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

[Jason Stajich]

You need an additional perl module.


install IO::String from CPAN

There is a section on how to install additional perl modules in the
INSTALL document.

-j

On Tue, 23 Mar 2004, Alberto Davila wrote:

> Hi,
>
> 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,
>
> Alberto
>
> ****
>
> #!/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 $s->seq,"\n";
>         }
>
>
>           exit;
>
>
> [davila at tryps script]$ 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/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.2/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.1/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
> /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/site_perl
> /usr/lib/perl5/vendor_perl/5.8.3/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.2/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.1/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
> /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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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu