im6A-TS-cnn.py

#!/usr/bin/env python
# -*- coding:utf-8-*-
# author: Liukewei time:2020/1/21 QQ:422209303 e-mail:Liukeweiaway@hotmail.com
# ----------------------------------------------------------------------------
import argparse
from mainf import preproces
import warnings
from mainf.formatCheck import formatCheck
warnings.filterwarnings("ignore")


def parse_args():
    """
    :return:进行参数的解析
    """
    description = "im6A-TS-cnn is able to identify m6A in brain/liver/kidney/heart/testis from Homo sapiens, Mus musculus and Saccharomyces cerevisiae. Thank you very much for submitting the error message to Liukeweiaway@hotmail.com.  Example: python im6A-TS-cnn.py -i sequence.txt -o ccc.html -s Human -m all -t normal "
    parser = argparse.ArgumentParser(description=description)
    help = "The correct path of address"
    parser.add_argument('--addresses', help=help)
    parser.add_argument('-i', '--inputFile', help='-i input.txt (The input file is a complete Fasta format sequence.)')
    parser.add_argument('-o', '--outputFile', help='-o output.html (Results are saved under results folder.)')
    parser.add_argument('-s', '--species', help='-s Human/Mouse/Rat (Choose one from three species to use.)')
    parser.add_argument('-t', '--tissues', help='-t Human(brain/liver/kidney/heart/testis) Mouse(brain/liver/kidney) Rat(brain/liver/kidney) (We can choose testis you want.)')
    parser.add_argument('-ts', '--threshold', help='-ts low/normal/high (We offer 3 options based on the difference in specificity, which are low, normal and high.)')
    args = parser.parse_args()
    return args


if __name__ == '__main__':
    args = parse_args()
    formatCheck = formatCheck(args.inputFile, args.outputFile, args.species, args.tissues)
    print(formatCheck)
    preproces.preprocesser(args.inputFile, args.outputFile, args.species, args.tissues)
    # previous_deal(args.inputFile, args.outputFile, args.featureList)  # feature extraction