[Bioperl-l] DBA_GenericHSP_output???

Brian Osborne osborne1 at optonline.net
Fri Aug 18 17:13:04 EDT 2006


Francois,

Something like:

use Bio::AlignIO;
# $aln will be a Bio::SimpleAlign object
my $aln = $hsps[0]->get_aln;
my $alnIO = Bio::AlignIO->new(-format =>"msf", -file => ">hsp.msf");
$alnIO->write_aln($aln);

Brian O.

On 8/18/06 3:33 PM, "francois fauteux" <ffauteux at gmail.com> wrote:

> Hi;
> 
>  DBA with non coding DNA; does something when launched:
> 
> Find start end points: [0,1001][0,1002] Score -2990
> Recovering alignment: Alignment recoveredplicit read off
> 
> I can't find a way to get the output (alignment)...
> 
> The code looks like this (see DBA.pm):
> 
>   my @params = ('matchA' => 0.75, 'matchB' => '0.55','dymem'=>'linear');
>   my  $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
>   $inputfilename = 'seqs.fasta';
>   #@hsps is an array of GenericHSP objects
>   my @hsps = $factory->align($inputfilename);
> 
> Missing the howto ouptut pretty alignment...
> 
> Many thanks;
> 
> François
> 
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