如何在iPython笔记本中调用用argparse编写的模块 [英] How to call module written with argparse in iPython notebook

问题描述

我正在尝试将BioPython序列传递给 Ilya Stepanov实施的Ukkonen后缀树算法在iPython的笔记本环境中。我在argparse组件上遇到了绊脚石。

I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component.

我以前从未直接与argparse打过交道。如何在不重写main（）的情况下使用它？

I have never had to deal directly with argparse before. How can I use this without rewriting main()?

通过by，这篇Ukkonen算法的写法很棒。

推荐答案

我之前有类似的问题，但是使用 optparse 而不是 argparse 。

I've had a similar problem before, but using optparse instead of argparse.

您无需更改原始脚本中的任何内容，只需将新列表分配给 sys.argv ，如下所示：

You don't need to change anything in the original script, just assign a new list to sys.argv like so:

if __name__ == "__main__":
    from Bio import SeqIO
    path = '/path/to/sequences.txt'
    sequences = [str(record.seq) for record in  SeqIO.parse(path, 'fasta')]
    sys.argv = ['-f'] + sequences
    main()

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