Metadata-Version: 2.1
Name: gopiscator
Version: 0.1.2
Summary: CLI tool for performing gene set enrichment analysis using the GO database.
Author-email: Dmitry Bespiatykh <d.bespiatykh@gmail.com>
License: MIT License
        
        Copyright (c) 2024 Dmitry Bespiatykh
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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Project-URL: Homepage, https://github.com/dbespiatykh/gopiscator
Project-URL: Documentation, https://github.com/dbespiatykh/gopiscator
Project-URL: Issues, https://github.com/dbespiatykh/gopiscator/issues
Project-URL: Repository, https://github.com/dbespiatykh/gopiscator/rich-click
Keywords: go,enrichment,gene,ontology,fisher
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: click
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: statsmodels
Requires-Dist: goatools
Requires-Dist: tabulate
Requires-Dist: tqdm

<p align="center">
  <img src="logo.png" alt="gopiscator Logo" height=200>
</p>
<hr>

`GOpiscator` is a command-line tool for performing gene set enrichment analysis using the Gene Ontology (GO) database.

[![PyPI version](https://badge.fury.io/py/gopiscator.svg)](https://badge.fury.io/py/gopiscator)
### Installation

```
pip install gopiscator
```

### Usage

```
Usage: gopiscator [OPTIONS]

  GOpiscator (Tool for performing gene set enrichment analysis)

Options:
  -i, --gene-list FILE      Genes of interest list.  [required]
  -a, --go-annotation FILE  GO annotation file.  [required]
  -o, --output FILE         Write output to a file.  [default: (standard output)]
  -g, --ontology FILE       GO '.obo' file.  [default: ('go-basic.obo'; will be downloaded if absent)]
  --threshold FLOAT         P-value threshold.  [default: 0.05]
  --gene-count INTEGER      Minimum No. of genes annotated to the specific GO term.  [default: 2]
  -v, --version             Show the version and exit.
  -h, --help                Show this message and exit.
```
> [!NOTE]
> `gene-list` should have your genes of interest, one gene per line:
> ||
>| --- |
>| Rv3861 |
>| Rv3862c |
>| Rv0083 |
>| Rv3371 |
>
> `go-annotation` should be tab-delimited with genes in the first column and GO terms in the second column (separated by comma):
> |||
>| --- | --- |
>| Rv0001 |	GO:0006172,GO:0006275,GO:0006270 |
>| Rv0002 |	GO:0046677,GO:0006260 |
>| Rv0003 |	GO:0009432,GO:0000731,GO:0006260 |
>| Rv0005 |	GO:0046677,GO:0006265,GO:0006261 |
