如何通过命令行为 python 脚本的函数提供参数？

发布于 2024-11-06 08:12:04 字数 855 浏览 1 评论 0原文

目前，这是我的Python脚本（TagGen），它有一个功能：

def SJtag(file,len_tag):

    import csv
    reader = csv.reader(open(file), dialect='excel-tab' )
    for row in reader:
        qstarts = row[1].split(",")[1:-1] 
        n = len_tag/2
        for i in qstarts:  
            name = row[0]

            start = int(i)-n
            if start<0:
                start = 0      

            end = int(i)+n
            if end>len(row[2]):
                end=len(row[2])

            tag = row[2][start:end]    
            print name, i, tag, len(tag)

SJtag("QstartRefseqhg19.head",80)

我想给出SJtag的file和len_tag参数 使用 bash 命令行的函数，如下所示：

python ./TagGen QstartRefseqhg19.head 80

我该如何做到这一点，或类似的事情？

感谢您的帮助！

原文

Currently this is my python script (TagGen) which has one function:

def SJtag(file,len_tag):

    import csv
    reader = csv.reader(open(file), dialect='excel-tab' )
    for row in reader:
        qstarts = row[1].split(",")[1:-1] 
        n = len_tag/2
        for i in qstarts:  
            name = row[0]

            start = int(i)-n
            if start<0:
                start = 0      

            end = int(i)+n
            if end>len(row[2]):
                end=len(row[2])

            tag = row[2][start:end]    
            print name, i, tag, len(tag)

SJtag("QstartRefseqhg19.head",80)

I want to give the file and len_tag parameters of the SJtag function using bash comand line, something like this:

python ./TagGen QstartRefseqhg19.head 80

How can I do this, or some thing similar?

Thanks for your help!

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坏尐絯 2024-11-13 08:12:04

您可以使用 argparse 模块来实现这一点。

从文档来看，

import argparse

parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('integers', metavar='N', type=int, nargs='+',
           help='an integer for the accumulator')
parser.add_argument('--sum', dest='accumulate', action='store_const',
           const=sum, default=max,
           help='sum the integers (default: find the max)')

args = parser.parse_args()
print args.accumulate(args.integers)

如果您使用的 python 版本早于 2.7，则应该使用 optparse模块，实现类似的效果。

You could use the argparse module for that.

From the docs,

import argparse

parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('integers', metavar='N', type=int, nargs='+',
           help='an integer for the accumulator')
parser.add_argument('--sum', dest='accumulate', action='store_const',
           const=sum, default=max,
           help='sum the integers (default: find the max)')

args = parser.parse_args()
print args.accumulate(args.integers)

If you are using a version of python earlier than 2.7, you should use the optparse module, to achieve a similar effect.

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水波映月 2024-11-13 08:12:04

sys.argv 是参数列表，第一个元素是脚本名称。它是一个字符串列表，因此如果任何参数是数字，则必须使用 int() 或 float() 对其进行转换。

因此，如果您像这样调用脚本：

$ python myscript.py 1 foo bar baz

sys.argv 将是这样的：

["myscript.py", "1", "foo", "bar", "baz"]

在您的情况下，您可以使脚本如下：

import sys
import csv

def SJtag(file,len_tag):
    reader = csv.reader(open(file), dialect='excel-tab' )
    for row in reader:
        qstarts = row[1].split(",")[1:-1] 
        n = len_tag/2
        for i in qstarts:  
            name = row[0]

            start = int(i)-n
            if start<0:
                start = 0      

            end = int(i)+n
            if end>len(row[2]):
                end=len(row[2])

            tag = row[2][start:end]    
            print name, i, tag, len(tag)

if __name__ == '__main__':
    SJtag(sys.argv[1], int(sys.argv[2]))

sys.argv is the arguments list, with the first element being the script name. It's a list of strings, so if any of the parameters are numbers, you'll have to convert them using int() or float().

So, if you called a script like so:

$ python myscript.py 1 foo bar baz

sys.argv would be this:

["myscript.py", "1", "foo", "bar", "baz"]

In your case, you could make your script this:

import sys
import csv

def SJtag(file,len_tag):
    reader = csv.reader(open(file), dialect='excel-tab' )
    for row in reader:
        qstarts = row[1].split(",")[1:-1] 
        n = len_tag/2
        for i in qstarts:  
            name = row[0]

            start = int(i)-n
            if start<0:
                start = 0      

            end = int(i)+n
            if end>len(row[2]):
                end=len(row[2])

            tag = row[2][start:end]    
            print name, i, tag, len(tag)

if __name__ == '__main__':
    SJtag(sys.argv[1], int(sys.argv[2]))

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╰◇生如夏花灿烂 2024-11-13 08:12:04

我推荐 argparse 和一个名为的漂亮包装器plac。在您的情况下，您需要做的就是：

if __name__ == '__main__':
    import plac; plac.call(SJtag)

...并且 plac 将处理所有事情，因为它能够从您的签名中找出要使用的命令行参数功能。非常酷，请查看文档了解更多信息（它可以做更多事情）。

I'd recommend argparse and a nice wrapper for it called plac. In your case all you'd need to do is:

if __name__ == '__main__':
    import plac; plac.call(SJtag)

...and placwill handle everything, as it is able to figure out the command-line arguments to use from the signature of your function. Very cool, check out the docs for more (it can do a lot more).

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