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Added legacy pgscatalog_utils scoring file validator to pygscatalog.validate (#45)
* Added legacy pgscatalog_utils scoring file validator to pygscatalog.validate * Added description * Renamed main function for consistency with other packages * Added basic doc for pgscatalog-validate * Added missing application pgscatalog-validate * update ruff to ignore validate * remove path filter * fix ruff * Added doc about validator installation --------- Co-authored-by: Benjamin Wingfield <bwingfield@ebi.ac.uk>
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.github/workflows/ruff.yml

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name: Ruff
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on:
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push:
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paths:
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- '**.py'
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pull_request:
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paths:
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- '**.py'
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jobs:
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ruff:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: chartboost/ruff-action@v1
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- uses: astral-sh/ruff-action@v3
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with:
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args: "check --exclude pgscatalog.validate/*.py"

README.md

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> [!TIP]
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> If you want to use all of the applications listed below, you can install the package `pgscatalog-utils` with [pip](https://pypi.org/project/pgscatalog-utils/) or [bioconda](http://bioconda.github.io/recipes/pgscatalog-utils/README.html)
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| Application | Description | Install | Link |
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|------------------------------|------------------------------------------------------------------------|---------------------------------|--------------------------------------|
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| `pgscatalog-download` | Download scoring files from the PGS Catalog in specific genome builds | `pipx install pgscatalog.core` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/download.html) |
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| `pgscatalog-combine` | Combine multiple scoring files into a consistent structure | `pipx install pgscatalog.core` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/combine.html) |
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| `pgscatalog-relabel` | Relabel values in a column based on values in a column in another file | `pipx install pgscatalog.core` | [README](pgscatalog.core/README.md) |
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| `pgscatalog-match` | Match structured scoring file to variants in target genomes | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
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| `pgscatalog-matchmerge` | Merge variant match results, useful on larger datasets | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
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| `pgscatalog-intersect` | Match variants across two different variant information files (e.g. reference & target genomes) | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/intersect.html) |
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| `pgscatalog-aggregate` | Aggregate calculated PGS split across multiple files | `pipx install pgscatalog.calc` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/aggregate.html) |
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| `pgscatalog-ancestry-adjust` | Adjust calculated PGS in the context of genetic ancestry | `pipx install pgscatalog.calc` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/ancestry.html) |
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| Application | Description | Install | Link |
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|------------------------------|-------------------------------------------------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------|
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| `pgscatalog-download` | Download scoring files from the PGS Catalog in specific genome builds | `pipx install pgscatalog.core` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/download.html) |
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| `pgscatalog-combine` | Combine multiple scoring files into a consistent structure | `pipx install pgscatalog.core` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/combine.html) |
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| `pgscatalog-relabel` | Relabel values in a column based on values in a column in another file | `pipx install pgscatalog.core` | [README](pgscatalog.core/README.md) |
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| `pgscatalog-match` | Match structured scoring file to variants in target genomes | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
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| `pgscatalog-matchmerge` | Merge variant match results, useful on larger datasets | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/match.html) |
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| `pgscatalog-intersect` | Match variants across two different variant information files (e.g. reference & target genomes) | `pipx install pgscatalog.match` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/intersect.html) |
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| `pgscatalog-aggregate` | Aggregate calculated PGS split across multiple files | `pipx install pgscatalog.calc` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/aggregate.html) |
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| `pgscatalog-ancestry-adjust` | Adjust calculated PGS in the context of genetic ancestry | `pipx install pgscatalog.calc` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/ancestry.html) |
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| `pgscatalog-validate` | Check if the scoring files match the PGS Catalog scoring file format | `pipx install pgscatalog.validate` | [README](https://pygscatalog.readthedocs.io/en/latest/how-to/guides/validate.html) |
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## Developer libraries
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docs/how-to/guides/validate.rst

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How to validate PGS Catalog scoring files
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==================================================
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``pgscatalog-validate`` is a CLI application that validates a set of scoring files
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to match the PGS Catalog scoring file formats.
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It can validate:
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* The formatted scoring file format (https://www.pgscatalog.org/downloads/#dl_ftp_scoring)
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* The harmonized (Position) scoring file format (https://www.pgscatalog.org/downloads/#dl_ftp_scoring_hm_pos)
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Installation
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-------------
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Download the source code:
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::
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$ git clone https://github.com/PGScatalog/pygscatalog.git
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$ cd pygscatalog/pygscatalog.validate
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Install the dependencies:
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::
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$ poetry install
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Run with a virtual environment
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Start a new local virtual envrironment:
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::
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$ poetry shell
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$ pgscatalog-validate --help
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Or install the package in the current environment
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Build the wheel package:
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::
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$ poetry build
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Install the built package in the current environment via pip:
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::
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$ pip install dist/pgscatalog_validate-0.1-py3-none-any.whl
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Run
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::
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pgscatalog-validate --help
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Usage
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-----
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Validating one scoring file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ mkdir log
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$ pgscatalog-validate -t formatted -f PGS000001.txt.gz --log_dir log/
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Validating all the scoring files in a directory
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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::
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$ mkdir log
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$ pgscatalog-validate -t formatted --dir scores_directory/ --log_dir log/
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Help
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----
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::
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$ pgscatalog-validate --help

docs/how-to/index.rst

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guides/intersect
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guides/aggregate
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guides/ancestry
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guides/validate

pgscatalog.validate/LICENSE

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