Script to bin chromosome

bin_chromosome.py

#!/usr/bin/env python
# Time-stamp: <2013-09-24 15:23:09 Tao Liu>

import os
import sys
# ------------------------------------
# Main function
# ------------------------------------
def main():
    if len( sys.argv ) < 4:
        sys.stderr.write( "Divid chromosomes into fixed sized bins. Bins could be overlapping.\n\n" )
        sys.stderr.write( "need 3 paras: %s <binsize> <stepsize> <chromlen file>\n" % sys.argv[0] )
        sys.stderr.write( "  binsize: fixed size of each bin\n" )
        sys.stderr.write( "  stepsize: fixed size of each bin (set as binsize if overlapping is not desired.)\n" )
        sys.stderr.write( "  chromlen file: chromsome name, chromosome length file from UCSC genome browser site\n\n" )
        sys.exit( 1 )

    binsize = int( sys.argv[1] )
    stepsize= int( sys.argv[2] )
    clfhd   = file( sys.argv[3], "r" )

    bin_index = 1

    for l in clfhd:
        l = l.strip()
        fs = l.split()
        chrname = fs[0]
        chrlen  = int( fs[ 1 ] )

        startpos = 0

        for endpos in xrange( binsize, chrlen + stepsize, stepsize ):
            if min( chrlen, endpos ) > startpos:
                print "%s\t%d\t%d\tbin_%d\t%d" % ( chrname, startpos, min( chrlen, endpos ), bin_index, min( chrlen, endpos ) - startpos )
            startpos += stepsize
            bin_index += 1

    #done


if __name__ == '__main__':
    main()