Metadata-Version: 2.4
Name: acidgenomics-acidgenomes
Version: 0.2.1
Summary: Toolkit for downloading and processing genome annotations.
Keywords: bioinformatics,genomics,annotation
Author: Michael Steinbaugh
Author-email: Michael Steinbaugh <mike@steinbaugh.com>
License-Expression: Apache-2.0
License-File: LICENSE
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Dist: biocframe>=0.7
Requires-Dist: genomicranges>=0.8
Requires-Dist: iranges>=0.7
Requires-Dist: pandas
Requires-Dist: requests
Requires-Dist: bumpver ; extra == 'develop'
Requires-Dist: coverage ; extra == 'develop'
Requires-Dist: interrogate ; extra == 'develop'
Requires-Dist: pyright[nodejs] ; extra == 'develop'
Requires-Dist: pytest ; extra == 'develop'
Requires-Dist: pytest-cov ; extra == 'develop'
Requires-Dist: ruff ; extra == 'develop'
Requires-Dist: ty ; extra == 'develop'
Requires-Dist: uv ; extra == 'develop'
Requires-Dist: myst-parser ; extra == 'docs'
Requires-Dist: numpydoc ; extra == 'docs'
Requires-Dist: sphinx ; extra == 'docs'
Requires-Python: >=3.12
Project-URL: Homepage, https://github.com/acidgenomics/py-acidgenomes
Project-URL: Documentation, https://python.acidgenomics.com/acidgenomes/
Project-URL: Repository, https://github.com/acidgenomics/py-acidgenomes
Project-URL: Changelog, https://github.com/acidgenomics/py-acidgenomes/blob/main/CHANGELOG.md
Provides-Extra: develop
Provides-Extra: docs
Description-Content-Type: text/markdown

# acidgenomes

Toolkit for downloading and processing genome annotations.

## Installation

This is a [Python][] package hosted on [PyPI][] as `acidgenomics-acidgenomes`.
The import name is unchanged: `acidgenomes`.
We recommend using [uv][] to install.

```sh
uv add acidgenomics-acidgenomes
```

Or with [pip][]:

```sh
pip install acidgenomics-acidgenomes
```

## Quick start

```python
import acidgenomes as ag

# Detect organism from Ensembl gene IDs
ag.detect_organism(["ENSG00000000003", "ENSG00000000005"])
# => "Homo sapiens"

# Current Ensembl genome build
ag.current_ensembl_genome_build("Homo sapiens")
# => "GRCh38"

# Strip version suffixes
ag.strip_gene_versions(["ENSG00000000003.14"])
# => ["ENSG00000000003"]

# Build a transcript-to-gene mapping
import pandas as pd
df = pd.DataFrame({"tx_id": ["ENST001", "ENST002"], "gene_id": ["ENSG001", "ENSG002"]})
t2g = ag.make_tx_to_gene(df)

# Build a gene-to-symbol mapping
df = pd.DataFrame({"gene_id": ["ENSG001"], "gene_name": ["TP53"]})
g2s = ag.make_gene_to_symbol(df, format="make_unique")
```

### Downloading reference data

```python
# HGNC (human gene nomenclature)
hgnc = ag.make_hgnc()

# MGI (mouse)
mgi = ag.make_mgi()

# NCBI gene info
ncbi = ag.make_ncbi_gene_info("Homo sapiens")

# JAX human-to-mouse orthologs
jax = ag.make_jax_human_to_mouse()

# Map gene names to HGNC IDs
ag.map_gene_names_to_hgnc(["TP53", "BRCA1"])

# Update outdated gene symbols
ag.update_gene_symbols(["ZCCHC11"], organism="Homo sapiens")
```

[pip]: https://pip.pypa.io/
[pypi]: https://pypi.org/project/acidgenomics-acidgenomes/
[python]: https://www.python.org/
[uv]: https://docs.astral.sh/uv/


## License

Apache-2.0 — Copyright 2026 Acid Genomics LLC — see [LICENSE](LICENSE).
