Metadata-Version: 2.1
Name: pgscatalog-utils
Version: 1.0.0
Summary: Utilities for working with PGS Catalog API and scoring files
License: Apache-2.0
Author: Benjamin Wingfield
Author-email: bwingfield@ebi.ac.uk
Requires-Python: >=3.11,<4.0
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Dist: pgscatalog.calc (>=0.1.0,<0.2.0)
Requires-Dist: pgscatalog.core (>=0.1.0,<0.2.0)
Requires-Dist: pgscatalog.match (>=0.1.0,<0.2.0)
Description-Content-Type: text/markdown

# `pgscatalog-utils`

This convenience package bundles every PGS Catalog application, including:

| 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](pgscatalog.core/README.md)                                                 |
| `pgscatalog-match`           | Match structured scoring file to variants in target genomes            | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html)     |
| `pgscatalog-matchmerge`      | Merge variant match results, useful on larger datasets                 | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html)     |
| `pgscatalog-aggregate`       | Aggregate calculated PGS split across multiple files                   | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/aggregate.html) |
| `pgscatalog-ancestry-adjust` | Adjust calculated PGS in the context of genetic ancestry               | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/ancestry.html)  |

Please note `v1.0.0` contains breaking changes: CLI applications have been renamed and the package has been significantly refactored.

See https://github.com/PGScatalog/pygscatalog for more details.

## Installation 

```
$ pip install pgscatalog-utils
```

## Documentation 

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

