Metadata-Version: 2.1
Name: genophenocorr
Version: 0.1.0
Summary: Search for genotype-phenotype correlations with GA4GH phenopackets
Author-email: Lauren Rekerle <lauren.rekerle@jax.org>, Daniel Danis <daniel.danis@jax.org>, Peter Robinson <peter.robinson@jax.org>
License: MIT License
        
        Copyright (c) 2023, The Monarch Initiative
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
Project-URL: homepage, https://github.com/monarch-initiative/genophenocorr
Project-URL: repository, https://github.com/monarch-initiative/genophenocorr.git
Project-URL: documentation, https://monarch-initiative.github.io/genophenocorr/stable
Project-URL: bugtracker, https://github.com/monarch-initiative/genophenocorr/issues
Keywords: Global Alliance for Genomics and Health,GA4GH Phenopacket Schema,Human Phenotype Ontology,GA4GH,Genotype-phenotype correlation,HPO
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3.5
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.5
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: hpo-toolkit >=0.3.0
Requires-Dist: protobuf >=3.15.0
Requires-Dist: pandas >=2.0.0
Requires-Dist: phenopackets >=2.0.2
Requires-Dist: requests >=2.25.0
Requires-Dist: scipy >=1.11
Requires-Dist: statsmodels >=0.13.0
Requires-Dist: numpy >=1.23
Provides-Extra: docs
Requires-Dist: sphinx >=7.0.0 ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme >=1.3.0 ; extra == 'docs'
Requires-Dist: sphinx-copybutton >=0.5.0 ; extra == 'docs'
Provides-Extra: test
Requires-Dist: pytest >=7.0.0 ; extra == 'test'

[![Build status](https://github.com/monarch-initiative/genophenocorr/workflows/CI/badge.svg)](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)
![PyPi downloads](https://img.shields.io/pypi/dm/genophenocorr.svg?label=Pypi%20downloads)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/genophenocorr)

Genophenocorr is a Python library for genotype-phenotype association analysis. 

An example of simple genotype-phenotype association analysis
```python
# Load HPO
import hpotk
hpo = hpotk.load_minimal_ontology('http://purl.obolibrary.org/obo/hp.json')

# Load a cohort of phenopackets 
from genophenocorr.data import get_toy_cohort
cohort = get_toy_cohort()

# Analyze genotype-phenotype associations 
from genophenocorr.analysis import CohortAnalysis
from genophenocorr.constants import VariantEffect

cohort_analysis = CohortAnalysis(cohort, 'NM_1234.5', hpo)
frameshift = cohort_analysis.compare_by_variant_type(VariantEffect.FRAMESHIFT_VARIANT)
print(frameshift)
```

prints a table with genotype-phenotype correlations:

```text
                            With frameshift_variant         Without frameshift_variant
                                              Count Percent                      Count Percent  p-value
HP:0001166 (Arachnodactyly)                       4  30.77%                         10  76.92%  0.04718
HP:0001250 (Seizure)                             11  84.62%                          9  69.23%  0.64472
HP:0001257 (Spasticity)                           8  61.54%                          9  69.23%  1.00000
```

## Documentation

Check out the User guide and the API reference for more info:

- [Stable documentation](https://thejacksonlaboratory.github.io/genophenocorr/stable) (last release on `main` branch)
- [Latest documentation](https://thejacksonlaboratory.github.io/genophenocorr/latest) (bleeding edge, latest commit on `development` branch)
