separateArms.py

#!/usr/bin/python

import sys, os, re, argparse

parser = argparse.ArgumentParser(description="Divide input copycaller file into p and q segments using an input bed file with centromere coordinates")
parser.add_argument('input', type=str,help="Tab separated copycaller file")
parser.add_argument('centro', type=str,help="Centromere bed file")

class cent(object):
    """centromere objects by chromosome"""
    def __init__(self, line):
        [id, start, end] = line.split("\t")
	self.name = id
        self.p = int(start)
        self.q = int(end)

def getChrom(id, centList, cur):
    if cur and id == cur.name:
	return cur
    for i in centList:
	if id == i.name:
	    return i
    return False

if len(sys.argv)==1:
    parser.print_help()
    sys.exit(1)
args = parser.parse_args()

# Main

centros=[]
f = open(args.centro,'r')
for line in f:
    line = line.strip()
    centobj = cent(line)
    centros.append(centobj)
f.close

splitfile = os.path.join(tmpdir, 'splitchrom.cnv')

with open 
curchrom = False
f = open(args.input,'r')
for line in f:
    line = line.strip()
    fields = line.split("\t")
    if fields[0] == 'chrom':
	print line
	continue
    id = fields[0]
    start = int(fields[1])
    end = int(fields[2])
    curchrom = getChrom(id, centros, curchrom)
    # centromere free chromosomes
    if not curchrom:
	print line
    # print only if segment does not overlap centromere
    elif end < curchrom.p:
	fields[0] = ('.').join([fields[0], 'p'])
	print ("\t").join(fields)
    elif start > curchrom.q:
	fields[0] = ('.').join([fields[0], 'q'])
	print ("\t").join(fields)
f.close