACK Bio::SeqIO::pir::next_seq /usr/local/lib/perl5/site_perl/5.8.0
> /Bio/SeqIO/pir.pm:122
> STACK toplevel pir.pl:15
>
>
> Is there a problem with my code ?
>
> Please help me!!!
>
>
>
>
>
>
>
> Sébastien Frade
> BioInformatic Team
> BAYER CropScience / BioScience
> 4 rue Pierre FONTAINE
> 91058 EVRY – France
>
>  tel:                                     33 (0) 1 69 47 61 52
>
>  fax:                                     33 (0) 1 69 47 61 42
>
>  mail:
>                                          sebastien.frade at bayercropscience.com
>
>  http://bioinfo.evry.fr.bayercropscience
>
>
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>

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