[Bioperl-l] get Seq by Acc - needs a start and end (what format is needed??)

[Wiepert, Mathieu]

Hi,

I am not sure what specific task you are trying to accomplish, is it remote fetching from genbank?  http://www.bioperl.org/Core/bptutorial.html#III_1_1_Accessing_remote_databas has some good tips on how you might retrieve data from remote databases.

Otherwise, this script at least retrieved a sequence, I am sure you would want something that can use variable substitution for you sequences?  Or did you want to retrieve sequences from a local db...  Or there are many other scripts that are better than this in the archives somewhere, though I didn't search.  I know I have seen plenty.  Have you installed bioperl?  I ran below with 1.0.1 (checked with 'perldoc -m Bio::Seq | grep VERSION'), it seemed to work.


#!/usr/bin/perl -w
#Test script to retrieve sequences from genbank and refseq.
use Bio::DB::GenPept;
use Bio::SeqIO;
use strict;

my $gb = new Bio::DB::GenPept(-retrievaltype => 'tempfile' ,
                               -format => 'Fasta');
$gb->request_format('fasta');
my $out = Bio::SeqIO->new('-file' => ">test.fa",
                         '-format' => 'FASTA'
                         );
my $seq = $gb->get_Seq_by_acc('AAF18306');
$out->write_seq($seq);
my $db = new Bio::DB::RefSeq;
$db->request_format('fasta');
$seq = $db->get_Seq_by_acc('NM_005252'); # RefSeq ACC
print "seq is ", $seq->seq, "\n"; 

-Mat

> -----Original Message-----
> From: Benjamin Breu [mailto:breu@proteosys.com]
> Sent: Tuesday, August 06, 2002 4:57 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] get Seq by Acc - needs a start and end 
> (what format
> is needed??)
> 
> 
> Hi,
> 
> I'm trying on Bioperl for a few days and would like to know 
> what format is needed to get the module get_Seq_by_acc working
> 
> 	
>  Thx for helping
> 
> Ben
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