[Bioperl-l] assistance with bioperl

[Mark A. Jensen]

Antonina--
Try the following:
Make sure that cysprot1a.msf and cysprot1b.fa are in the current directory, 
or use full path names for the files. 
MAJ
----- Original Message ----- 
From: "Antonina Iagovitina" <antonina.iagovitina at epfl.ch>
To: <bioperl-l at lists.open-bio.org>
Sent: Wednesday, September 30, 2009 2:09 PM
Subject: [Bioperl-l] assistance with bioperl


> Here is the error message I get when I try to align a sequence to an existing
> alignment. Please help
> I am using Windows XP and Clustalw version1.83
> 
> MSG:
> ERROR: Could not open sequence file (-profile) 
> No. of seqs. read = -1. No alignment!
> 
> use Bio::AlignIO;
> use Bio::SeqIO;
> use Bio::Seq;
> use Bio::Tools::Run::Alignment::Clustalw;
> 
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> $str = Bio::AlignIO->new(-file=> 'cysprot1a.msf');
> $aln = $str->next_aln();
> $str1 = Bio::SeqIO->new(-file=> 'cysprot1b.fa');
> $seq = $str1->next_seq();
> $aln = $factory->profile_align($aln,$seq);
> end
> 
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