Utilities for working with PGS Catalog API and scoring files
Project description
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 |
pgscatalog-combine |
Combine multiple scoring files into a consistent structure | README |
pgscatalog-relabel |
Relabel values in a column based on values in a column in another file | README |
pgscatalog-match |
Match structured scoring file to variants in target genomes | README |
pgscatalog-matchmerge |
Merge variant match results, useful on larger datasets | README |
pgscatalog-intersect |
Match variants across two different variant information files (e.g. reference & target genomes) | README |
pgscatalog-aggregate |
Aggregate calculated PGS split across multiple files | README |
pgscatalog-ancestry-adjust |
Adjust calculated PGS in the context of genetic ancestry | README |
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
or install via pip:
$ pipx install pgscatalog-utils
Documentation
Documentation is available at https://pygscatalog.readthedocs.io/.
Developer instructions
You'll need nox and uv installed.
To get set up with a development environment run:
$ nox -s dev
$ source .venv/bin/activate
This will create a virtual environment in the current directory.
$ pgscatalog-download --help
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