ma2cWigToBedGraph fix MA2C wig output

ma2cWigToBedGraph.py

#!/usr/bin/env python
# Time-stamp: <2012-01-10 17:21:24 Tao Liu>

# in the wiggle file from MA2C, the 1st column -- position is actually
# the center of each probe. Some probes may overlap. In order to
# convert them to appropriate bigwig, I need to create bedGraph file
# with above two problems fixed.

import os
import sys
# ------------------------------------
# Main function
# ------------------------------------
def main():
    if len(sys.argv) < 3:
        sys.stderr.write("""need 2 paras: %s <shift> <MA2C wig file>

        shift: if the position in wig file is not the leftmost position of the represented region, use this option to fix. For example, if a probe is 50bp, and in wig, 1st column is
 the middle points of probes, use -25. Otherwise, use 0
        
        **Make sure your variableStep wig file is from MA2C!
        **In the output, gaps will be filled with 0 and if two regions are overlapped, the later value will be used.
""" % sys.argv[0])
        sys.exit(1)

    ssize = int(sys.argv[1])
    wigfile = open(sys.argv[2],"r")

    #fs = bdgfile.readline().rstrip().split()
    #prev_region = (fs[0],int(fs[1]),int(fs[2]),float(fs[3]))
    prev_region = None


    for l in wigfile:
        if l.startswith("track"):
            continue
        if l.startswith("variableStep"):
            chrom = l.rstrip().split()[1].split("=")[1]
            span = int(l.rstrip().split()[2].split("=")[1])
            continue
        (pos,value) = l.rstrip().split()
        startpos = int(pos) + ssize
        endpos = startpos + span
        curr_region = (chrom,startpos,endpos,float(value))
        
        if not prev_region:
            prev_region = curr_region
            continue
            
        if prev_region[0] == curr_region[0]:
            # only if they are in the same chromosome
            right_pos_of_prev_region = min(curr_region[1],prev_region[1]+span)
            if right_pos_of_prev_region > prev_region[1]:
                print "%s\t%d\t%d\t%.4f" % (prev_region[0],prev_region[1],right_pos_of_prev_region,prev_region[3])
            # fill in gaps with 0
            if curr_region[1] > prev_region[1]+span:
                print "%s\t%d\t%d\t%.4f" % (prev_region[0],prev_region[1]+span,curr_region[1],0)
        else:
            right_pos_of_prev_region = prev_region[1]+span
            if right_pos_of_prev_region > prev_region[1]:
                print "%s\t%d\t%d\t%.4f" % (prev_region[0],prev_region[1],right_pos_of_prev_region,prev_region[3])
        prev_region = curr_region

    # last region
    right_pos_of_prev_region = prev_region[1]+span
    if right_pos_of_prev_region > prev_region[1]:
        print "%s\t%d\t%d\t%.4f" % (prev_region[0],prev_region[1],right_pos_of_prev_region,prev_region[3])


if __name__ == '__main__':
    main()