def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument(dest="bamfile")
parser.add_argument('-o', dest='outfile')
parser.add_argument('-w', dest='window')
parser.add_argument('-e', dest="extend", default=0)
parser.add_argument('--paired-end', dest="pe", action="store_true")
args = parser.parse_args()
# Split BAM by strand
split_bam = splitByStrand(args.bamfile, args.pe)
# Split BAM to Wig
for bam in split_bam:
print "BAM to WIG..."
print bam
w = b2w.windower(bam, bam.split(".bam")[0] + ".wig", args.window, args.extend, args.pe, "", "", "", "")
w.window()
#Wig to Track
for bam in split_bam:
print "WIG to Track..."
print bam
wig2Track(bam.split(".bam")[0] + ".wig", args.outfile, args.window)
def wig(self):
window_size = str(200)
bamname = "/".join([self.output, "accepted_hits_sort.bam"])
wigdir = "/".join([wig_dir, self.input_prefix])
if not os.path.exists(wigdir): os.makedirs(wigdir)
wigfile = "/".join([wigdir, "_".join([self.input_prefix, window_size]) + ".wig"])
extend = self.mean
pe = not self.single_end
wi = BAMtoWIG.windower(bamname, wigfile, window_size, extend, pe)
print "Writing WIG..."
wi.window()
wi.wigfile.close()
wi.tdf()
def wig(self):
#pdb.set_trace()
window_size = str(25)
bamname = "/".join([self.output, "accepted_hits.bam"])
wigdir = "/".join([wig_dir, self.sample])
if not os.path.exists(wigdir): os.makedirs(wigdir)
wigfile = "/".join([wigdir, "_".join([self.sample, window_size]) + ".wig"])
extend = self.mean
pe = not self.single_end
wi = BAMtoWIG.windower(bamname, wigfile, window_size, extend, pe, False, False)
print "Writing WIG..."
wi.window()
wi.wigfile.close()
wi.tdf()
