convert FREEC ratio.txt file to bedGraph format

freec2bedgraph.py

"""
Chromosome      Start   Ratio   MedianRatio     CopyNumber
1       1       -1      -1      5
1       9854    4.28786 2.74942 5
1       19707   3.38082 2.74942 5
1       29560   2.56094 2.74942 5
1       39413   2.87198 2.74942 5
1       49266   2.47    2.74942 5
1       59119   2.62686 2.74942 5
1       68972   2.0109  1.81246 4
1       78825   1.51216 1.81246 4
"""
import argparse
with args.txt as infile, args.bedgraph as outfile:
    header = next(infile)
    prev_rname = None
    prev_start = None
    prev_cn = cn
    for line in infile:
        rname, start, ratio, med, cn = line.split()
        if rname == prev_rname:
            outfile.write("chr{0}\t{1}\t{2}\t{3}\n".format(rname, start, prev_start, prev_cn))
            prev_start = start
            prev_cn = cn
        elif rname != prev_rname:
            prev_rname = rname
            prev_start = start
            prev_cn = cn
    outfile.write("chr{0}\t{1}\t{2}\t{3}\n".format(rname, start, prev_start, prev_cn))

def main():
    parser = argparse.ArgumentParser(prog='freec2bedgraph', description="Convert FREEC ratio.txt file to bedgraph format")
    parser.add_argument('txt', type=argparse.FileType('r', 1), help="FREEC ratio.txt file (- as stdin)")
    parser.add_argument('bedgraph', type=argparse.FileType('w', 4096), help="bedgraph output file (- as stdout)")
    args = parser.parse_args()
    freec2bedgraph(args)
    
if __name__ == "__main__":
    main()