Fields, Christopher J | 30 Oct 16:38 2013

Re: Perl script uses all my cpu

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 <antony.vincent.1 <at> ulaval.ca> 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
> 
> 
> 
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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

Gmane