chip-job-music 818 Bytes
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#!/usr/bin/env python

import argparse
import os
import subprocess
import shutil
import glob

parser = argparse.ArgumentParser(description="Run music peak caller prep & peak calling.")
parser.add_argument("--prefix", dest="prefix", required=True, help="Unique prefixectory to create")
parser.add_argument("--controls", dest="controls", required=True, nargs="+", help="Control files to process.")
parser.add_argument("--signals", dest="signals", required=True, nargs="+", help="Signal files to process.")
parser.add_argument("--mapp", dest="mapp", required=True, help="Path to mapability profile")

parser.add_argument("--peak_type", dest="peak_type", required=True, default="narrow", choices=["narrow", "punctate", "broad"], help="Peak calling type to use.")
parser.add_argument("--lmapp", dest="lmapp", default="50")