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
--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki@xxxxxxxxx
_/_/_/_/_/ 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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