55 lines
1.3 KiB
Factor
Executable File
55 lines
1.3 KiB
Factor
Executable File
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 unicode.case continuations io.encodings.latin1 ;
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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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latin1 <file-writer> [
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swap latin1 <file-reader> [
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swap <duplex-stream> [
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500000 <vector> (reverse-complement)
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] with-stream
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] with-disposal
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] with-disposal ;
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: reverse-complement-in
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"reverse-complement-in.txt" temp-file ;
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: reverse-complement-out
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"reverse-complement-out.txt" temp-file ;
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: reverse-complement-main ( -- )
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reverse-complement-in
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reverse-complement-out
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reverse-complement ;
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MAIN: reverse-complement-main
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