import glob
import os
import argparse
import sys
import subprocess
from datetime import datetime

now = datetime.now()

parser = argparse.ArgumentParser()
parser.add_argument('-input_directory', '-i', type=str, help='path to data')
parser.add_argument('-project_req', '-pr', type=str, help='quast folder')
opts = parser.parse_args()


def check_directories_exist(filepath, file_description):
    """ to check if the directory exist"""
    if not os.path.exists(filepath):
        print(file_description + "," + filepath + "," + " doesn't exist")
        sys.exit(1)
    else:
        print(file_description + " detected")


def quast_quality_assembler(quast_file, quast_dir, ref_file, assembly_dir):
    """ to check the quality of the assemblies using a reference fasta
    file for Serratia marcencens
    :param  quast_file
    :param quast_dir
    :param ref_file
    :param assembly_dir"""
    cmd = [quast_file, '-o', quast_dir, '-r', ref_file, '-L', assembly_dir]
    my_assemblies = subprocess.Popen(cmd)
    my_assemblies.wait()


def main():
    # if not enough arguments are key, it will show the help

    if len(sys.argv) <= 2:
        parser.print_help()
        sys.exit()
    else:
        # this will write all the print statement into a file
        timenow = datetime.now()
        sys.stdout = open('runlog.txt', 'wt')
        # to check if the directories exist
        check_directories_exist(opts.input_directory, 'input_directory' + "\t" + str(timenow))
		check_directories_exist(opts.project_req, 'project_req' + "\t" + str(timenow))
        ref_file = opts.project_req + "/ref_serratia.fasta"
        quast_file = opts.project_req + "/quast-5.2.0/quast.py"
        quast_dir = opts.input_directory + "/quast_results/"
		# Using glob.glob I get the error "TypeError: expected str, bytes or os.PathLike object, not list" but if I don't using
        assembly_dir = glob.glob(opts.input_directory + '/unicycler_assemblies/*/*.fasta')
		#removing glob.glob I get the error "ERROR! File not found (contigs): /home/my_name/my_project/test_assemblies/unicycler_assemblies/*/*.fasta
	assembly_dir = opts.input_directory + '/unicycler_assemblies/*/*.fasta'
	quast_quality_assembler(quast_file, quast_dir, ref_file, assembly_dir)


main()