[Bioperl-l] clustalw.pm: could not open sequence file error

[Scott Markel]

Olena,

Are you getting a BioPerl error or a ClustalW error?

What happens if you invoke ClustalW directly on your input
file, i.e., without using BioPerl?

Scott

Olena Morozova wrote:

> Hi all,
> 
> I am trying to use this script
> 
> use Bio::Tools::Run::Alignment::Clustalw;
> 
> $ENV{CLUSTALDIR} = 'C:/perl/clustalw1.8/';
>  my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
> 
> 'outfile'=> 'al_mouse.txt');
>  my $factory =
> 
> Bio::Tools::Run::Alignment::Clustalw->new(@params);
>  $inputfilename = 'c:/perl/mouse_unique.txt';
>  my $aln = $factory->align($inputfilename);
> 
> to do a MSA, and it works for a test file with 2 or 3 sequences.
> However, when I try to run it on my actual file (has 97 sequences)
> which is in exactly the same format as the test file (fasta), I get a
> "could not open the sequence file" error.
> Is this because the file is too big and is there a way to fix this?
> Thanks a lot for your help!
> 
> Olena

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Scott Markel, Ph.D.
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