Python script that converts a bedGraph format file to a wig file.

bedgraph_to_wig.py

#!/usr/bin/env python
#
# Convert bedgraph file into wig format
#
# Based on perl script by Dave Tang
# http://davetang.org/wiki/tiki-index.php?page=wig
import optparse
import os
import gzip

if __name__ == "__main__":
     
    # Process command line
    p = optparse.OptionParser(usage="%prog [OPTIONS] BDG [WIG]")
    p.add_option('-c','--compress',action="store_true",dest="compress",default=False,
                 help="Compress (gzip) the output wig file")
    p.add_option('-n','--name',action="store",dest="name",default=None,
                 help="Set the 'name' field in the wig file")
    p.add_option('-d','--description',action="store",dest="desc",default=None,
                 help="Set the 'description' field in the wig file")
    p.add_option('-s','--step',action="store",dest="step_size",type='int',default=1,
                 help="Set the step size (default is 1)")
    options,args = p.parse_args()
    if len(args) != 1:
        p.error("Need to supply input bdg file name")
    bdg = args[0]
    if len(args) == 1:
        wig = os.path.splitext(os.path.basename(bdg))[0] + '.wig'
    elif len(args) == 2:
        wig = args[1]
    else:
        p.error("Too many arguments")
    if options.compress:
        if not wig.endswith('.gz'):
            wig += '.gz'
        fwig = gzip.GzipFile(filename=wig,mode='wb',compresslevel=9)
    else:
        fwig = open(wig,'w')
    if options.name is not None:
        name = options.name
    else:
        name = os.path.basename(bdg)
    if options.desc is not None:
        desc = options.desc
    else:
        desc = os.path.basename(bdg)
    step = options.step_size
    fwig.write("track type=wiggle_0 name=\"%s\" description=\"%s\" visibility=full\n" %
               (name,desc))
    for line in open(bdg,'r'):
        chrom,start,end = line.strip().split('\t')[:3]
        data = '\t'.join(line.strip().split('\t')[3:])
        fwig.write("fixedStep chrom=%s start=%s step=%d span=1\n" % (chrom,start,step))
        for i in xrange(int(start),int(end)+1,step):
            fwig.write("%s\n" % data)
    fwig.close()