add fasta.py benchmark from pypy. adopted output to display md5 instead of string

minibenchmarks/fasta.py

+# -*- coding: utf-8 -*-
+# The Computer Language Benchmarks Game
+# http://shootout.alioth.debian.org/
+#
+# modified by Ian Osgood
+# modified again by Heinrich Acker
+
+import sys, bisect
+
+
+# pyston change:
+import hashlib
+class HashOutput:
+    def __init__(self):
+        self.m = hashlib.md5()
+    def write(self, string):
+        self.m.update(string)
+    def md5hash(self):
+        return self.m.hexdigest()
+hash_output = HashOutput()
+old_stdout = sys.stdout
+sys.stdout = hash_output
+
+alu = (
+   'GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG'
+   'GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA'
+   'CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT'
+   'ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA'
+   'GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG'
+   'AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC'
+   'AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA')
+
+iub = zip('acgtBDHKMNRSVWY', [0.27, 0.12, 0.12, 0.27] + [0.02]*11)
+
+homosapiens = [
+    ('a', 0.3029549426680),
+    ('c', 0.1979883004921),
+    ('g', 0.1975473066391),
+    ('t', 0.3015094502008),
+]
+
+
+def genRandom(lim, ia = 3877, ic = 29573, im = 139968):
+    seed = 42
+    imf = float(im)
+    while 1:
+        seed = (seed * ia + ic) % im
+        yield lim * seed / imf
+
+Random = genRandom(1.)
+
+def makeCumulative(table):
+    P = []
+    C = []
+    prob = 0.
+    for char, p in table:
+        prob += p
+        P += [prob]
+        C += [char]
+    return (P, C)
+
+def repeatFasta(src, n):
+    width = 60
+    r = len(src)
+    s = src + src + src[:n % r]
+    for j in xrange(n // width):
+        i = j*width % r
+        print s[i:i+width]
+    if n % width:
+        print s[-(n % width):]
+
+def randomFasta(table, n):
+    width = 60
+    r = xrange(width)
+    gR = Random.next
+    bb = bisect.bisect
+    jn = ''.join
+    probs, chars = makeCumulative(table)
+    for j in xrange(n // width):
+        print jn([chars[bb(probs, gR())] for i in r])
+    if n % width:
+        print jn([chars[bb(probs, gR())] for i in xrange(n % width)])
+
+
+#n = int(sys.argv[1])
+#for i in range(int(sys.argv[2])):
+
+n = 1000
+
+for i in range(int(1000)):
+    print '>ONE Homo sapiens alu'
+    repeatFasta(alu, n*2)
+
+    print '>TWO IUB ambiguity codes'
+    randomFasta(iub, n*3)
+
+    print '>THREE Homo sapiens frequency'
+    randomFasta(homosapiens, n*5)
+    
+sys.stdout = old_stdout
+print hash_output.md5hash()