[Bioperl-l] Bio::Tools::Run::StandAloneBlast

[Qiang TU]

Dear Luc Gauthier,

If you make a StandAloneBlast object by the parameter 'outfile', 
it is what you want. or you can get the file name by $blast_report->file.

happy coding,

Qiang Tu

========================

#!/usr/bin/perl

use strict;
use warnings;
use Bio::Tools::Run::StandAloneBlast;

my @params = ('database' => 'swissprot',
              'outfile' => 'myblast.txt',
              'program'  => 'blastp',
              '_READMETHOD' => 'Blast');
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $io = Bio::SeqIO->new('-file' => 'try.fas',
                         '-format' => 'fasta',
                        );
my $Oseq = $io->next_seq;
my $blast_report = $factory->blastall($Oseq);

print $blast_report->file;


---Original Message---
From: Luc.Gauthier<Luc.Gauthier at aventis.com>
Subject: [Bioperl-l] Bio::Tools::Run::StandAloneBlast
 
>Hi everyone,
>
>I am currently trying to write a small tool to locally run NCBI Blast. I
>quickly found out about the "Bio::Tools::Run::StandAloneBlast" module and
>decided to use it. I am using Bioperl v1.0. Now what I would like to have as
>the final result is the plain raw blast result, as it is normally generated
>when running blast as a unix command-line tool.
>
>The reason why I want to do that is that I want to wrap that small tool as a
>SOAP web service that can be remotely called. One would call a simple method
>and get the plain raw blast result back.
>
>I am new to Bioperl and the answer to my problem may be quite simple ... I
>just can't find out how to get the raw blast report from the BPlite object
>reference I get back when calling the "blastall" method from a
>StandAloneBlast factory.
>
>Can someone help ???
>
>Thank you very much in advance and have a pleasant day !
>Luc Gauthier
>
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>Bioperl-l at bioperl.org
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>

 
---End of Message---

 
Qiang Tu
Institute of Biochemistry and Cell Biology
Chinese Academy of Sciences
Email: tuqiang at mail.shcnc.ac.cn, tuqiang_cn at yahoo.com