From OpenWetWare
#!/usr/bin/env python
# encoding: utf-8
# toehold.py
# Copyright (c) 2006 Shawn Douglas
import sys
import os
import random
import string
import fileinput
N = 7 # Number of toeholds
L = 12 # Length in bases
def nowhite(s):
return ''.join([c for c in s if c in string.letters])
def rev(s):
return s[::-1]
complement = string.maketrans('ACGTacgt','TGCAtgca')
def comp(s):
return rev(s.translate(complement))
def getinput():
s = ''
for line in fileinput.input("-"):
s += nowhite(string.rstrip(line)).upper()
return s
def randseq(l):
s = []
for i in range(l):
s.append(random.choice(['A', 'C', 'G', 'T']))
return ''.join(s)
def main():
s = getinput()
r = comp(s)
toehold = []
while (len(toehold) < N):
foo = randseq(L)
if (s.find(foo) > 0) | (r.find(foo) > 0):
continue
toehold.append(foo)
for toe in toehold:
print toe
if __name__ == '__main__':
main()
