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

Ryan Golhar golharam at umdnj.edu
Fri May 11 22:11:47 UTC 2007

No, I didn't, but I will now.  Thanks.  Interestingly enough ClustalW
removes the files from within the temp directory, but not the temp directory
-----Original Message-----
From: Jason Stajich [mailto:jason.stajich at gmail.com] On Behalf Of Jason
Sent: Friday, May 11, 2007 4:53 PM
To: golharam at umdnj.edu
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Bio:Tools::Run::Alignment::ClustalW not cleaning up
after itself

Did you try adding this after your calls getting the CDS aln.



On May 11, 2007, at 1:20 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
How can I force the cleanup of these directories after I am done with the

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);


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Jason Stajich
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