61 lines
1.6 KiB
Factor
61 lines
1.6 KiB
Factor
! Copyright (C) 2008, 2009 Slava Pestov.
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! See http://factorcode.org/license.txt for BSD license.
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USING: accessors io io.encodings.ascii io.files kernel sequences
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assocs math.parser namespaces regexp benchmark.knucleotide ;
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IN: benchmark.regex-dna
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! Based on http://shootout.alioth.debian.org/gp4/benchmark.php?test=regexdna&lang=ruby&id=1
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: strip-line-breaks ( string -- string' )
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R/ >.*\n|\n/ "" re-replace ;
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: count-patterns ( string -- )
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{
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R/ agggtaaa|tttaccct/i
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R/ [cgt]gggtaaa|tttaccc[acg]/i
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R/ a[act]ggtaaa|tttacc[agt]t/i
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R/ ag[act]gtaaa|tttac[agt]ct/i
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R/ agg[act]taaa|ttta[agt]cct/i
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R/ aggg[acg]aaa|ttt[cgt]ccct/i
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R/ agggt[cgt]aa|tt[acg]accct/i
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R/ agggta[cgt]a|t[acg]taccct/i
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R/ agggtaa[cgt]|[acg]ttaccct/i
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} [
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[ raw>> write bl ]
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[ count-matches number>string print ]
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bi
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] with each ;
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: do-replacements ( string -- string' )
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{
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{ R/ B/ "(c|g|t)" }
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{ R/ D/ "(a|g|t)" }
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{ R/ H/ "(a|c|t)" }
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{ R/ K/ "(g|t)" }
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{ R/ M/ "(a|c)" }
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{ R/ N/ "(a|c|g|t)" }
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{ R/ R/ "(a|g)" }
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{ R/ S/ "(c|t)" }
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{ R/ V/ "(a|c|g)" }
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{ R/ W/ "(a|t)" }
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{ R/ Y/ "(c|t)" }
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} [ re-replace ] assoc-each ;
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SYMBOL: ilen
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SYMBOL: clen
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: regex-dna ( file -- )
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ascii file-contents dup length ilen set
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strip-line-breaks dup length clen set
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dup count-patterns
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do-replacements
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nl
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ilen get number>string print
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clen get number>string print
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length number>string print ;
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: regex-dna-main ( -- )
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knucleotide-in regex-dna ;
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MAIN: regex-dna-main
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