[Bioperl-l] Blast to Clustalw Format

Mark A. Jensen maj at fortinbras.us
Thu Jan 14 08:54:31 EST 2010


Thanks Marcelo-- code snips always appreciated! MAJ
----- Original Message ----- 
From: "Marcelo Iwata" <marcelo011982 at gmail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Thursday, January 14, 2010 8:46 AM
Subject: Re: [Bioperl-l] Blast to Clustalw Format


> Sorry , the correct code is:
>
>
>
> #!/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 Thu, Jan 14, 2010 at 11:44 AM, Marcelo Iwata 
> <marcelo011982 at gmail.com>wrote:
>
>> 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
>>>>
>>>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



More information about the Bioperl-l mailing list