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

Chris Fields cjfields at uiuc.edu
Tue Jul 10 10:35:03 EDT 2007


That will work as well; the key difference between my example and  
this one is that the seq stream retrieved using Bio::DB::GenBank  
passes through Bio::SeqIO while Bio::DB::EUtilities saves the raw seq  
record directly to a file (or callback or HTTP::Response) for  
optionally parsing later.

If you have problems with Bio::SeqIO you can always use  
Bio::DB::EUtilities to get around the issue until we resolve it.

chris

On Jul 10, 2007, at 9:15 AM, Diogo Tschoeke wrote:

> 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)
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list