#!/usr/bin/python

import re

# 1 # Read sequences and store them in a hash/dictionary

nonhuman = {}
id = ''
seq = ''
id_human = ''
humanseq = ''

for line in open('foxp2.fasta'):
    line = line.rstrip()
    if re.search('^>', line):
        if id != '':
            if not re.search('HUMAN', id):
                nonhuman[id] = seq
            else:

                humanseq = seq
                id_human = id

        id = line.replace('>', '')
        seq = ''
    else:

        seq += line

nonhuman[id] = seq    # this assumes that we know that the
                      # final sequence read is non human

# 2 # Analyze the multiple alignment

for i in range(0, len(humanseq)):
    unique = 1
    for key in nonhuman.keys():

        # check if the amino acid in the human sequence
        # is the same as in the non-human sequence

        if humanseq[i] == nonhuman[key][i]:
            unique = 0
    if unique:
        print 'At position i'
        aa = humanseq[i]
        print id_human, '\t', aa
        for key in nonhuman.keys():
            aa = nonhuman[key][i]
            print key, '\t', aa