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benchmark.fasta: make it about 2x faster

release
Slava Pestov 2010-04-14 21:49:41 -07:00
parent f40b313be5
commit b87171ff00
1 changed files with 18 additions and 21 deletions
extra/benchmark/fasta

39
extra/benchmark/fasta/fasta.factor
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@ -1,8 +1,9 @@
! Based on http://shootout.alioth.debian.org/gp4/benchmark.php?test=fasta&lang=java&id=2
USING: alien.c-types math kernel io io.files locals multiline
assocs sequences sequences.private benchmark.reverse-complement
hints io.encodings.ascii byte-arrays specialized-arrays ;
SPECIALIZED-ARRAY: double
USING: assocs benchmark.reverse-complement byte-arrays fry io
io.encodings.ascii io.files locals kernel math sequences
sequences.private specialized-arrays strings typed ;
QUALIFIED-WITH: alien.c-types c
SPECIALIZED-ARRAY: c:double
IN: benchmark.fasta
CONSTANT: IM 139968
@ -11,10 +12,8 @@ CONSTANT: IC 29573
CONSTANT: initial-seed 42
CONSTANT: line-length 60
: random ( seed -- n seed )
>float IA * IC + IM mod [ IM /f ] keep ; inline
HINTS: random fixnum ;
: random ( seed -- seed n )
>float IA * IC + IM mod dup IM /f ; inline
CONSTANT: ALU "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
@ -46,34 +45,32 @@ CONSTANT: homo-sapiens
{ CHAR: t 0.3015094502008 }
}
: make-cumulative ( freq -- chars floats )
TYPED: make-cumulative ( freq -- chars: byte-array floats: double-array )
[ keys >byte-array ]
[ values >double-array ] bi unclip [ + ] accumulate swap suffix ;
[ values >double-array unclip [ + ] accumulate swap suffix ] bi ;
:: select-random ( seed chars floats -- seed elt )
floats seed random -rot
[ >= ] curry find drop
chars nth-unsafe ; inline
seed random floats [ <= ] with find drop chars nth-unsafe ; inline
: make-random-fasta ( seed len chars floats -- seed )
[ iota ] 2dip [ [ drop ] 2dip select-random ] 2curry "" map-as print ; inline
TYPED: make-random-fasta ( seed: fixnum len: fixnum chars: byte-array floats: double-array -- seed: fixnum )
'[ _ _ select-random ] "" replicate-as print ;
: write-description ( desc id -- )
">" write write bl print ; inline
">" write write bl print ;
:: split-lines ( n quot -- )
n line-length /mod
[ [ line-length quot call ] times ] dip
quot unless-zero ; inline
: write-random-fasta ( seed n chars floats desc id -- seed )
TYPED: write-random-fasta ( seed: fixnum n: fixnum chars: byte-array floats: double-array desc id -- seed: fixnum )
write-description
[ make-random-fasta ] 2curry split-lines ; inline
'[ _ _ make-random-fasta ] split-lines ;
:: make-repeat-fasta ( k len alu -- k' )
TYPED:: make-repeat-fasta ( k: fixnum len: fixnum alu: string -- k': fixnum )
alu length :> kn
len iota [ k + kn mod alu nth-unsafe ] "" map-as print
k len + ; inline
k len + ;
: write-repeat-fasta ( n alu desc id -- )
write-description
@ -81,7 +78,7 @@ CONSTANT: homo-sapiens
:> alu
0 :> k!
[| len | k len alu make-repeat-fasta k! ] split-lines
] ; inline
] ;
: fasta ( n out -- )
homo-sapiens make-cumulative