rosalind_hamming(hamm).py

# -*- coding: utf-8 -*-
# Diane Kaplan
# Rosalind Problem: hamm (counting point mutations)
# May 30, 2015


    
DEBUG = True
# hamming_distance finds the number of differences between two sequences:
# compare values for inequality at each position in the sequence and increment counter

def hamming_distance (seq, comparison_seq):  
    cursor = 0
    string_length = len(seq)
    difference_counter = 0

    while cursor < string_length:  #ours are all the same length, could also add a check/flexbility
        if seq[cursor] != comparison_seq[cursor]:        
    	   difference_counter += 1
        cursor += 1
    return difference_counter


string1 = 'TTCGAGGCTTTTGCGGACCTTAATCTTTATTGAGTTCCGCTACCTCTCAGCTCAATGACGTTTCGTGTGAATTTTTGTGAGTTCGGGCGGGAAGACCTCGCACCCCCGACACTTTCCCTAAAACTCGGATAGAAATGTTGACGGCCTTCACTGGCAGGGGAATCCCACATCTTGGCGCGTAGTGGTCTGGTGGATAGACAGATGGTACCAGTCGCAAGCGTCTGACTAGTGGCGATGAGTGCTAGACCCACCTAAGGTAACGGCAACGAATTGCTTAATCTACTTCAGGTTAGTAATGTCAGACGGTGTAGCACCCCTAAAGAGAAGGACAGGGGTGGGGCGCGCCAGGCTGATCTCCCGGCCTAATTCAAAGCGGATGTAAACCGTCTAGGTACTCTAGGATGCAGGGCAAGTACAGGACAAATCCTCATCGAGCCTGTACTCTTGCGAATACCGGACCTAGGCTCCTAACTTTGTCCTTTCTGTTACGATGATTGTACGCTAAGAGTTAGAAATTACCATGTCACACGGATTTTCGTCGCCACTAGCTATTCACGCGCACGAGAGTTGGTCTCACTTCTAAACGGTCGTATATGCTTAGATTACAGTATGCCCAGACGGGTTGTCTCTTTAGCCGCTACCATCCACCGGATCGACGACCCCCTAAGATTGGGGGAGAACTCCAGCAATTTCCTAGACAGCCAATCTAGGGGGTCATAAATCCGGGCAATTCCTGTAGTATACCCAATAACCCCAGCATGGCGGATCGCTATGTACATACTAATAACTTGCAACCGGGCCGTCCGACAGACATGCCTTCGCGCTCTATTCCCTAGCCGAGTCTACGCTAACATAAAGGTAGCTTCGAGTGGTGCCGAGTCATCCCCTCGGGAGATCCCCGCTTAACCCCTAAGATCTTGCACAAGAT'
string2 = 'CGTATGACGTTGACGGAAATTGACCCATAGTCTGTTAACGGCCCGGTGATCACCAAGACTGCAGCGAGTAATGGGGGTAAGGTTTGGCTCGCAGACCTGTGCGTCCGTTCTCTTACCCTGAGACTCGAAGCAATATGTGATACGCCTTCAAGGCCAGGCGAATCCCTCGGCTTTGCGAGTAGTTTTACGATGTTCGTAGGGATTCGAACTCGAGCAACCTTCGCCCCGGTCGAAAAGTGTTCTATATCAACCGACGATTCGTGCTACGCAGTCCTGCTCCTGCGCGAGTGAGAATCTCTCACGTGATGCAGCTCCCCGATGATGACTGACTGGCTTGGTTCGCGCAGGGACTTCCCTCCGGTATAAACCCTAGGCGATATCCATTAGGGTTGTAAGCACGAATACAAGGCAACGAAAGTGCAAAAGCTTCCCGCGTGTATTAGCTAGTCATCACTCGTCCTAGGTGACATACCTACGCCAACATAATTAGATGACAATAGACTATTGTCACAAACCCATCTTGTCACCCGAACGACCCTTCACACTCTATTTCACTCAATTTATGATTTGGTGTTTGGGCTCAAGAGAAGTACATGATTATAGCACAGCCTGATACGAAACATTAATGCTTAATCCCTAACCCTAGTTCGCACAGCCGTTCCCGCATTGTTGGAAGACAAATCCTCAAAGATCTAGGGCTGACAATCCACGGCAGCTCGAACGCGTGCATTTGCTGGAGATCACTCCCCATGAGCCTCATAAACTGTCCCTAACTCAGTACGAAAATCATTCTTGACGGCATCCCCCAAGATCTGCTTTCGCGCCCACTGCCGCCGCTGACACAACGCTAAAATAATGTTCGCCGGCCTATCTGAGGGGAATGTTTCTTGTAAATAACCCGGTACAAGGTTATCATCTAGCGGAAGAG'

print hamming_distance(string1, string2)