[Bioperl-l] Bio::Tools::Run::Alignment::ClustalW output redirect?

Chris Fields cjfields at uiuc.edu
Sat Jun 24 21:21:56 EDT 2006


According to the docs ( ;> ) the default behaviour is to return "a BioPerl
Bio::SimpleAlign object which can then be printed and/or saved in multiple
formats using the AlignIO.pm module"; you should be able to do something
like:

use Bio::AlignIO;
...
my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new();
my $aa_aln = $aln_factory->align(\@aa_seq);

my $al_out = Bio::AlignIO::new(-format => 'clustalw',
                               -fh     => \*STDERR);

$al_out->write_aln($aa_aln);

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ryan Golhar
> Sent: Saturday, June 24, 2006 5:37 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Bio::Tools::Run::Alignment::ClustalW output redirect?
> 
> I'm using Bio::Tools::Run::Alignment::ClustalW to generate some
> alignments and parsing the resulting alignments.
> 
> The ClustalW output is being sent to STDOUT.  Is there a way I can
> redirect the output to STDERR instead?
> 
> Here's how I'm using it:
> 
> my $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new();
> my $aa_aln = $aln_factory->align(\@aa_seq);
> 
> (Forgive me if it in the docs - I've been coding for a week straight now
> including saturday)
> 
> Thanks, Ryan
> 
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