def main(argv=None):
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser()
parser.add_argument("bed", help="input bed")
parser.add_argument("pdf", help="output pdf")
parser.add_argument("--bin", default=10, type=int, help="bin size")
parser.add_argument("--events",
default=" ".join(BedMutations.defaultEvents),
type=str, help="event tags")
parser.add_argument("--xlimit", default=None, type=int,
help="maximum x value to plot")
parser.add_argument("--backgroundBed", default=None, type=float,
help="regions for computing background rate")
parser.add_argument("--title", default=None, type=str,
help="title of plot")
args = parser.parse_args()
binSize = args.bin
events = args.events.split()
bh = BedHistogram()
bh.linearY = False
bh.xlimit = args.xlimit
bgRate = None
if args.backgroundBed is not None:
count, size = getBackgroundRate(args.bed, args.backgroundBed, events)
bgRate = float(count) / float(size)
bh.loadFile(args.bed, binSize, bgRate, events)
bh.writeFigure(args.pdf, args.title)
def main(argv=None):
if argv is None:
argv = sys.argv
parser = argparse.ArgumentParser()
parser.add_argument("bed", help="input bed")
parser.add_argument("pdf", help="output pdf")
parser.add_argument("--bin", default=10, type=int, help="bin size")
parser.add_argument("--events",
default=" ".join(BedMutations.defaultEvents),
type=str,
help="event tags")
parser.add_argument("--xlimit",
default=None,
type=int,
help="maximum x value to plot")
parser.add_argument("--backgroundBed",
default=None,
type=float,
help="regions for computing background rate")
parser.add_argument("--title",
default=None,
type=str,
help="title of plot")
args = parser.parse_args()
binSize = args.bin
events = args.events.split()
bh = BedHistogram()
bh.linearY = False
bh.xlimit = args.xlimit
bgRate = None
if args.backgroundBed is not None:
count, size = getBackgroundRate(args.bed, args.backgroundBed, events)
bgRate = float(count) / float(size)
bh.loadFile(args.bed, binSize, bgRate, events)
bh.writeFigure(args.pdf, args.title)
def computeBackgroundRate(self, mutationsBed, backgroundBed, events):
self.count, self.size = getBackgroundRate(mutationsBed,
backgroundBed, events)
self.rate = float(self.count) / float(self.size)
self.events = events
def computeBackgroundRate(self, mutationsBed, backgroundBed, events):
self.count, self.size = getBackgroundRate(mutationsBed, backgroundBed,
events)
self.rate = float(self.count) / float(self.size)
self.events = events
