generateGregorConf

#! /usr/bin/env python3

# TheParkerLab
# Vivek Rai
# GPLv3

__description__ = """Generate a GREGOR config file using supplied options.

The Parker Lab
"""

import argparse
import glob
import sys
import os


def create_index_bed(bedfilename, annotfiles, annotdir):
    with open(bedfilename, 'w') as f:
        if annotfiles is not None:
            for bed_file in annotfiles:
                f.write("{path}\n".format(path=os.path.abspath(bed_file)))
        elif annotdir is not None:
            for bed_file in glob.glob(os.path.join(annotdir + "*.bed")):
                f.write("{path}\n".format(path=os.path.abspath(bed_file)))
        else:
            print("NO OPTIONS: generated skeleton config file (gregor.conf) in current dir")


def getopts():
    parser = argparse.ArgumentParser(description=__description__)
    parser.add_argument('--outfile', type=str, default='gregor.conf',
                        help="""Name of output .conf file""")
    parser.add_argument('--annotfiles', nargs='+', type=str,
                        help="""File with paths of annotation files to calculate enrichment in.""")
    parser.add_argument('--annotdir', type=str,
                        help="""The directory with (unzipped) bed files if --annotfiles are not specified. Will take all .bed files in this directory""")
    parser.add_argument('--snpfile', type=str,
                        help="""chr:pos formatted SNP files. IMPORTANT: filename should not contain '_'""")
    parser.add_argument('--indexbed', type=str, default='indexbed.txt',
                        help="""Name of file to be created with paths of annotfiles""")
    parser.add_argument('--refdir', type=str, default='/lab/data/sw/GREGOR/1.4.0/0.7',
                        help="""GREGOR reference. Default = /lab/data/sw/GREGOR/1.4.0/0.7 """)
    parser.add_argument('--population', type=str, default='EUR',
                        help="""Population. Default = EUR """)
    parser.add_argument('-r2', '--gregorR2Threshold', default='0.8',
                        help="""Minimum LD r2 for proxy SNPs (default: 0.8)""")
    parser.add_argument('--ldwindow', type=int, default=1000000,
                        help="""Minimum LD r2 for proxy SNPs (default: 0.8)""")
    parser.add_argument('-d', '--outdir', type=str,
                        help="""Name of the output directory""")
    parser.add_argument('--neighbor', type=int, default=500,
                        help="""Min neighbors for GREGOR""")
    parser.add_argument('--issorted', type=str, default="true",
                        help="""true or false if bed files are sorted""")
    parser.add_argument('--topnbed', type=int, default=2, help="""Top n bed""")
    parser.add_argument('--cores', type=str, default='6',
                        help="""Number of cores for each GREGOR job. (default: 6)""")
    parser.add_argument('--batchtype', type=str, default='local',
                        help="""Batch job submission type (default: local)""")
    return parser


if __name__ == '__main__':
    parser = getopts()
    args = parser.parse_args()

    args.indexbed = os.path.abspath(args.indexbed)
    create_index_bed(args.indexbed, args.annotfiles, args.annotdir)

    with open(args.outfile, 'w') as f:
        f.write("INDEX_SNP_FILE = {} \n".format(args.snpfile))
        f.write("BED_FILE_INDEX = {} \n".format(args.indexbed))
        f.write("REF_DIR = {} \n".format(args.refdir))
        f.write("POPULATION = {} \n".format(args.population))
        f.write("R2THRESHOLD = {} \n".format(args.gregorR2Threshold))
        f.write("LDWINDOWSIZE = {} \n".format(args.ldwindow))
        f.write("OUT_DIR = {} \n".format(args.outdir))
        f.write("MIN_NEIGHBOR_NUM = {} \n".format(args.neighbor))
        f.write("BEDFILE_IS_SORTED = {} \n".format(args.issorted))
        f.write("TOPNBEDFILES = {} \n".format(args.topnbed))
        f.write("JOBNUMBER = {} \n".format(args.cores))
        f.write("BATCHTYPE = {} \n".format(args.batchtype))