peakseq_wrapper.py

#!/usr/bin/env python

# Simple PeakSeq wrapper. Simply returns if the input file isn't
# found, instead of failing.

import sys
import os
import subprocess

if __name__ == '__main__':
    if len(sys.argv) < 8:
        print "Usage: peakseq_wrapper.py <PeakSeq_binary> <sample_input_file> <control_input_file> <output_sgr_file> <output_hits_file> <bin_size> <mappability_file>"
        raise SystemExit(1)
    if not os.path.exists(sys.argv[2]):
        print "Cannot find sample eland file %s, skipping scoring."  % sys.argv[2]
        raise SystemExit(0)
    subprocess.call(' '.join(sys.argv[1:]), shell=True)