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)
Download the source code:
$ git clone https://github.com/PGScatalog/pygscatalog.git $ cd pygscatalog/pygscatalog.validate
Install the dependencies:
$ poetry install
Start a new local virtual envrironment:
$ poetry shell $ pgscatalog-validate --help
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
$ mkdir log $ pgscatalog-validate -t formatted -f PGS000001.txt.gz --log_dir log/
$ mkdir log $ pgscatalog-validate -t formatted --dir scores_directory/ --log_dir log/
$ pgscatalog-validate --help