[Bioperl-l] Blast to Clustalw Format

Marcelo Iwata marcelo011982 at gmail.com
Thu Jan 14 08:44:25 EST 2010


Thanks Mark.
I think that most of you already know it.
But , i'll put it for new users:


#!/usr/bin/perl -w

use strict;
use Bio::SearchIO;
use Bio::AlignIO;

my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => '
../../fontes/exemplos/blat/teste2/output.blast ');
my $aln;
my $alnIO;
$alnIO = Bio::AlignIO->new(-format =>"clustalw", -file => ">hsp.aln");
while ( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while ( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while ( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      $aln = $hsp->get_aln;
      $alnIO->write_aln($aln);

    }
  }
}


On Wed, Jan 13, 2010 at 4:44 PM, Mark A. Jensen <maj at fortinbras.us> wrote:

> Marcelo-
> Yes-- look at the code snip at
> http://www.bioperl.org/wiki/HOWTO:SearchIO#Using_SearchIO
> combined with the snip at
> http://www.bioperl.org/wiki/HOWTO:SearchIO#Using_the_methods
> (using -format => 'clustalw')
> cheers MAJ
> ----- Original Message ----- From: "Marcelo Iwata" <
> marcelo011982 at gmail.com>
> To: <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, January 13, 2010 1:12 PM
> Subject: [Bioperl-l] Blast to Clustalw Format
>
>
>  Hi..
>> I have an simple Blast result, such as blastn.
>> Is there an  scrip  to transform such result to Clustalw format in Bioperl
>> ?(.aln)
>>
>> Thanx for any help.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>


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