Utilities for working with PGS Catalog API and scoring files

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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

install with bioconda

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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