[Bioperl-l] Blast parser.

Chris Fields cjfields at uiuc.edu
Mon Oct 2 11:01:44 EDT 2006


The alignment that you get should come from GenericHSP, not BLASTHSP.
Either way, the HSP alignment that is retrieved using $hsp->get_aln() should
be a Bio::SimpleAlign object.  You can then output that to the proper
AlignIO format using an AlignIO stream object or use the Bio::SimpleAlign
methods for further analysis.  

my $aln = $hsp->get_aln();
my $alnout = Bio::AlignIO->new(-format => 'msf',
                               -fh  => \*STDOUT);
$alnout->write_aln($aln);

Quick note: not all AlignIO formats have write_aln() support at this time,
but most do.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of JK (Jesper Agerbo Krogh)
> Sent: Monday, October 02, 2006 9:06 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Blast parser.
> 
> 
> Hi.
> 
> I've tried to use the blast-parser but I cannot get the original alignment
> out of the parser. Is it possible to get that out of the
> Bio::Search::HSP::BlastHSP in some way. It seems quite odd to get a
> clustalw alignment out when it isn't that type of alignment people are
> used to get from blast.
> 
> Thanks
> 
> Jesper
> 
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> Bioperl-l at lists.open-bio.org
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