[Bioperl-l] parse cds and peptide from genbank file with identifier

Guoqi4 at aol.com Guoqi4 at aol.com
Sun May 25 02:05:05 EDT 2003


Dear group, 
I am interested in parsing cds and peptide from genbank file. I run the 
following script:

#!/usr/bin/perl -w
# Contributed by Jason Stajich <^S HYPERLINK "mailto:jason at bioperl.org" 
^Tjason at bioperl.org^U>

# simple extract the CDS features from a genbank file and
# write out the CDS and Peptide sequences

use strict;
use Bio::SeqIO;
my $filename = shift || die("pass in a genbank filename on the cmd line");
my $in = new Bio::SeqIO(-file => $filename, -format => 'genbank');
my $out = new Bio::SeqIO(-file => ">$filename.cds");
my $outpep = new Bio::SeqIO(-file => ">$filename.pep");

while( my $seq = $in->next_seq ) {
   my @cds = grep { $_->primary_tag eq 'CDS' } $seq->get_SeqFeatures();
   foreach my $feature ( @cds ) {
     my $featureseq = $feature->spliced_seq;
     #print 'featureseq:'.$featureseq;
     my $featureseqid=$feature->display_name;
         #print my $featureseqid;
    # $out->write_seq($featureseq);
     $out->write_seq($featureseqid);
$outpep->write_seq($featureseq->translate);
   }
}

There are two problems found. The first lines are all the same in   for One 
is the fasta format 


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