make_indices.py

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

def options():
    parser = argparse.ArgumentParser(description="Generate Indices for STAR",
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument("-nThreads", help="Number of threads to use for STAR", default="8")
    parser.add_argument("-read_length", help="Input max(ReadLength)-1", default="49")
    parser.add_argument("-st",
                        metavar="Star Indices",
                        default = "/shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/assembly/STAR_indices_masked",
                        help="Directory for STAR indices")
    parser.add_argument("-mg",
                        metavar = "Genome (masked)",
                        default = "/shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/assembly/Bdistachyon_314_v3.0.hardmasked.fa",
                        help="Masked genome fasta file")
    parser.add_argument("-gff",
                        default = "/shares/tmockler_share/clizarraga/Brachypodium_distachyon/Phytozome/v3.1/annotation/Bdistachyon_314_v3.1.gene_exons.gff3",
                        help="GFF file for STAR")
    parser.add_argument("-usegtf", action="store_true", help="Use GTF with STAR instead of GFF (pass GTF to -gff)")
    parser.add_argument("-config", help="Use Config file instead of CLI parameters", default=None)
    args = parser.parse_args()
    return args


def main():
    args = options()
    # Either using a Config file or straight command line parameters.
    if args.config:
        if sys.version_info[0] < 3:
            import ConfigParser
            Config = ConfigParser.ConfigParser()
        else:
            import configparser
            Config = configparser.ConfigParser()
        Config.read(args.config)
        nThreads = Config.get("ALL", "nThreads")
        read_length = Config.get("STAR", "read_length")
        st = Config.get("STAR", "star_indices")
        mg = Config.get("STAR", "reference")
        gff = Config.get("STAR", "annotation")
        usegtf = Config.getboolean("STAR", "usegtf")
    else:
        nThreads = args.nThreads
        read_length = args.read_length
        st = args.st
        mg = args.mg
        gff = args.gff
        usegtf = args.usegtf
    if usegtf:
        cmd = "STAR --runThreadN {0} --runMode genomeGenerate --genomeDir {1} --genomeFastaFiles {2} --sjdbGTFfile {3} --sjdbOverhang {4}" \
          .format(nThreads, st, mg, gff, read_length)
    else:
        cmd = "STAR --runThreadN {0} --runMode genomeGenerate --genomeDir {1} --genomeFastaFiles {2} --sjdbGTFfile {3} --sjdbGTFtagExonParentTranscript Parent --sjdbOverhang {4}" \
          .format(nThreads, st, mg, gff, read_length)
    print("Running cmd: ")
    print(cmd)
    subprocess.call(cmd, shell=True)


if __name__ == "__main__":
    main()