readsep

#!/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 read_extract import read_extract
import argparse
parser = argparse.ArgumentParser(prog="readsep",usage='%(prog)s -h [options] <reads> <read_titles>',description='Extract reads from fasta or fastq, part of GALA Gap-free Long-reads Assembler',)
parser.add_argument("reads",nargs=1,type=str,help='raw/corrected reads \t [required]')
parser.add_argument("read_titles",nargs=1,type=str,help='read names\t[required]')
parser.add_argument("-f",nargs=1, type=str, default=['fa'], metavar='input file format (fa/fq)',dest="format")
parser.add_argument('-v','--version', action='version', version='%(prog)s 1.0.0')
args = parser.parse_args()
reads=args.reads[0]
names=args.read_titles[0]
formats=args.format[0]
read_extract(reads,names,formats)
if '-v':
	parser.parse_args(['-v'])