python点击：“获得了意外的额外参数”

Question

我用Click编写了一个小而简单的界面，出现此错误“错误：收到了意外的额外参数”，但我不知道为什么会发生这种情况？

这是我的setup.py：

from setuptools import setup, find_packages

setup(
    name = "transcov",
    description = "A software for mapping coverage around transcription start sites",
    packages=find_packages("src"),
    package_dir={"": "src"},
    #test_suite="test",
    install_requires=['pysam>=0.15.4', 'numpy>=1.18.1', 'attrs>=19.3.0', 'click>=7.1.1'],
    entry_points={
        'console_scripts': ['transcov = transcov.cli:cli'],
    },
    include_package_data=True,
)

这是我的cli.py文件：

import click

from .generator import generate_coverage_matrix
from .preprocessor import preprocess
from .collapser import collapse

@click.group()
def cli():
    pass

@cli.command()
@click.argument('annotation_file')
@click.option('-o', '--output-file', default='transcription_start_sites.tsv')
def preprocess(annotation_file, output_file):
    preprocess(annotation_file, output_file)

@cli.command()
@click.argument('bam_file')
@click.argument('tss_file')
@click.option('-k', '--region-size', default=10000)
@click.option('-o', '--output-file', default='coverage_matrix.npy')
def generate(bam_file, tss_file, region_size, output_file):
    generate_coverage_matrix(bam_file, tss_file, region_size, output_file)

@cli.command()
@click.argument('matrices', nargs=-1)
@click.option('-o', '--output-file', default='collapsed_matrix.npy')
@click.option('--uint32', is_flag=True)
def collapse(matrices, output_file, uint32):
    if len(matrices) > 0:
        collapse(matrices, output_file, uint32)

这是调用程序时出现的错误：

$ transcov preprocess -o gencodes/gencode.v19.annotation.tss.tsv gencodes/gencode.v19.annotation.gff3
Usage: gencodes/gencode.v19.annotation.tss.tsv [OPTIONS] ANNOTATION_FILE
Try 'gencodes/gencode.v19.annotation.tss.tsv --help' for help.

Error: Got unexpected extra arguments (e n c o d e s / g e n c o d e . v 1 9 . a n n o t a t i o n . g f f 3)

有人知道为什么会这样吗？我错过了什么吗？

Answer 1

您的preprocess函数调用自身，导致此错误（类似情况请参见Click: "Got unexpected extra arguments" when passing string）。这是因为其定义隐藏了您从.preprocessor导入的定义。

您应该改用其他名称导入外部preprocess函数，例如：

from .preprocessor import preprocess as _preprocess

@cli.command()
@click.argument('annotation_file')
@click.option('-o', '--output-file', default='transcription_start_sites.tsv')
def preprocess(annotation_file, output_file):
    _preprocess(annotation_file, output_file)