[Bioperl-l] problem with pir sequence

[sebastien.frade at bayercropscience.com]

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