Metadata-Version: 2.1
Name: pgscatalog.core
Version: 0.3.1
Summary: Core tools for working with polygenic scores (PGS) and the PGS Catalog
License: Apache-2.0
Author: Benjamin Wingfield
Author-email: bwingfield@ebi.ac.uk
Requires-Python: >=3.10
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: httpx (>=0.26.0,<0.27.0)
Requires-Dist: natsort (>=8.4.0,<9.0.0)
Requires-Dist: pydantic (>=2.9.0,<3.0.0)
Requires-Dist: pyliftover (>=0.4,<0.5)
Requires-Dist: tenacity (>=8.2.3,<9.0.0)
Requires-Dist: tqdm (>=4.66.1,<5.0.0)
Requires-Dist: xopen[zstd] (>=1.8.0,<2.0.0)
Description-Content-Type: text/markdown

# `pgscatalog.core`

[![Run pytest on pgscatalog.core](https://github.com/PGScatalog/pygscatalog/actions/workflows/core-pytest.yml/badge.svg)](https://github.com/PGScatalog/pygscatalog/actions/workflows/core-pytest.yml)
[![Documentation Status](https://readthedocs.org/projects/pygscatalog/badge/?version=latest)](https://pygscatalog.readthedocs.io/en/latest/autoapi/pgscatalog/core/index.html)

This Python package contains:

* CLI applications to download scoring files from the PGS Catalog and normalise them into a consistent structure
* core library classes and functions for working with PGS data

| Application           | Description                                                            | Link                                                                               |
|-----------------------|------------------------------------------------------------------------|------------------------------------------------------------------------------------|
| `pgscatalog-download` | Download scoring files from the PGS Catalog in specific genome builds  | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/download.html) |
| `pgscatalog-combine`  | Combine multiple scoring files into a consistent structure             | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/combine.html)  |
| `pgscatalog-relabel`  | Relabel values in a column based on values in a column in another file | [README](README.md)                                                |

If you want to write Python code to work with PGS data, the library may be helpful for you.

If you want to do automatic PGS calculation check out the [PGS Catalog Calculator](https://github.com/PGScatalog/pgsc_calc), which uses these tools internally.

## Installation 

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pgscatalog.core/README.html)

or [install via `pip`](https://pypi.org/project/pgscatalog.core/):

```
$ pipx install pgscatalog.core
```

## Documentation

Documentation is available at https://pygscatalog.readthedocs.io/.


