eggnog-mapper-fixurl

Fix outdated URLs in eggnog-mapper's download_eggnog_data.py.

Installation

First, ensure that eggnog-mapper is installed in your environment. Then install the eggnog-mapper-fixurl package with pip:

pip install eggnog-mapper-fixurl

Usage

You can confirm that download_eggnog_data.py is detected in your current environment by running:

which download_eggnog_data.py

If it's detected, you can make the fix by simply running

eggnog-mapper-fixurl

This will update the outdated URLs in download_eggnog_data.py, after which the script should work correctly.

The fix will also take place if this package is imported in a Python script

import eggnog_mapper_fixurl

If you need to specify the location of download_eggnog_data.py, there are a few ways to do so:

1. By command line option: eggnog-mapper-fixurl --pyscript <path/to/download_eggnog_data.py>
2. By environment variable: export EGGNOG_MAPPER_FIXURL_PYSCRIPT="<path/to/download_eggnog_data.py>"
3. By configuration file, add download_eggnog_data_pysript = "<path/to/download_eggnog_data.py>" to ~/.eggnog-mapper-fixurl-config.toml
4. In a Python script:

import eggnog_mapper_fixurl
eggnog_mapper_fixurl.fixurl(
    download_eggnog_data_pysript="<path/to/download_eggnog_data.py>"
)