pgscatalog.core 1.1.0

Core tools for working with polygenic scores (PGS) and the PGS Catalog

pgscatalog.core

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
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

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, which uses these tools internally.

Installation

or install via pip:

$ pipx install pgscatalog.core

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

nox can also be used to run tests and lint the package:

$ nox