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删除帮助功能中的冗余

python

-1

F.Lira · 技术社区 · 6 年前

我可以编写参数,但如果命令没有提供正确的参数,我就无法避免编写函数“help”来打印它。

任何建议都将不胜感激。

def get_arguments():
    parser = argparse.ArgumentParser(prog = 'contig2genbank.py', usage= '\n\t%(prog)s [contig ID/ or list of contigs] [output prefix]' , description = "Split a .gbk (.gbff) file and retrieve the information of the contig of interest.",formatter_class=RawTextHelpFormatter)
    parser.add_argument('-s', required = False, type = str, help='Name of input file (mandatory with -g)', metavar='') # used to extract single contigs
    parser.add_argument('-l', required = False, type = str, help='Name of input file  when in list (mandatory)', metavar='') # when giving a list of genomes and contigs to be extracted; see above the list example
    parser.add_argument('-g', required = False, type = str, help='Name of genome file (mandatory with -i)', metavar='') # when using a single genome, -g is the name of genome file in .gbk (.gbff) format
    return parser.parse_args()


def help():
    parser = argparse.ArgumentParser(prog = 'contig2genbank.py', usage= '\n\t%(prog)s [contig ID/ or list of contigs] [output prefix]' , description = "Split a .gbk (.gbff) file and retrieve the information of the contig of interest.",formatter_class=RawTextHelpFormatter)
    parser.add_argument('-s', required = False, type = str, help='Name of input file (mandatory with -g)', metavar='') # used to extract single contigs
    parser.add_argument('-l', required = False, type = str, help='Name of input file  when in list (mandatory)', metavar='') # when giving a list of genomes and contigs to be extracted; see above the list example
    parser.add_argument('-g', required = False, type = str, help='Name of genome file (mandatory with -i)', metavar='') # when using a single genome, -g is the name of genome file in .gbk (.gbff) format 
    parser.print_help()


def main():
    args = get_arguments()  # check arguments

    if args.s and args.g:
        with open(args.g, "rU") as genome: #open(args.c + '.gbk','w') as outgbk:
            for record in SeqIO.parse(genome, "genbank"):
                if args.s == record.id:
                    #with open(args.c + '.gbk','w') as outgbk:
                    SeqIO.write([record], open(record.id + ".gbk", "w"), "genbank")
        print record.id + ".gbk created."

    else:
        help()

我期望的是避免get_参数和帮助函数中的行重复。

2 回复 | 直到 5 年前

Dani Mesejo 6 年前

编写函数 get_parser 这样地:

def get_parser():
    parser = argparse.ArgumentParser(prog = 'contig2genbank.py', usage= '\n\t%(prog)s [contig ID/ or list of contigs] [output prefix]' , description = "Split a .gbk (.gbff) file and retrieve the information of the contig of interest.",formatter_class=RawTextHelpFormatter)
    parser.add_argument('-s', required = False, type = str, help='Name of input file (mandatory with -g)', metavar='') # used to extract single contigs
    parser.add_argument('-l', required = False, type = str, help='Name of input file  when in list (mandatory)', metavar='') # when giving a list of genomes and contigs to be extracted; see above the list example
    parser.add_argument('-g', required = False, type = str, help='Name of genome file (mandatory with -i)', metavar='') # when using a single genome, -g is the name of genome file in .gbk (.gbff) format
    return parser

main 功能如下:

def main():
    parser = get_parser()
    args = parser.parse_args()  # check arguments

    if args.s and args.g:
        with open(args.g, "rU") as genome: #open(args.c + '.gbk','w') as outgbk:
            for record in SeqIO.parse(genome, "genbank"):
                if args.s == record.id:
                    #with open(args.c + '.gbk','w') as outgbk:
                    SeqIO.write([record], open(record.id + ".gbk", "w"), "genbank")
        print record.id + ".gbk created."

    else:
        parser.print_help()

Kings85 6 年前

我不是专家,但如果您只需在两个原始函数中添加第三个函数,名为: get_parser

def get_parser():
parser = argparse.ArgumentParser(prog = 'contig2genbank.py', usage= '\n\t%(prog)s [contig ID/ or list of contigs] [output prefix]' , description = "Split a .gbk (.gbff) file and retrieve the information of the contig of interest.",formatter_class=RawTextHelpFormatter)
parser.add_argument('-s', required = False, type = str, help='Name of input file (mandatory with -g)', metavar='') # used to extract single contigs
parser.add_argument('-l', required = False, type = str, help='Name of input file  when in list (mandatory)', metavar='') # when giving a list of genomes and contigs to be extracted; see above the list example
parser.add_argument('-g', required = False, type = str, help='Name of genome file (mandatory with -i)', metavar='') # when using a single genome, -g is the name of genome file in .gbk (.gbff) format
return parser

然后,原来的两个函数只有两行: 获取分析器 得到它,然后解析/打印