[Bioperl-l] Bio:Tools::Run::Alignment::ClustalW not cleaning up after itself

[Chris Fields]

cleanup() is supposed to clean up temp directory stuff; it's  
inherited from Bio::Tools::Run::WrapperBase.

chris

On May 11, 2007, at 3:20 PM, Ryan Golhar wrote:

> I'm running a large series of clustalw alignments.  After a large  
> number of
> alignments, my perl script would die indicating too many links were  
> open.  I
> checked my /tmp directory (while the script is running) and noticed  
> that the
> temp directory created for ClustalW are not removed until after the  
> script
> exists.
> How can I force the cleanup of these directories after I am done  
> with the
> alignment?
>
> My code is essentially this;
>
> $aln_factory = Bio::Tools::Run::Alignment::Clustalw->new();
> $aa_aln = $aln_factory->align(\@aa_seqs);
> open(STDOUT, ">&OLDOUT");
> $dna_aln = &aa_to_dna_aln($aa_aln, \%dna_seqs);
>
>
> Ryan
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign