seprator

#!/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 bam_seprator import bam_seprator
import argparse
parser = argparse.ArgumentParser(prog="seprator",usage='%(prog)s -h  [options] <contig_names> <bam_file>',formatter_class=argparse.RawDescriptionHelpFormatter,description='Separate each contig correlated read names, part of GALA Gap-free Long-reads Assembler',epilog="Use the following command to produce contig_names file:""\n\t""samtools view -H <bam_file> |grep 'SQ'|cut -f 2|cut -d : -f 2 > contig_names")

parser.add_argument("contig_names",nargs=1,type=str,help='contig_names \t [required]')
parser.add_argument("bam_file",nargs=1,type=str,help='mapping bam file\t[required]')
parser.add_argument("-o",nargs=1, type=str, default=[os.getcwd()], metavar='output files path\t[default current directory]',dest="output")
parser.add_argument("-f",nargs=1, type=str, default=['bam_seprator'], metavar='Output files name\t[default bam_seprator]',dest="name")
parser.add_argument("-b",nargs=1, type=str, default=['bams'], metavar='output folder name\t [default bams]',dest="folders")
parser.add_argument('-v','--version', action='version', version='%(prog)s 1.0.0')
args = parser.parse_args()
contig_names=args.contig_names[0]
bam_file=args.bam_file[0]
output=args.output[0]
name=args.name[0]
folders=args.folders[0]
bam_seprator(contig_name=contig_names,bam_file=bam_file,out_put_path=output,out_put_name=name,folder_name=folders)
if '-v':
	parser.parse_args(['-v'])