测试使用命令行输入_20211209

# -*- coding: utf-8 -*-
import click

@click.command()
@click.option('-f', '--fastafile', help='Input a fasta file', required=True)
@click.option('-i', '--idfile', help='Input an idlist', required=True)
@click.option('-o', '--outfile', help='Input the name of result file', default='result.fa')


def get(fastafile, idfile, outfile):
    """
    Extract seqences from a fasta file
    according to a id list.
    """
    idfile = open(idfile, 'r')
    resultfile = open(outfile, 'w')
    for id in idfile:
        qid = id.strip()
        flag = 0
        with open(fastafile,'r') as ffile:
            for line in ffile:
                line = line.strip()
                if line.startswith('>'):
                    name = line.replace('>','').split()[0]
                    if name == qid:
                        flag = 1
                        resultfile.write(line + '\n')
                    else:
                        flag = 0
                else:
                    if flag == 0:
                        pass
                    else:
                        resultfile.write(line + '\n')
    resultfile.close()

if __name__ == '__main__':
    get()

import pandas.api
import numpy