main_salmon.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2020/6/23 9:34
# @Author : Yuancong Wang
# @Site : 
# @File : main.py
# @Software: PyCharm
# @E-mail: wangyuancong@163.com
'''
Description:
Output: 
Input:
Other notes:
'''

import argparse


import argparse
from processors.file_proc import FilePorcessor
from processors.cmd_proc import CmdProcessor

def fozu():
    print("                            _ooOoo_                     ")
    print("                           o8888888o                    ")
    print("                           88  .  88                    ")
    print("                           (| -_- |)                    ")
    print("                            O\\ = /O                    ")
    print("                        ____/`---'\\____                ")
    print("                      .   ' \\| |// `.                  ")
    print("                       / \\||| : |||// \\               ")
    print("                     / _||||| -:- |||||- \\             ")
    print("                       | | \\\\\\ - /// | |             ")
    print("                     | \\_| ''\\---/'' | |              ")
    print("                      \\ .-\\__ `-` ___/-. /            ")
    print("                   ___`. .' /--.--\\ `. . __            ")
    print("                ."" '< `.___\\_<|>_/___.' >'"".         ")
    print("               | | : `- \\`.;`\\ _ /`;.`/ - ` : | |     ")
    print("                 \\ \\ `-. \\_ __\\ /__ _/ .-` / /      ")
    print("         ======`-.____`-.___\\_____/___.-`____.-'====== ")
    print("                            `=---='  ")
    print("                                                        ")
    print("         .............................................  ")
    print("                  Prey for no bug                      ")
    print("                  Zen of python:                       ")
    print("                  Beautiful is better than ugly.；      ")
    print("                  Explicit is better than implicit.     ")
    print("                  Simple is better than complex.        ")
    print("                  Complex is better than complicated.   ")
    print("                  Flat is better than nested.           ")
    print("                  Sparse is better than dense.          ")
    print("                  Readability counts.                   ")
    print("                  Now is better than never.             ")


def main():
    fozu()
    parser = argparse.ArgumentParser(description="Trim the sequencing data in the directory.")
    parser.add_argument('-d', '--directory', help='The directory where you put the sequencing files.', default='')
    parser.add_argument('-p', '--program', help='chose the program you wang to use. (salmon)')
    parser.add_argument('-g', '--is_genome', help='"T" for sequencing data without poly A (genome sequencing data, default),\
                                                   "F" for sequencing data with poly A (transcriptome sequencing data).\
                                                  This option is only useful if you use fqtrim.',

                        default='T')
    parser.add_argument('-r', '--reference', help='The path of the reference file')
    args = parser.parse_args()
    f_proc = FilePorcessor()
    f_proc = f_proc.fit(args.directory)
    paired_seq_files = f_proc.get_paired_seq_fpaths()
    cmd_proc = CmdProcessor()
    cmd_proc.fit(lst_paired_fpath=paired_seq_files, ref_path=args.reference)
    if args.program.lower() == 'salmon':
        print('Program: salmon')
        cmd_proc.execute_salmon()


if __name__ == '__main__':
    main()