Speed up Bio::DB::Fasta using compiled regular expressions or Inline::C #96
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rocky
commented
Dec 20, 2014
rocky
commented
- If available, use Inline::C
- As a fallback, using compiled regexps in s/// speeds up subseq() by about 7% from 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data. See my gist benchmarks
- Compile regular expression for compound_id in Bio::DB::IndexedBase
added 4 commits
December 18, 2014 11:35
…m 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data.
…urns and line feeds (\n) and (\r).
…ocument better Build.PL: add Inline::C recommended dependency. .gitignore: ignore _Inline directories that Inline::C creates.
fjossandon
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Dec 24, 2014
Speed up Bio::DB::Fasta using compiled regular expressions or Inline::C
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