45 lines
1.2 KiB
Factor
45 lines
1.2 KiB
Factor
! Copyright (C) 2006, 2008 Slava Pestov.
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! See http://factorcode.org/license.txt for BSD license.
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USING: io io.files io.files.temp io.streams.duplex kernel
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sequences sequences.private strings vectors words memoize
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splitting grouping hints tr continuations io.encodings.ascii
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ascii ;
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IN: benchmark.reverse-complement
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TR: trans-map ch>upper "ACGTUMRYKVHDB" "TGCAAKYRMBDHV" ;
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: translate-seq ( seq -- str )
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concat reverse! dup trans-map-fast ;
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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 ">;" member-eq?
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[ over show-seq print dup delete-all ] [ over push ] 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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ascii [
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ascii [
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500000 <vector> (reverse-complement)
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] with-file-reader
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] with-file-writer ;
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: reverse-complement-in ( -- path )
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"reverse-complement-in.txt" temp-file ;
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: reverse-complement-out ( -- path )
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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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