python click: "got unexpected extra arguments"

Question

I have written a small and simple interface with Click, I get this error "Error: Got unexpected extra arguments" and I just can't figure out why this occurs?

Here is my 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,
)

Here is my cli.py file:

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)

And here is the error that I get when calling my program:

$ 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)

Does anyone have any idea why this is happening? Have I missed something?

dspencer · Accepted Answer · 2020-04-06 07:11:55Z

4

Your preprocess function calls itself, resulting in the "unexpected extra arguments" error (see Click: "Got unexpected extra arguments" when passing string for a similar case). This is because its definition hides the one that you imported from .preprocessor.

You should instead import the external preprocess function using a different name, e.g.:

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)

Alternatively, you can import the preprocessor module:

from . import preprocessor

and then access the function using:

preprocessor.preprocess

answered Apr 6, 2020 at 7:11

dspencer

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1 Comment

dspencer Over a year ago

The same thing will happen for collapse, just so you're aware

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