ngssim

#!/bin/env python
# -*- coding: utf-8 -*-


import sys
import argparse
import subprocess
import time


def main():
    ## Run ART to simulate NGS reads
    art_cmd = "%s -ss MSv3 \
                        -i %s \
                        -o %s \
                        -l 250 \
                        -f 4 \
                        -p \
                        -m 500 \
                        -s 10 \
                        -na \
                        -rs %d \
                        "%(artPath, inf, basename, seed_value)
    
    subprocess.call(art_cmd, shell=True)


if __name__ == "__main__":
    ## Specify the default value
    scriptDir = sys.path[0]
    artDefault="%s/art_illumina"%scriptDir
    iDefault = 'clonally_expanded_sequences.fasta'
    oDefault = 'illumina.sequencing.reads'
    dtime = int(time.strftime("%Y%m%d", time.localtime()))
    
    ## define the argument parser module
    parser = argparse.ArgumentParser(description='''ngssim simulates next
    generation sequencing reads via ART''')
    parser.add_argument("-art", "--art_path", type=str, default=artDefault, \
                help="Path to ART executable")
    parser.add_argument("-i", "--input", type=str, default=iDefault, \
                help="Path to input fasta file")
    parser.add_argument("-d", "--dir", type=str, default="./", \
                help="Path to output directory")
    parser.add_argument("-b", "--basename", type=str, default=oDefault, \
                help="basename for output")
    parser.add_argument("-s", "--seed", type=int, default=dtime, \
                help="Seed used for generating random value")
    args = parser.parse_args()
    artPath = args.art_path
    inf = args.input
    basename = args.basename
    dirt = args.dir
    seed_value = args.seed
    
    ## Prompt message
    print (''' +-++-++-++-++-++-+
|n||g||s||s||i||m|
+-++-++-++-++-++-+
''')
    ## Run main function
    main()