bedFixBlockOverlaps

#!/usr/bin/env python

import logging, sys, optparse
from collections import defaultdict
from os.path import join, basename, dirname, isfile

# === COMMAND LINE INTERFACE, OPTIONS AND HELP ===
parser = optparse.OptionParser("usage: %prog [options] filename - fix overlapping blocks in a bed file, produced e.g. by pslMap") 

parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages") 
#parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
#parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
(options, args) = parser.parse_args()

if options.debug:
    logging.basicConfig(level=logging.DEBUG)
else:
    logging.basicConfig(level=logging.INFO)
# ==== FUNCTIONs =====
    
# ----------- MAIN --------------
if args==[]:
    parser.print_help()
    exit(1)

filename = args[0]
if filename=="stdin":
    ifh = sys.stdin
else:
    ifh = open(filename)

for line in ifh:
    row = line.rstrip("\n").split("\t")
    bSizes = [int(x) for x in row[10].strip(",").split(",")]
    bStarts = [int(x) for x in row[11].strip(",").split(",")]
    newLens = []
    newStarts = []

    pos = 0
    for bs, bl in zip(bStarts, bSizes):
        if pos>bs:
            diff = pos-bs
            bs = pos
            bl = bl-diff
        #print bs, bl, pos, bs, bl
        pos+= bl
        newLens.append(str(bl))
        newStarts.append(str(bs))
    row[10] = ",".join(newLens)
    row[11] = ",".join(newStarts)
    print "\t".join(row)