ehitk 1.1.0

Earth Hologenome Initiative Toolkit

EHItk

The Earth Hologenome Initiative ToolKit (EHItk) is a Python package and command-line tool for finding, summarizing, exporting, and downloading EHI specimens, hologenomes, and metagenome-assembled genomes.

Installation

pip install ehitk

Example

ehitk specimens query --host-species "Podarcis muralis" --limit 5
ehitk hologenomes values --field country --limit 10
ehitk mags stats --quality high --species "Escherichia coli"
ehitk mags query --quality high --csv | head
ehitk specimens values --field sex --csv --output-file specimen-sex-values.csv

Python API:

import ehitk

with ehitk.Database() as ehidb:
    mags = ehidb.mags.query(quality="high", host_taxid=562, limit=5)

for mag in mags:
    print(mag.mag_id, mag.quality, mag.host_species)

Documentation

Full installation instructions, command reference, examples, output formats, and download guidance, and Python API examples are available at:

https://ehitk.readthedocs.io/

Use the built-in help for local command details:

ehitk --help
ehitk specimens --help
ehitk hologenomes fetch --help
ehitk mags query --help

Testing and continuous integration

EHItk includes a pytest-based unit test suite in the tests/ directory. The repository also uses GitHub Actions continuous integration to run the test suite, build source and wheel distributions, and perform CLI smoke tests across Python 3.10, 3.11, 3.12, 3.13, and 3.14.