#!/usr/bin/env python3.7
import argparse
from bfg_analysis import read_counts
# Author: Roujia Li
# email: Roujia.li@mail.utoronto.ca
parser = argparse.ArgumentParser(description='BFG-Y2H')

# make fasta from summary file (AD and DB)
# -- create: creates fasta file from summary.csv
# parser.add_argument('--pfasta', help="Path to fasta file")

# parameters for cluster
if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='BFG-Y2H')

    # make fasta from summary file (AD and DB)
    # -- create: creates fasta file from summary.csv
    # parser.add_argument('--pfasta', help="Path to fasta file")

    # parameters for cluster
    parser.add_argument("-r1", help="Read 1 SAM file")
    parser.add_argument("-r2", help="Read 2 SAM file")
    # parser.add_argument("--AD_GROUP", help="AD group number")
    # parser.add_argument("--DB_GROUP", help="DB group number")
    # parser.add_argument("--mode", help="Mode (yeast, human, virus, hedgy)")
    parser.add_argument("--cutoff", help="SAM reads quality cutoff", type=int)
    parser.add_argument("--genes", help="path to file that contains all gene (AD and DB) for this sample")
    parser.add_argument("-o", "--output", help="Output path")
    args = parser.parse_args()

    read_counts.RCmain(args.r1, args.r2, args.output, args.cutoff, args.genes)
