pgscatalog-utils 2.0.2

Utilities for working with PGS Catalog API and scoring files

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