[Bioperl-l] oligo_count script

[Heikki Lehvaslaiho]

Charles,

It might interest you that while we are refactoring the bioperl scripts
directory (scripts will be installable into users path), I took a look
at your oligo_count code and did some speed optimization there. 

In the core of your script you have a very tight loop over the sequence.
I moved all possible code outside the loop and rewrote the remaining
lines to have no object calls. The speed increase is over 100x; in one
test it was ~300x.

The script is now in the CVS head only as:
	scripts/seqstats/oligo_count.PLS

Enjoy,
	-Heikki

  
-- 
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      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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