[Bioperl-l] How to download EST files via bioperl script?

Diogo Tschoeke diogoat at gmail.com
Tue Jul 10 10:15:20 EDT 2007


Deal All,
I use this script bellow, and it`s work very fine!
I only changed the query! And the script gave me the 5133 EST from T.
brucei.

#################################################################################
use strict;
use warnings;
use Bio::Seq;
use Bio::SeqIO;
use Bio::DB::GenBank;

my $query = Bio::DB::Query::GenBank->new
                                (-query   =>'gbdiv est[prop] AND Trypanosoma
brucei [organism]',
                                db      => 'nucleotide');
my $gb = new Bio::DB::GenBank;
my $seqio = $gb->get_Stream_by_query($query);

my $out = Bio::SeqIO->new(-format => 'Genbank',
                          -file => '>>Tbrucei.EST.fasta');
while (my $seq = $seqio->next_seq){
         $out->write_seq($seq);
                        }
####################################################################

Diogo Tschoeke/Fiocruz (Alberto`s Student)


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