updated snpTable2GenomeAlignment.py to python 3 version

snpTable2GenomeAlignment.py

@@ -1,46 +1,47 @@
-#!/bin/env python
+#!/usr/bin/env python3
 
 '''
 Copyright (c) 2015, David Edwards, Bernie Pope, Kat Holt
 All rights reserved. (see README.txt for more details)
+
+Updated to python3 by Kelly Wyres, 2018
 '''
+
+
+
 # input = reference sequence and table of SNP alleles
 # output = mfasta whole genome alignment of pseudosequences
 import string, re, collections
 import os, sys, subprocess
-from optparse import OptionParser
+import argparse
 from Bio import SeqIO
 from Bio.SeqRecord import SeqRecord
 from Bio.Seq import MutableSeq
 
-def main():
-
-	usage = "usage: %prog [options]"
-	parser = OptionParser(usage=usage)
+def get_arguments():
+	parser = argparse.ArgumentParser(description='create whole genome pseudo aln using snp matrix and reference')
+	parser.add_argument("-r", "--ref", action="store", dest="ref", help="reference (fasta)", default="")
+	parser.add_argument("-s", "--snps", action="store", dest="snps", help="snp table (CSV)", default="")
+	parser.add_argument("-o", "--offset", action="store", dest="offset", help="offset (added to SNP positions in table to match reference coordinates)", default="0")
 
-	parser.add_option("-r", "--ref", action="store", dest="ref", help="reference (fasta)", default="")
-	parser.add_option("-s", "--snps", action="store", dest="snps", help="snp table (CSV)", default="")
-        parser.add_option("-o", "--offset", action="store", dest="offset", help="offset (added to SNP positions in table to match reference coordinates)", default="0")
-#	parser.add_option("-f", "--format", action="store", dest="format", help="format (fasta)", default="fasta")
-
 	return parser.parse_args()
 
-if __name__ == "__main__":
+def main():
 
-	(options, args) = main()
+	# Get arguments
+	args = get_arguments()
 
 	# read in ref seq
-#	ref = SeqIO.read(options.ref, options.format)
-	ref = SeqIO.read(options.ref, "fasta")
+	ref = SeqIO.read(args.ref, "fasta")
 
 	# read in SNP info
-	f = file(options.snps,"r")
+	f = open(args.snps,"r")
 	strains = []
 	snps = collections.defaultdict(dict) # key 1 = strain, key2 = pos (corrected by offset), value = allele
 	for line in f:
 		fields = line.rstrip().split(",")
 		if len(strains) > 0:
-			pos = int(fields[0]) + int(options.offset)
+			pos = int(fields[0]) + int(args.offset)
 			for i in range(1,len(fields)):
 				snps[strains[i]][pos] = fields[i]
 		else:
@@ -52,6 +53,8 @@ def main():
 		seq = ref.seq.tomutable()
 		for snp in snps[strain]:
 			seq[snp-1] = snps[strain][snp]
-		print ">" + strain
-		print str(seq)
+		print(">" + strain)
+		print(str(seq))
 
+if __name__ == '__main__':
+	main()