catt

#!python3
import argparse
import os
import sys

def CommandLineParser():
    parser = argparse.ArgumentParser(
        prog="CATT",
        description="What the program does",
        epilog='Text at the bottom of help'
    )
    group = parser.add_mutually_exclusive_group()
    group.add_argument('-f', '--file', action='append', default=[], help="Input file path")
    group.add_argument("--f1", action='append', default=[], help='Input file path with #1 mates')
    parser.add_argument("--f2", action='append', default=[], help='Input file path with #2 mates')
    parser.add_argument('-o', '--output', action='append', default=[], required=True, help='Output path, prefix shoulde be included.')
    parser.add_argument('-t', '--thread', default=4, type=int, help='Thread number used by CATT')
    parser.add_argument('-k', '--kmer', default=10000, type=int)
    parser.add_argument("--chain", default="TRB", choices=['TRB', 'TRA', 'IGH', 'IGL', 'TRD', 'TRG'])
    parser.add_argument("--region", '-r', default="CDR3", choices=['CDR1', 'CDR2', 'CDR3'])
    parser.add_argument("--bowt", type=int, default=8, help="Thread used for bowtie align.")
    parser.add_argument("--sc", action="store_true", default=False)
    parser.add_argument("--debug",  action='store_true', default=False)
    parser.add_argument("--bowsc",  default=12, type=int)
    parser.add_argument('--penality',default=1, type=int)
    parser.add_argument("--bam", action="store_true", dest='bam', default=False)
    parser.add_argument("--species", default='hs', choices=['hs', 'ms', 'pig'])
    parser.add_argument('--proV', dest='proV', action='append', default=[], help="processed file pathV ")
    parser.add_argument('--proJ', dest='proJ', action='append', default=[], help="processed file pathJ ")
    return parser.parse_args()


def convert( arg ):

    if arg is None:
        return "nothing"

    if type(arg) == str:
        return '"' + arg + '"'
    elif type(arg) == int:
        return arg
    elif type(arg) == bool:
        return "true" if arg else "false"
    else:
        return arg

if __name__ == '__main__':
    
    abp = os.path.abspath(sys.argv[0])[0:-5]
    args = CommandLineParser()

    #Index check
    if not os.path.exists("./resource/TR/hs/%sV.fa.bwt" % getattr(args, 'chain')):
        os.system("bwa index ./resource/TR/hs/%sV.fa" % getattr(args, 'chain'))
        os.system("bwa index ./resource/TR/hs/%sJ.fa" % getattr(args, 'chain'))

    with open("%s/config.jl" % abp, "w") as handle:
        handle.write("parsed_args = Dict(\n")
        for arg in vars(args):
            line = "{} => {},\n".format(convert(arg), convert((getattr(args, arg))))
            handle.write(line.replace('\'', "\""))
        handle.write(")")

    os.system('export JULIA_NUM_THREADS=%d && julia %s/catt.jl' % (getattr(args, "thread"), abp) )