Metadata-Version: 2.4
Name: ghfc-utils
Version: 0.1.2
Summary: Various genomics tools and scripts used in the GHFC lab
Project-URL: Repository, https://gitlab.pasteur.fr/ghfc/ghfc-utils
Project-URL: Issues, https://gitlab.pasteur.fr/ghfc/ghfc-utils/-/issues
Project-URL: Changelog, https://gitlab.pasteur.fr/ghfc/ghfc-utils/-/blob/master/CHANGELOG.md
Author-email: Freddy Cliquet <fcliquet@pasteur.fr>, Alexandre Mathieu <amathieu@pasteur.fr>
License: MIT License
        
        Copyright (c) 2023 bourgeron-lab
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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License-File: LICENSE
Keywords: WGS,de novo mutations,genomics,slivar,variant filtering
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: <3.13,>=3.10
Requires-Dist: gwaslab==3.5.2
Requires-Dist: numpy<2
Requires-Dist: pandas>=2.2.3
Requires-Dist: pyranges>=0.1.2
Requires-Dist: python-docx>=1.1.2
Requires-Dist: pyyaml>=6.0.2
Requires-Dist: scikit-learn>=1.6.0
Requires-Dist: scipy>=1.15.0
Requires-Dist: setuptools>=75.7.0
Requires-Dist: simple-slurm>=0.3.5
Requires-Dist: statsmodels>=0.14.4
Requires-Dist: tabulate>=0.9.0
Requires-Dist: tqdm>=4.67.1
Description-Content-Type: text/markdown

# ghfc-utils

set of small tools designed to help automatize simple task locally or on Pasteur's cluster.

- **slivar-reannotate** for the postprocessing of slivar files including filtering and geneset reannotation.
- **slivar-dnm** for the computation of a prediction score about the veracity of *de novo* mutations

## Installation

```bash
pip install ghfc-utils
```

PS. on maestro, do not forget to load Python first (not needed anymore once installed):

```bash
module load Python/3.9.16
```

### Installation using **uv**

TODO
