BioPerl tip for the day

/ nsaunders

So you have an NCBI Entrez uid and you want to grab that sequence from NCBI and convert it directly to a Bio::Seq object? Try this.

use strict;
use Bio::SeqIO;
use IO::String;
use LWP;

# the URL for fasta as plain text looks like this
my $url='http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?'.
              'db=protein&dopt=fasta&sendto=t&list_uids=47157325';
my $fasta = get($url);
# open filehandle on string
my $seqio = Bio::SeqIO->new('-fh' => IO::String->new($fasta), '-format' => 'fasta');
# voila!
my $seqobj = $seqio->next_seq;
# do whatever with the object

It’s easy to have a base URL, loop through a bunch of UIDs, append to the end and fetch.