convert_hg19_bed_to_b37.py

#!/usr/local/Anaconda/envs/py3.4.3/bin/python


"""
Converts hg19 bed files to b37

e.g. 
chr1 100 110 will be converted to 1 100 110 
chrM 100 110 to MT 100 110
"""

import sys

counter = 0
output = []
for line in open(sys.argv[1]):
	line = line.split()
	if line[0][0:3] != "chr":
		counter += 1
	# remove hap contigs
	elif "hap" in line[0]:
		continue
	# rename GLxxxxx contigs to mtach 1000g phaseII notation
	elif "gl" in line[0]:
		line[0] = line[0].split("_")[1].upper() + ".1"
		print('\t'.join(line))
	# Need to hand convert chrM to MT
	elif line[0] == "chrM":
		line[0] = "MT"
		print('\t'.join(line))
	elif counter > 1:
		print("ERROR, multiple non chr lines")
		break
	else:
		line[0] = line[0][3:]
		print('\t'.join(line))