factor/extra/benchmark/reverse-complement/reverse-complement.factor

45 lines
1.2 KiB
Factor

! Copyright (C) 2006, 2008 Slava Pestov.
! See http://factorcode.org/license.txt for BSD license.
USING: io io.files io.files.temp io.streams.duplex kernel
sequences sequences.private strings vectors words memoize
splitting grouping hints tr continuations io.encodings.ascii
ascii ;
IN: benchmark.reverse-complement
TR: trans-map ch>upper "ACGTUMRYKVHDB" "TGCAAKYRMBDHV" ;
: translate-seq ( seq -- str )
concat reverse! dup trans-map-fast ;
: show-seq ( seq -- )
translate-seq 60 <groups> [ print ] each ;
: do-line ( seq line -- seq )
dup first ">;" member-eq?
[ over show-seq print dup delete-all ] [ over push ] if ;
HINTS: do-line vector string ;
: (reverse-complement) ( seq -- )
readln [ do-line (reverse-complement) ] [ show-seq ] if* ;
: reverse-complement ( infile outfile -- )
ascii [
ascii [
500000 <vector> (reverse-complement)
] with-file-reader
] with-file-writer ;
: reverse-complement-in ( -- path )
"reverse-complement-in.txt" temp-file ;
: reverse-complement-out ( -- path )
"reverse-complement-out.txt" temp-file ;
: reverse-complement-main ( -- )
reverse-complement-in
reverse-complement-out
reverse-complement ;
MAIN: reverse-complement-main