[Bioperl-l] get cds from genbank record

[Heikki Lehvaslaiho]

Perdo,

It should work again if you spesify the sequence format for the output:

  my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa", -format => 'fasta');

It should have been spesified even before 1.4, I an surprised that it worked 
without it.

	-Heikki


On Thursday 15 Jan 2004 20:35, Pedro Antonio Reche wrote:
> !/usr/sbin/perl -w
> #use strict;
> use Bio::SeqIO;
> use Bio::Seq;
>
>
> my $in = new Bio::SeqIO(-file => "$ARGV[0]", -format => 'genbank');
> my $out = new Bio::SeqIO(-file => ">$ARGV[0].tfa");
>
> while( my $seq = $in->next_seq ) {
>
>     foreach my $f ( grep { $_->primary_tag eq 'CDS' }
>        $seq->top_SeqFeatures ) {
>     my ($gname);
>     if( $f->has_tag('gene') ) {
>         ($gname) = $f->each_tag_value('gene');
>     } elsif( $f->has_tag('product') ) {
>         ($gname) = $f->each_tag_value('product');
>     }
>
>     my ($ref) = $f->has_tag('protein_id') &&
> $f->each_tag_value('protein_id');
>     my ($gi)  = $f->has_tag('db_xref') && $f->each_tag_value('db_xref');
>
>     my ($translation) = $f->has_tag('translation') &&
>                           $f->each_tag_value('translation');
>
>     unless( $gi && $ref && $gname && $translation ) {
>       print STDERR "not fully annotated CDS ($gi,$ref,$gname),
> skipping...\n";
>       next;
>     }
>     my $outseq = Bio::PrimarySeq->new(-seq => $translation,
>                                       -display_id =>
>             sprintf("gi|%s|gb|%s|%s",$gi,$gname,$ref));
>     $out->write_seq($outseq);
>   }

-- 
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      _/      _/                      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
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