# File: hw3_4.py
# This program introduces single base-pair mutations 
# (i.e. replacement of A by T/C/G, G by A/T/C, etc...)
# into a DNA string at a rate of 1%
# (i.e. ~1 mutation every 100 base pairs)

import random

print 'Enter path to file containing DNA string:'

# Ask for path to file containing DNA string
# and load DNA string into memory
dna = open(raw_input(), 'U').read()

print "Enter name of output string:"

# Ask under what name to store output string
# and create output file
output = open(raw_input(), 'w')

# Initialize random variable
mutation = 1

# Go through the DNA string
for letter in dna:
    # Read every base pair
    if letter == 'g' or letter == 'G' \
        or letter == 'c' or letter == 'C' \
        or letter == 'a' or letter == 'A' \
        or letter == 't' or letter == 'T':

            # Generate a random number in [0,1) according to the uniform
            # distribution in order to determine if a mutation occurs
            mutation = random.random()

            # If it does, replace the current base pair by a 
            # different base pair chosen at random (uniformly)
            if 0.1 < mutation and mutation < 0.11:
                #output.write('R')
                mutation = random.randint(1, 3)
                if letter == 'g' or letter == 'G':
                    if mutation == 1:
                        output.write('c')
                    elif mutation == 2:
                        output.write('a')
                    elif mutation == 3:
                        output.write('t')
                elif letter == 'c' or letter == 'C':
                    if mutation == 1:
                        output.write('g')
                    elif mutation == 2:
                        output.write('a')
                    elif mutation == 3:
                        output.write('t')
                elif letter == 'a' or letter == 'A':
                    if mutation == 1:
                        output.write('g')
                    elif mutation == 2:
                        output.write('c')
                    elif mutation == 3:
                        output.write('t')
                elif letter == 't' or letter == 'T':
                    if mutation == 1:
                        output.write('c')
                    elif mutation == 2:
                        output.write('a')
                    elif mutation == 3:
                        output.write('g')
            else:
                output.write(letter)
    # Maintain layout
    elif letter == '\n':
        output.write(letter)