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

[Alberto Davila]

Thanks Jason,

I installed the IO::String, then it is working fine now. However I have
a doubt, the "get_Stream_by_id" is returning me more than the "sequence
per se", what is it ? My script and results are listed below. Finally I
would like to save (in my local disk) the retrieved sequences as fasta
files... is there any argument for that ?

Thanks again, Alberto


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

use lib "/usr/local/bioperl14";
use 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\n\n";
	}			  
				  
 	  
	  exit;




[davila at tryps script]$ perl gb-fetch-1.pl
agtagtgtactaccaagtatagataacgtttaaatattaaagttttggatcaaagccaaagatgattcgcat
gctggtgctgattgtagttacagctgcaagcccagtgtatcagagatgtttccaagatggggctatagtgaa
gcaaaacccatccaaagaggcagtcacagaagtgtccctaaaagatgatgttagca
                                                                                
                                                                                
cctggacctcctgtgcaagaacatgaaacanctgtggttcttccttctcctggtggcagctcccagatgggt
cctgtcccaggtgcacctgcaggagtcgggcccaggactggggaagcctccagagctcaaaaccccacttgg
tgacacaactcacacatgcccacggtgcccagagcccaaatcttgtgacacacctcccccgtgcccacggtg
cccagagcccaaatcttgtgacacacctcccccatgcccacggtgcccagagcccaaatcttgtgacacacc
tcccccgtgcccnnngtgcccagcacctgaactcttgggaggaccgtcagtcttcctcttccccccaaaacc
caaggatacccttatgatttcccggacccctgaggtcacgtgcgtggtggtggacgtgagccacgaagaccc
nnnngtccagttcaagtggtacgtggacggcgtggaggtgcataatgccaagacaaagctgcgggaggagca
gtacaacagcacgttccgtgtggtcagcgtcctcaccgtcctgcaccaggactggctgaacggcaaggagta
caagtgcaaggtctccaacaaagccctcccagcccccatcgagaaaaccatctccaaagccaaaggacagcc
cnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngaggagatgaccaagaaccaagtcagcctgacctg
cctggtcaaaggcttctaccccagcgacatcgccgtggagtgggagagcaatgggcagccggagaacaacta
caacaccacgcctcccatgctggactccgacggctccttcttcctctacagcaagctcaccgtggacaagag
caggtggcagcaggggaacatcttctcatgctccgtgatgcatgaggctctgcacaaccgctacacgcagaa
gagcctctccctgtctccgggtaaatgagtgccatggccggcaagcccccgctccccgggctctcggggtcg
cgcgaggatgcttggcacgtaccccgtgtacatacttcccaggcacccagcatggaaataaagcacccagcg
ctgccctgg




On Tue, 2004-03-23 at 22:44, Jason Stajich wrote:
> 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.