fix_coords.py

#!/usr/bin/python
usage = """
Ensures start/stop coords in a BED file are integers
and not in exponential notation (like 9.3e+07)

Usage:

    python fix_coords.py input.bed > fixed.bed
"""
import sys
if len(sys.argv)<2:
    print usage
    sys.exit()
for line in open(sys.argv[1]):
    L = line.strip().split('\t')
    start = float(L[1])
    stop = float(L[2])
    L[1] = '%d' % start
    L[2] = '%d' % stop
    sys.stdout.write('\t'.join(L)+'\n')