#!/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 joining import reformated

import argparse

parser = argparse.ArgumentParser(prog="reformat",usage='%(prog)s -h [options] <path/to/mapping_files> <number of drafts>',description='Re-formatting mapping files tool, part of GALA Gap-free Long-reads Assembler')

parser.add_argument("mapping_files",nargs=1,type=str,help='mapping paf file \t [required]')

parser.add_argument("drafts",nargs=1,type=int,help='Number of drafts\t[required]')

parser.add_argument("-b",nargs=1, type=int, default=[5000], metavar='Alignment block length\t [default 5000]',dest="block")

parser.add_argument("-p",nargs=1, type=int, default=[70], metavar='Alignment identity percentage\t [default 70%]',dest="percent")

parser.add_argument("-c",nargs=1, type=int, default=[5000], metavar='Shortest contig length\t [default 5000]',dest="contig")

parser.add_argument("-q",nargs=1, type=int, default=[20], metavar='Mapping quality\t [default 20]',dest="qty")

parser.add_argument("-f",nargs=1, type=str, default=['reformated'], metavar='Output files name\t[default reformated]',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()

paf=args.mapping_files[0]

drafts=args.drafts[0]

block=args.block[0]

percent=args.percent[0]

qty=args.qty[0]

output=args.output[0]

name=args.name[0]

contig=args.contig[0]

reformated(path=paf,number_of_drafts=drafts,block=block,percentage=percent,shortage_contig=contig,quality=qty,files=True,output=name '_',out_path=output)

if '-v':

parser.parse_args(['-v'])