How to validate PGS Catalog scoring files

pgscatalog-validate is a CLI application that validates a set of scoring files to match the PGS Catalog scoring file formats. It can validate:

• The formatted scoring file format (https://www.pgscatalog.org/downloads/#dl_ftp_scoring)

• The harmonized (Position) scoring file format (https://www.pgscatalog.org/downloads/#dl_ftp_scoring_hm_pos)

Installation

Download the source code:

$ git clone https://github.com/PGScatalog/pygscatalog.git
$ cd pygscatalog/pygscatalog.validate

Install the dependencies:

$ poetry install

Run with a virtual environment

Start a new local virtual envrironment:

$ poetry shell
$ pgscatalog-validate --help

Or install the package in the current environment

Build the wheel package:

$ poetry build

Install the built package in the current environment via pip:

$ pip install dist/pgscatalog_validate-0.1-py3-none-any.whl

Run

pgscatalog-validate --help

Usage

Validating one scoring file

$ mkdir log
$ pgscatalog-validate -t formatted -f PGS000001.txt.gz --log_dir log/

Validating all the scoring files in a directory

$ mkdir log
$ pgscatalog-validate -t formatted --dir scores_directory/ --log_dir log/

Help

$ pgscatalog-validate --help