[Bioperl-l] Genbank LOCUS entry
Matthias Adams
matze at bioinf.uni-leipzig.de
Wed Feb 2 16:38:10 EST 2005
Hello!
I have a problem concerning the genbank LOCUS entry:
As described in the BioPerl documentation
(http://search.cpan.org/~birney/bioperl-1.4/Bio/Seq.pm):
"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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