[Bioperl-l] Genbank LOCUS entry

Matthias Adams matze at bioinf.uni-leipzig.de
Wed Feb 2 16:38:10 EST 2005


I have a problem concerning the genbank LOCUS entry:
As described in the BioPerl documentation
"The display_id() method returns the LOCUS name of a Genbank entry"
(also described somewhere else)

I can not reproduce this behavior, some test code:
#!/usr/bin/perl -w
use Bio::DB::GenBank;
use Bio::Perl;

use strict;
use Error qw(:try);

my $seqio;

        my $gb = new Bio::DB::GenBank();
        my $q;
        my $qstring="BV421351";
        $q =Bio::DB::Query::GenBank->new
                (-query   =>$qstring,
                -db      => 'nucleotide',
                -verbose => 0);
        $seqio = $gb->get_Stream_by_query($q);
        while( my $seq =  $seqio->next_seq ) {
        #       print $seq->desc(), "\n";
                print "LOCUS: \"", $seq->display_id(), "\"\n";

The only output is:
LOCUS: "BV421351"

It's just the accession number.
But I need the LOCUS line as in genbank:
BV421351                 590 bp    DNA     linear   STS 01-FEB-2005

So whats my problem? Do I have to call another sub?

Thanks for your help, Matze.

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