newgenome

#!/usr/bin/env python3
################################################################
#  This file part of GALA Gap-free Long-reads Assembler        #
#  Auther: Mohamed awad                                        #
#  Company: Xiangchao Gan lab (MPIPZ)                          #
#  Released under the (MIT) license (see LICENSE file)         #
################################################################
import os
import sys
scr='src'
path=os.path.dirname(os.path.abspath(__file__))
absolute=os.path.join(path,scr)
sys.path.insert(0, absolute)
from new_genome import genomes
import argparse
parser = argparse.ArgumentParser(prog="newgenome",usage='%(prog)s -h  [options] <draft_names & paths> <path to cut files>',description='Produce mis-assembly free genomes, part of GALA Gap-free Long-reads Assembler')

parser.add_argument("draft",nargs=1,type=str,help='Draft names and paths\t[required]')
parser.add_argument("cut_files",nargs=1,type=str,help='path_to_cut_files" \t [required]')
parser.add_argument("-f",nargs=1, type=str, default=['gathering'], metavar='Output files name\t[default gathering]',dest="name")
parser.add_argument("-o",nargs=1, type=str, default=[os.getcwd()], metavar='output files path\t[default current directory]',dest="output")
parser.add_argument('-v','--version', action='version', version='%(prog)s 1.0.0')
args = parser.parse_args()
gathering=args.cut_files[0]
draft=args.draft[0]
output=args.output[0]
name=args.name[0]
genomes(genomes=draft,gathering=gathering,gathering_name=name,outpath=output)
if '-v':
	parser.parse_args(['-v'])