run_sicer.py

#!/usr/bin/python
from __future__ import print_function
import argparse
import subprocess
import os


def options():
    parser = argparse.ArgumentParser(description="Run SICER on Treatment vs Control")
    parser.add_argument("InputDir", help="Directory where input files are located")
    parser.add_argument("bed_file", help="Treatment bed file for sample size")
    parser.add_argument("control_file", help="Control bed file for sample size")
    parser.add_argument("OutputDir", help="Directory where output files go")
    parser.add_argument("--species", dest="species", help="Species in SICER", default="bdist")
    parser.add_argument("--rdthresh", dest="rdthresh", help="SICER redundancy threshold", default="1")
    parser.add_argument("--winsize", dest="winsize", help="SICER window size", default="200")
    parser.add_argument("--fragsize", dest="fragsize", help="SICER fragment size", default="150")
    # Maybe efg for Brachy should be: 0.84 or 0.98 depending on how you look at it.
    parser.add_argument("--egf", dest="egf", help="SICER Effective Genome Fraction", default="0.95")
    parser.add_argument("--gap_size", dest="gap_size", help="SICER gap size", default="600")
    parser.add_argument("--FDR", dest="FDR", help="SICER False Discovery Rate", default="1E-2")
    args = parser.parse_args()
    return args


def main():
    args = options()
    print(args)
    # Getting the absolute path to file if relative path given.
    # args.input_file = os.path.abspath(args.bed_file)
    # args.control_file = os.path.abspath(args.control_file)
    # Getting just the filename
    args.OutputDir = os.path.abspath(args.OutputDir)
    args.InputDir = os.path.abspath(args.InputDir)
    basepre = '-'.join(args.bed_file.split('-')[3:7])
    OutputDir = os.path.join(args.OutputDir, basepre)
    print(OutputDir)
    try:
        os.makedirs(OutputDir)
    except OSError:
        if not os.path.isdir(OutputDir):
            raise
    # Creating the output file path.
    SICER = "/shares/tmockler_share/clizarraga/usr/local/SICER_V1.1/SICER/SICER.sh"
    # Generate Indices
    # sh DIR/SICER.sh ["InputDir"] ["bed file"] ["control file"] ["OutputDir"]
    # ["Species"] ["redundancy threshold"] ["window size (bp)"] ["fragment size"]
    # ["effective genome fraction"] ["gap size (bp)"] ["FDR"]
    cmd = "sh {0} {1} {2} {3} {4} {5} {6} {7} {8} {9} {10} {11}" \
          .format(SICER, args.InputDir, args.bed_file, args.control_file, OutputDir, args.species,
                  args.rdthresh, args.winsize, args.fragsize, args.egf, args.gap_size, args.FDR)
    print("Running cmd: ")
    print(cmd)
    subprocess.call(cmd, shell=True)

if __name__ == "__main__":
    main()