46 lines
1.2 KiB
Factor
46 lines
1.2 KiB
Factor
USING: io io.files io.streams.duplex kernel sequences
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sequences.private strings vectors words memoize splitting
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hints ;
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IN: benchmark.reverse-complement
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MEMO: trans-map ( -- str )
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256 >string
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"TGCAAKYRMBDHV" "ACGTUMRYKVHDB"
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[ pick set-nth ] 2each ;
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: do-trans-map ( str -- )
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[ ch>upper trans-map nth ] change-each ;
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HINTS: do-trans-map string ;
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: translate-seq ( seq -- str )
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concat dup reverse-here dup do-trans-map ;
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: show-seq ( seq -- )
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translate-seq 60 <groups> [ print ] each ;
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: do-line ( seq line -- seq )
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dup first ">;" memq? [
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over show-seq print dup delete-all
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] [
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over push
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] if ;
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HINTS: do-line vector string ;
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: (reverse-complement) ( seq -- )
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readln [ do-line (reverse-complement) ] [ show-seq ] if* ;
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: reverse-complement ( infile outfile -- )
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<file-writer> >r <file-reader> r> <duplex-stream> [
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500000 <vector> (reverse-complement)
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] with-stream ;
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: reverse-complement-main ( -- )
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"extra/benchmark/reverse-complement/reverse-complement-test-in.txt"
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"extra/benchmark/reverse-complement/reverse-complement-test-out.txt"
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[ resource-path ] 2apply
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reverse-complement ;
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MAIN: reverse-complement-main
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