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|
#!./parrot -R cgp
# Copyright (C) 2005-2009, Parrot Foundation.
# $Id$
#
# fasta.pir N (N = 2500000 for shootout)
# by Joshua Isom
# modified by karl : fixed bug in default value (N=1000) assignment
# 48.2 sec on AMD@2000/512K cache
.sub makeCumulative
.param pmc genelist
.param int count
.local num cp
.local int i
cp = 0.0
i = 0
beginfor:
unless i < count goto endfor
$N0 = genelist[i;1]
cp += $N0
genelist[i;1] = cp
inc i
goto beginfor
endfor:
.end
.sub selectRandom
.param pmc genelist
.param int count
.local num r
r = gen_random(1.0)
.local int i, lo, hi
$N0 = genelist[0;1]
unless r < $N0 goto endif
$S0 = genelist[0;0]
.return($S0)
endif:
lo = 0
hi = count - 1
beginwhile:
$I0 = lo + 1
unless hi > $I0 goto endwhile
i = hi + lo
i /= 2
$N0 = genelist[i;1]
unless r < $N0 goto else_1
hi = i
goto endif_1
else_1:
lo = i
endif_1:
goto beginwhile
endwhile:
$S0 = genelist[hi;0]
.return($S0)
.end
.const int LINE_LENGTH = 60
.sub makeRandomFasta
.param string id
.param string desc
.param pmc genelist
.param int count
.param int n
.local int todo, i, m
todo = n
print ">"
print id
print " "
print desc
print "\n"
.local string pick
beginfor:
unless todo > 0 goto endfor
unless todo < LINE_LENGTH goto else
m = todo
goto endif
else:
m = LINE_LENGTH
endif:
i = 0
beginfor_1:
unless i < m goto endfor_1
$S0 = selectRandom(genelist, count)
pick .= $S0
inc i
goto beginfor_1
endfor_1:
print pick
print "\n"
pick = ''
todo -= LINE_LENGTH
goto beginfor
endfor:
.end
.sub makeRepeatFasta
.param string id
.param string desc
.param string s
.param int n
.local int todo, k, kn, m
todo = n
k = 0
kn = length s
print ">"
print id
print " "
print desc
print "\n"
beginfor:
unless todo > 0 goto endfor
unless todo < LINE_LENGTH goto else
m = todo
goto endif
else:
m = LINE_LENGTH
endif:
beginwhile:
$I0 = kn - k
unless m >= $I0 goto endwhile
$S0 = substr s, k
print $S0
$I0 = kn - k
m -= $I0
k = 0
goto beginwhile
endwhile:
$S0 = substr s, k, m
print $S0
print "\n"
k += m
todo -= LINE_LENGTH
goto beginfor
endfor:
.end
.macro InitStruct (iub, i, char, num)
$P0 = new 'FixedPMCArray'
$P0 = 2
.iub[.i] = $P0
.iub[.i;0] = .char
.iub[.i;1] = .num
.endm
.sub main :main
.param pmc argv
.local pmc stdout
.local int n
# stdout is linebuffered per default - make it block buffered
stdout = getstdout
stdout.'buffer_size'(40960)
$I0 = argv
if $I0 > 1 goto argsok
n = 1000
goto argsdone
argsok:
$S0 = argv[1]
n = $S0
argsdone:
.local pmc iub
iub = new 'FixedPMCArray'
iub = 15
.InitStruct(iub, 0, "a", 0.27)
.InitStruct(iub, 1, "c", 0.12)
.InitStruct(iub, 2, "g", 0.12)
.InitStruct(iub, 3, "t", 0.27)
.InitStruct(iub, 4, "B", 0.02)
.InitStruct(iub, 5, "D", 0.02)
.InitStruct(iub, 6, "H", 0.02)
.InitStruct(iub, 7, "K", 0.02)
.InitStruct(iub, 8, "M", 0.02)
.InitStruct(iub, 9, "N", 0.02)
.InitStruct(iub, 10, "R", 0.02)
.InitStruct(iub, 11, "S", 0.02)
.InitStruct(iub, 12, "V", 0.02)
.InitStruct(iub, 13, "W", 0.02)
.InitStruct(iub, 14, "Y", 0.02)
.local pmc homosapiens
homosapiens = new 'FixedPMCArray'
homosapiens = 4
.InitStruct(homosapiens, 0, "a", 0.3029549426680)
.InitStruct(homosapiens, 1, "c", 0.1979883004921)
.InitStruct(homosapiens, 2, "g", 0.1975473066391)
.InitStruct(homosapiens, 3, "t", 0.3015094502008)
.local string alu
alu = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA"
makeCumulative(iub, 15)
makeCumulative(homosapiens, 4)
$I0 = n * 2
makeRepeatFasta("ONE", "Homo sapiens alu", alu, $I0)
$I0 = n * 3
makeRandomFasta ("TWO", "IUB ambiguity codes", iub, 15, $I0)
$I0 = n * 5
makeRandomFasta ("THREE", "Homo sapiens frequency", homosapiens, 4, $I0)
.end
.const num IM = 139968.0
.const num IA = 3877.0
.const num IC = 29573.0
.sub gen_random
.param num max
.local num last
last = 42.0
loop:
$N0 = last
$N0 *= IA
$N0 += IC
$N0 %= IM
$N1 = max
$N1 *= $N0
$N1 /= IM
last = $N0
.yield($N1)
get_params "0", max
goto loop
.end
# Local Variables:
# mode: pir
# fill-column: 100
# End:
# vim: expandtab shiftwidth=4 ft=pir:
|
