genomon_virus_checker

#! /usr/bin/env python

from genomon_virus_checker.run import *
import argparse

parser = argparse.ArgumentParser(prog = "genomon_virus_checker")

parser.add_argument("--version", action = "version", version = "genomon_virus_checker-0.1.0")

parser.add_argument("fastq_file_1", metavar = "sequence1.fastq", default = None, type = str,
                    help = "the path to the read 1 fastq file")

parser.add_argument("fastq_file_2", metavar = "sequence2.fastq", default = None, type = str,
                    help = "the path to the read 2 fastq file")

parser.add_argument("output_prefix", metavar = "output_prefix", default = None, type = str, 
                    help = "the prefix of the output")

parser.add_argument("virus_reference_file", metavar = "virus_reference.fa", default = None, type = str,
                    help = "the path to virus reference file")

parser.add_argument('-q', metavar = "minimum_match_thres", default='30', type=int,
                    help = "threshold for match score for calculating base counts")


args = parser.parse_args()

main(args)