patternmatching.py

__author__ = 'ssen'
def patternmatching(pattern, genome):
    indexMatch = []
    lenPattern = len(pattern)
    lenGenome = len(genome)
    count = 0
    for i in range(0, lenGenome-lenPattern):
        if (pattern == genome[i:i+lenPattern]):
            count = count + 1
            indexMatch.append(i)
    return indexMatch

#print patternmatching('ATAT','GATATATGCATATACTT' )
#f=open('C:/vibrio_cholerae.txt')
#s=f.read()
a=""
indicesCombined = patternmatching('GCGCATCGC','GCGCATCAGCGCATCGCGCATCACACGCAGCGCATCAGTGCGCATCTGCGCATCTGCGCATCGGAAGGCGCATCGGCGCATCTTGTGCGCATCGCGCATCTAGCGCATCTGCGCATCGTCCTGCGCATCAGGGTAGCGCATCGCGCATCGGCGCATCGCGCATCGCGCATCCCGCGCATCTGCGAACACAGCGCATCGTAATGCGCATCGCGCATCCGGAGCGCATCGCGCATCGCGCATCAAACTACCTTTGCGCATCTCCCATGCGCATCTTCGGGCGCATCGCGCATCGCGCATCTGCGCGCATCACATGCGCATCTCGCGCATCGCAAGCGCATCAGCGCATCGCGCATCCGCTACAGCGCATCTGGCGCATCGCGCATCATTCAAGCGAGGCGCATCGGCGCATCGCGCATCGCGCATCGCGCATCAGTTCCGCGCATCGCGCATCATTCGGTTGCGCATCGCGCATCAAGCGCATCCGACCGCGCGTTGCACCGCGCATCGCAACTACTGCGCATCGCGCATCTCACGGGTTGCGCATCGCGCATCTAGCGCATCGGGCGCATCGCGCATCTCTGCGCATCAACCGAGCGCATCGGCGCATCGCGCATCAGCGCATCATGCGCATCGGCGCGCATCCGCGCATCTGCGCATCACGCGCATCGCGCATCTAGCGTCGCGCATCGCGCATCGCGCATCAAGCGCATCGCGCATCGCGCATCAAGGCGTACGCGCATCCGCGCATCGCGCATCGCGCATCGTGCGCATCATAGCGCATCGCGCATCCAGAATAGGCGCATCAGCGCATCGTGCGCATCGGCGCATCGCGCATCAGGCGCATCGGCGCATCCGATCGCGCATCTGCGATGCGCATCGGCGCATCACGTTTGCGCATCGCGCATCCGCGCATCACGGCGCATCCCGCGCATCGCGCATCCTAGCGCATCCGAGCGCATCGAGGACGCGCATCGAGGCGCATCTGCGCATCGCGCATCTCGCGCATCGCGCATCTTCAGCGCATCTGCGCATCGCGGCGCATCGATTTTGCGCATCCCGAATGCGCATCGCGCATCTGCGCATCGGGCGCATCTCGCGCATCGCGCATCGCGCATCGGCGCATCGCGCATCGGGAGGGCGCATCGCGCATCGCGCATCAAGCGCATCCGCGCATCTGGCGCATCCCTGCGCATCAGCGCATCTTGCGCATCGCGCATCGGCGCGCATCAGCGCATCCTGGCGCATCAGCGCATCGCGCATCGAGCGCATCTAGCGCATCCCTGGCGCATCGCGCATCGCGCATCGAGCGCATCCTCCCGCGCATCCATGCGCATCGCGCATCGGCGCATCCGCGCATCGATGTGGCGCATCCAGCGCATCGCGATAAGCGCATCGGGCGCATCGATCAGCGCATCCTTGCGCATCGCGCATCATAAAGCGCATCGGGTGCGCATCAGGCGCATCTTGTCGCGCATCGCGCATCTGCGCATCGAGGAGCGCATCAGGCGCATCATGCGCATCGCGCATCGCGCATCCAATCGCGCATCCAGGACGGCGCATCCGCGCATCATGGCGCATCCGCGCATCAATGGCGCATCAGCGCATCGGAGCCGCGCATCTCAACGTAGCGCATCGGGCGCATCTTACCGACAATAGCGCATCTGGGCGCATCAGCGCATCTGGCGCATCTGGTTCAGGTTCCCCCGCGCATCCGTGCGCATCATGCGCATCAAGCGCATCCTTGAGGCGCATCGCGCATCCGCGCATCGCGCATCCTCGCGCATCGCGCATCATGGCGCATCATGCGCATCATGCGTTGCGCATCATGCGCATCAAGGGCGCATCCGGGGCGCATCGCGCATCGCAATCTGGCGCATCCTGCGCATCGCCGCGCATCGCGCATCCTATAGCGCATCCCAAGCGCATCATCGTGTAGTGGCAGCGCATCGCGCATCAGCGCATCGCGCATCTCTTTGGCGCATCGCGCATCAGCGCATCGACACTTAGCGCATCGCGCATCCATAATGCGCATCCAGCGGAAGGATTGCGCATCGATCTGCGCATCGCGCATCGCGCATCAGCGCATCGCGCATCAACGAACAATCAACTTTAGTATAAGCGCATCAGCGCATCGCGGCGCATCAGAGCGCATCGCGCATCGCGCATCGGCGCATCGAGCGCATCGCGCATCAGGCGCATCGGAACCGCGCATCGCGCATCTGCGCATCGGGCGCATCGCGCGCATCTCCTACCCATGCGCATCCGCGCATCAGCGTACGCGCATCGGCCGGTTTTGGCGCATCAGGGCGCGCATCGGCGCATCATTTTGCGCGCATCCCCCGGATTGCGCGCATCGGCGCGCATCAGGATTTAGCGCATCGGCGCATCTAGCGCATCTGTGCGCATCGCGCATCGGCGCATCTTCGCGCATCTCGGGCGCATCGCCGCTCCGCGCATCTGCGCATCGCGCATCCAGCGCATCTCGCGCATCTTATGCAGCCAACGCGCATCTCATCGCGCATCTCGCGCATCCTCACGCGCATCGGTGAAGGCGCATCGCGCATCGAAAGCGCATCTTTGCGCATCTGCGCATCGTCTGCGCATCGCGCATCTGAGAGGGGCGCATCCAGTAACCGCGCATCTTGCGCATCAGAACGCGCATCGCGCATCTGCGCATCATCATTTTGCGCATCGACCGCGCATCAAGTGCGCATCGCGCATCGCGCATCCCGCGCATCCCGCGCATCTTCGCGCATCCGGCGCATCTGCGCATCACGCGCATCAGTGCGCATCGGCGCATCAGCGCATCGCGCATCTAGCGCATCGCGCATCATTCTTAAGCGCATCTAAGCGCATCACTCGGCGCGCATCGCGCATCTGCGTTGCAGCGCATCCTTAAGGCCAAGCTTTCGCGCATCAGGGCGCATCACGCGCATCGCGCATCCGCGCATCGGATGGCGCATCACATGGACACGGCGCATCTGGAGCATCTAAGCGCATCGCGCATCCCCAGCGCATCGTGTAGCGCATCTTGGTCACTTGCTCGGCGCATCGCGCATCCGCGCATCGGCGCATCAGGAGCGCATCTAGGCTATTCAGGTATCCAGCGCATCCGGCGCATCCGCGCATCCAAGGGCGCATCAAGCGCATCGAGCGCATCAGGCGCATCTAAATTAGGTAGTAGCGCGCATCGCGCATCAGCGCATCGCGCATCTAGGGACCCGTGGCGCATCCGCGCATCTGCGCATCAGGGCTTAATGAACTCGGATCGACGCGCGCATCGCGCATCTCAGCGCATCCGCGCATCACGGGCAGCGCATCGGCGCATCGCCGGCGCATCGATGCGCATCGCGCATCCGGCGCATCCGATGCGCATCCCGCGCATCAAGCGCATCGCGCATCGGGCGCATCGCGCATCGCGCATCGGCGCATCGTAGCGCATCTGCGCATCGGCGCATCGCGCATCACCGCGCATCCGCGCATCGCGAACGTCGCGCATCGTGCGCATCCGAGCGCATCCGGAGCGCATCGACTCGATGCGCATCGGGAGAACGCGCATCCCGTGTGACCTCGCGCATCGCGCATCGGATGCGCATCTAGGAGCGCATCTGCGCATCGGACTACGAGCGCATCGCGCATCCACAGCGAAGGGCGCATCCAGCGCATCATCTATGCGCATCGCGGCGCATCGCGCATCGCGCATCGCGCATCCCCGCGCATCAAGGGGGCGCATCCGCGCATCAGGCGCATCGCGCGCATCGCGCATCGATGTGACCGCGCATCCAGCGCATCAAGCGCATCATCGCTCTTGCATTAATCCAACAATGCGCATCCAGCGCATCATGTCGCTTGTATACGAGCGCATCTTCCATGCGCATCGGTGCGCATCTACGCGCATCATAACGCGCATCCGAAGCCTGCGCATCCACATGCGCATCGCGCATCCAGGCGCATCAGCGCATCTCTAGCTGCGCATCTGGCGCATCGCGCATCGCGCATCGTTCGCGCATCGTGCTGCGCATCGCGCATCGCGCATCGCGCATCCCGCGCATCCGCGCATCTATGCGCATCTGCGCATCAGCGCATCAGCGCATCAGCGCATCGCGCATCTGCGCATCGCGCATCATACGCGCATCAGGCGCATCGGCGCATCGGCGCATCTCGCGCATCGGCGCATCGCGCATCCTCTGGCTGCGCATCTCTGCGCATCGGGCGCATCGCGCATCTGCGCATCGCGCATCGCGCATCTGGGCGCATCACACTGTGGCCGCGCATCCGTGACGCGCATCGCGCATCCGTTGGGACGCGCATCCCGGCGCATCAGCGCATCGCGCATCTTCGCCTATTATGCGCATCGCGCATCGCGCATCGGTGCGCATCGGCCAATCCCGCGCATCCGCTTCCAGCGCATCGCGCATCGCGCATCGCGCATCTGCTGGAGCGCATCGACGTGCGCATCGCGCATCCCAGCGCATCTGCGCATCAGCGCATCTCGCGCATCCGCGCATCACATCGGAGGCCCCCCAGCGCATCTCGCGCGCATCCTGCGCATCCCGCGCATCCTTCGTGCGCATCCGCGCATCGCGCATCTGTGGCGCATCGTGCGCATCTCGCCATTATGCGCATCGCGCATCTAGGCGCATCGGCGCATCGCGCATCAGCGCATCGGGCGCATCGATAGAAATGGCGCATCAGAGTGCGCATCGCGCATCTGGCGCATCCGGCGCATCAGCGCATCTCACTCCGCGCATCATGCGCATCGCGCATCTTGAGGTAGTGCAGGCGCATCGGCGGCGCATCTGCGCATCGGCGCATCATGCGCATCACACTCGCGCATCTTGCGCATCTCGCGCATCGTGAGCGCATCCCGAGCGCATCGCGCATCTAGCGCATCGCGCATCTCGCGCATCGCGCATCGGCGCATCTCTGGCGCATCGCGCATCGTGACTTGCGCATCGCGCATCGCGCATCGCGCATCCAAGCGCATCGCGCATCCTTGGCGCATCAAATAGGGCGCATCAGCGCATCTCCCGGCGCATCAGCGCATCACTGGCGCATCGAATAAGCGCATCACGACGAAAAACGAGCGCATCGCGCATCATAGCGCATCCTGCGCATCACACCGCGCATCGGCGCATCCTTCTGCGCATCGACGCGCATCGGCGAGCGCATCATACGCGCATCGCGCATCGCGCATCGCGCATCGGGGCGCATCACCAGACGCGTCAGCGCATCCATGCGCATCACCGCGCATCGCGCATCAAGGCGCATCCGGCGCGCGCATCGCGCATCGGCGCATCAGCGCATCGCGCATCGCTCGCGCATCGGGCGCATCTGCGCGCATCGCGCATCGCGCATCGCGCATCGCGCATCTCCCGGTCAATGGGCGCATCGCGCATCCCCCATTAAAAGACCAGATGCGCATCAAGCGCATCGCGCATCGCGCATCGCGCATCTAGCGCATCGGCGCATCAACCAGGCGCATCGCGCATCGACCTGTCTGCGCATCGTAGCGCATCTCCGCGCATCTCCTGGCGCATCCTACGCGCATCTTTTAGCGCATCGCGCATCCGAAGGCGCATCTCGCGCATCAATGCGCATCGGGCGCATCGCGCATCTTAGCGCATCAGTGGCGCATCGCCGCGAAACGCGCATCCTTGCGCATCGCGCATCCGCGCATCGGTACACTTTGCGCATCGGGGGCGCATCTGCGCATCATCAGCGCATCGGAGCGCATCGGAGTGCGCATCTGCGCGCATCTCCGGCGCATCTGCGCATCTGAGGCGCATCGCGCATCACGCGCATCTGTCTCTGCGCATCCTGCGCATCTGCGCATCTTTCAGGAGCGCATCAAGTGGATGGCGCATCTAGCGCATCGGCGCATCTGCGCATCGCTCGCGCATCAACACAGCGCATCGCGCATCACGCGCATCTTTGGGCGCATCGGCGCATCAACGCGCGCATCGGGCGCATCGCGCATCCTACTGTAGTGCGCATCGCGCATCGCCTGCGCATCGGGCGCATCGCGCATCTTGTATGCGCATCGTTTGAGCCGCGCATCCCGCGGTGTGCGCATCGCGCGCATCAAACGCGCATCAGCGCATCTTCCGACGCGCATCCAAGCGCATCCTGCGGCGCATCGCTAAGCGCATCAAGGCGCATCACATATCGAGCGCATCGGGCGCATCAAAGCGCATCGCGCATCGCGCATCGGCCAGCGCATCAACCTCGCGCATCTAGCGCATCGCCGCGCATCACCCCGCGCATCGCGCATCATGCGCATCTGCGCATCGAATAGCGCATCACCAGTAGCGCATCCCGCGCATCTCGCGCATCGTGCGCATCGCATAGCGCATCGCGCATCGGGCGCATCATCTAACGGCGCATCGCGCATCAGGCGCATCATGTCGCGCATCGCGCATCTAGCGCGCATCATTGCGCATCAGGCGCATCGCGCATCCACACTCAGCGCATCACGCGCATCGACATATGCGCATCTTGCGCATCGCGCATCGCGCATCTAGCGCATCTAGCGCATCCGGCGCATCATAGAGGCGCATCCGGCGCATCCGGGTGGGATGGCGCATCTCTGGGCGCATCGTCTGCGCATCGCGCATCTACGCGCATCCGCGCATCTGCCCGCTGCTTGCGCATCCGCGCATCGGCGCATCGCGCATCACCGCGCATCGCGCATCTCAGCGCATCAGCGCATCGGGCGCATCGCGCATCCGTTAGGCGCATCATGCGCATCTTCTGCTGTTGGCGCATCGCGCATCACTTAGCGCATCAGCGCATCCGCGCATCGCGCATCCTGCGCATCGCGCATCGCAACGAGAGCAATAGACCCCTGCGCGCATCCGCGCATCCCCCGTTGCGCATCTTTGCGCATCCCAAAAGCTGCGCATCGCGCATCCACAACAAGCGCGCATCTGCGCATCAGCGCATCGAGCGCATCAGTCGGCGCGACAAGCGCATCGCGCATCATATAGCGCATCGAGGGCGCATCTGCGCATCGCGCATCCCCGCGCATCGCGCATCGCGCATCGCGCATCAGCCGAGCGCGCATCTGCGCATCGCGCATCCGCGCATCCGGCGCATCGCGCATCATACGCGCATCTGCGCATCCCCCCGAGCGGAGGGCGCATCTCCGCGCATCTGCGCATCTCTGGCGCATCACGACCCTCATGGCGCATCCAAGCGCATCGAGCGCATCCGCGCGCATCCAGCGCATCGCGCATCAGCGCATCGTACGCGCATCGGCGCATCATCACGCGCATCGCGCATCTCGCGCATCAGCGCATCCCTAAGCGCATCGGGCGCATCGGGGCGCATCTGCGCATCAGCGCATCGTACGCGCATCAGTGCGCATCCACGCGCATCGATGGGGCGCATCGGCGCATCTGCGCATCAACTCGCGCGCATCAGCGCATCGTGAATGCGCATCTAGTGCGCATCGGGATGCGCATCTGGCTGCGCATCGAACTAGTGCGCATCCGCGCATCGTGCGCATCGGGTTAGTGCGCATCAAACGGCGCATCATTTGCGCATCTGCGCATCTAATGCGCATCAGCAAGTCAGCGCATCGCGCATCGCGCATCTCACCCGGGCGCATCGTGCTGCGCATCGCGCATCGCGCATCCTTGCGCATCATAGGCAGCGCATCCGCGCATCACTGACGCGCATCCACCGTCGCGCATCGCGCATCGCGCATCGCGCATCGCGCATCTGCGCATCAGGCGCATCGAGGGGGCGCATCGCGCATCGGCGCATCTGGCGCATCTGCTACTCAGCGCATCCCGCGCATCAGCGCATCGCGCATCAGGCGCATCTGTCACTTGGGCGCATCTCCGCGCATCACAGGAAGCGCATCAGGCGCATCCGCGCATCTGCGCATCCCGGCGCATCGCGCATCACGCGCATCATTCGCGCATCGCGCATCTCCGGCGCATCGGCGCATCCGAGAAGCGCATCGGGACCGCGCATCCGCGCATCCGCGCATCGCGCATCCAGTCGCGCATCGCGCATCCGCGCGCATCGCGCATCAGCGCATCGGCGCATCGGCGCATCGCGCATCGCGCATCTCTCGCGCATCACGAGCGCATCGCGCATCGTGTTCGCGCATCTTGCGCATCGGCGCATCAATGCGCATCGCGCATCCTTTCAGCGCATCGCGCATCGCGCATCGCGCATCGGGCATCGATCGTGCGCATCGCGCATCGCGGCGCATCGCGCATCCGCGCATCATGCGCATCCTCGGGCGCATCGCGCATCGCAGGCAGCGCATCTGCTAGCATTGATGCGCATCGCGCATCCGCGCATCAAATAGCGCATCATACGCGCATCGCGCATCGCGCATCTGCGCATCAGCGCATCTGCGCATCGCGCATCCGCGCATCACAGCGCATCCATCCCCGCGCATCGCGCATCGCGCATCGCGCATCGCGGAGCGCATCGCGCATCGTGCGCATCGGCGCGCATCGCGCATCAGGCGCATCATTACGCGCATCGCGCATCGCGCATCTCTATGGCGCGCATCCTTAGGCGCATCGTCTAGCGCATCACTCCCTAGACTGCGCATCTAGCGCATCCGCGCATCTTACTTACTCGCGCATCGCGCATCAGCGCATCAAGTTTCGCGCATCTCCGCGCATCCGCGCATCGTGCGCATCAGCGCATCGGTAGGCGCATCACCAGCGCATCTGTGCGCATCGCGCATCGCGCATCCGTTGCGCATCTCACCTGTACAATTGCGCATCACGGCGCATCGCGCATCCTCGGCGCGCATCGGCGCATCGCGCGCATCCACACTGCGCATCGCAACGCGCATCGCGCATCGGCGCATCGGCGCATCGCGCATCTAGCGCATCTAGCAAATTGCGCGCATCGCGCATCTGCGCATCCATGCTAGCGCATCTGCGCATCGCGCATCTTTAGGCGCATCAACTCGCGCGCATCGCGCATCGCTTTACGCTCTGCGCATCCTGTGCGCATCAGCGCATCGGCGCATCGCGCATCGGGTAGATGCGCGCATCGCGCATCCATCGCGCATCAACGCGCATCCGCTGCGCATCCAGACAAGCGCATCGCGCATCGCCGCGCATCTCCGCGCATCGGCGCATCACCCAGCGCATCTCGCGCATCATGTCTGCGCATCTCTAGGCGCATCTGCGCATCAGCGCATCCCAGCGCATCGCGCATCGCGCATCCGCGCATCGCGCATCGGAAGCGCATCTAGCGCATCCGCGCATCCCAGCGCATCGCGCATCTCGCGCATCTGGCGCATCGGCGCGCATCCCATCCCGCGCATCAGTGTTGCGCATCGCGCATCAAGCGCATCGCGCATCGCGCATCTGAGCGCGCATC')
#indicesCombined = patternmatching('GCGCATCGC',s)
#indicesCombined = indices + indicesComp
#indicesCombined.sort()
#print indicesCombined
for i in range(0,len(indicesCombined)):
    a = a+' ' + str(indicesCombined[i])

print(a)