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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Perl script uses all my cpu
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 30th October 2013 15:38:48 UTC (over 2 years ago)
There are wrappers that can do this in bioperl-run (submit the sequence to
fasta36, runs the analysis, returns the SearchIO result I believe).  I
haven’t extensively used it myself, but here it is:

  https://github.com/bioperl/bioperl-run/blob/master/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm

chris

On Oct 30, 2013, at 9:02 AM, Antony03  wrote:

> Effectively, with -T 1 it's correct.
> 
> Do I really need to pass by an intermediate file to make an input for
fasta?
> It's really slow. Do you know how can I pass the sequence in $seq
directly
> to fasta?
> 
> Thanks
> 
> 
> 
> --
> View this message in context: http://bioperl.996286.n3.nabble.com/Perl-script-uses-all-my-cpu-tp17189p17196.html
> Sent from the Bioperl-L mailing list archive at Nabble.com.
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Chris Fields
Technical Lead in Genome Informatics
High Performance Computing in Biology
W.M. Keck Center for Comparative and Functional Genomics
Institute for Genomic Biology
1206 W. Gregory Dr., MC-195
Urbana, IL 61801
Phone: (217) 244-1890
http://www.hpcbio.illinois.edu
 
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