[Bioperl-l] [Quick help needed] Getting Organism info using NCBI Accession numbers : sample code included

[shalabh sharma]

Hey Abhishek,
                I think you can use this:
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#I_want_a_list_of_database_.27x.27_UIDs_that_are_linked_from_a_list_of_database_.27y.27_UIDs

Also there are few files maintained by refseq that can convert accession to
GIs.

-Shalabh


On Wed, Apr 20, 2011 at 1:14 PM, Abhishek Pratap <abhishek.vit at gmail.com>wrote:

> Hi John
>
> Thanks for your reply. I think your code does exactly what I needed. In
> batch cases it runs a bit slow but still able to fetch lineage using NCBI
> Accession.
>
> FYI : I love the speed of Bio::LITE::Taxonomy but it only works on NCBI GI.
>
> So I am wondering if I can convert Accession -> GI quickly then I can get
> my
> results far more faster.
>
> -Abhi
>
> On Mon, Apr 18, 2011 at 10:30 AM, John SJ Anderson <genehack at genehack.org
> >wrote:
>
> > 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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-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636