[Bioperl-l] [Quick help needed] Getting Organism info using NCBI Accession numbers : sample code included
John SJ Anderson
genehack at genehack.org
Mon Apr 18 13:30:18 EDT 2011
On Fri, Apr 15, 2011 at 18:39, Abhishek Pratap <abhishek.vit at gmail.com> wrote:
> I want to seach NCBI for Locus name "CP000490" and get the organism lineage
Maybe this will at least get you started:
#! /opt/perl/bin/perl
use strict;
use warnings;
use 5.010;
use Bio::DB::GenBank;
my @ids = qw( NW_001884661 EZ361133 CP000490 );
my $gbh = Bio::DB::GenBank->new();
foreach my $id( @ids ) {
say "* ID: $id";
my $seq = $gbh->get_Seq_by_acc( $id );
my $org = $seq->species;
say join ' ' , $org->classification , "\n";
}
j.
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