# score_oligo.py
# Author: Neha Bhagwat
# Last updated: December 31, 2017
# Purpose: Program to score a sequence using the pwm generated by create_pwm.py
# Program uses the Python function open() and the Python methods read(), write(),
#    close() and split()
#
from __future__ import division

# Read a list of sequences of size 9, one per line, from the file Donor_MOG.txt
input_file = open("Donor_MOG.txt", "r")
input_data = input_file.read()
input_file.close()

input_list = input_data.split("\r\n")

# Take as input Donor_MOG_matrix.txt to read the values of the PWM
pwm = open("Donor_MOG_matrix.txt","r")
pwm_data = pwm.read()
pwm_set = pwm_data.split("\n")
a = pwm_set[0].split('\t')
a = a[0:9]
c = pwm_set[1].split('\t')
c = c[0:9]
g = pwm_set[2].split('\t')
g = g[0:9]
t = pwm_set[3].split('\t')
t = t[0:9]
 
pwm.close()
output_file = open("Donor_MOG_scores.txt", "w")
# Compute the score of each sequence read from the file Donor_MOG.txt
for ele in input_list:
    total = 0
    for i in range(9):
        if ele[i] == 'A':
            total = total + float(a[i])
        elif ele[i] == 'C':
            total = total + float(c[i])
        elif ele[i] == 'G':
            total = total + float(g[i])
        elif ele[i] == 'T':
            total = total + float(t[i])
    # Write each input sequence followed by it's score into the file
    #     Donor_MOG_scores.txt
    output_file.write(ele + "\t" + str(total) + "\n")

output_file.close()