[Bioperl-l] Fetching Fasta seqs from GenBank - Help request

Alberto Davila davila at ioc.fiocruz.br
Tue Mar 23 13:07:03 EST 2004


May I ask for some help ?

I am trying to use the BioFetch module in order to download several seqs
(from specific Organisms) from GenBank in fasta format, but looks like I
am missing "IO/String.pm" and other things.. should I install additional
bioperl modules (I have the Bioperl Core 1.4 installed) ? or use a
different module for my purpose ?

My script and error msg are listed below.

Thanks and besr regards,



#!/usr/local/bin/perl -w

use lib "/usr/local/bioperl14";
package Bio::DB::BioFetch;
use strict;
use Bio::DB::WebDBSeqI;
use HTTP::Request::Common 'POST';

my $format_type='fasta';
my $stream;

my $bf = new Bio::DB::BioFetch(-format        =>$format_type',
                               -retrievaltype =>'tempfile',
                               -db            =>'EMBL');
 $stream = $bf->get_Stream_by_id(['BUM','J00231']);
 while (my $s = $stream->next_seq) {
    print $s->seq,"\n";

[davila at tryps script]$ perl gb-fetch-1.pl
Can't locate IO/String.pm in @INC (@INC contains:
/usr/local/bioperl14/i386-linux-thread-multi /usr/local/bioperl14
/usr/lib/perl5/5.8.3/i386-linux-thread-multi /usr/lib/perl5/5.8.3
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2
/usr/lib/perl5/vendor_perl/5.8.1 /usr/lib/perl5/vendor_perl/5.8.0
/usr/lib/perl5/vendor_perl .) at
/usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90.
BEGIN failed--compilation aborted at
/usr/local/bioperl14/Bio/DB/WebDBSeqI.pm line 90.
Compilation failed in require at gb-fetch-1.pl line 6.
BEGIN failed--compilation aborted at gb-fetch-1.pl line 6.

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