base_changer2.py

import csv
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from sys import argv
script, ref, subs, outfile = argv
out = open(outfile, 'wb')
seq_string = []
user_descrip=raw_input("Give the file a description: ")
with open(ref, "r") as infile:
	for k, line in enumerate(infile):
        
                if ">" in line:
                	pass
            	else:
                	seq_string.append(line.strip("\n"))

seq_str = "".join(seq_string)
print len(seq_str)
new_indexed_seq=list(seq_str)
with open(subs) as subs_file:
	subs_reader=csv.reader(subs_file, delimiter='\t')
	for line in subs_reader:
		pos = (int(line[0]) - 1)
		base = line[1]
		original_base=seq_str[pos]
		
		
		new_indexed_seq[pos]=base

out_string="".join(new_indexed_seq)

with open(outfile, 'wb') as out:
	out_seq = SeqRecord(Seq(out_string), id = 'anscestral_sequence', description=user_descrip)
	SeqIO.write(out_seq, out, 'fasta')