https://github.com/loremod/go2hpo
GO2HPO is a Python package designed to create association rules that classify genes to related phenotypes based on their annotations.
https://github.com/loremod/go2hpo
Last synced: about 1 year ago
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GO2HPO is a Python package designed to create association rules that classify genes to related phenotypes based on their annotations.
- Host: GitHub
- URL: https://github.com/loremod/go2hpo
- Owner: loremod
- License: mit
- Created: 2024-12-06T12:43:32.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-02-03T09:36:00.000Z (over 1 year ago)
- Last Synced: 2025-02-03T10:32:12.551Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 135 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# GO2HPO
GO2HPO is a Python package designed to create association rules that classify genes to related phenotypes based on their annotations.
---
## Features
- Extract and process annotation data related to genes and phenotypes.
- Analyze data to create association rules. (TO DO)
- Allows to be easily configurable and extendable. (TO DO)
---
## Installation
To install GO2HPO, follow these steps:
### **1. Clone the Repository**
Clone this repository to your local machine:
```bash
git clone https://github.com/loremod/GO2HPO.git
cd GO2HPO
```
### **2. Set Up a Virtual Environment**
Create and activate a virtual environment:
```bash
# On Windows
python -m venv venv
venv\Scripts\activate
# On Linux/Mac
python3 -m venv venv
source venv/bin/activate
```
### **3. Install the Package**
Install the package in editable mode (TEMPORARILY):
```bash
pip install -e .
```
---
## Usage
### **Importing the Modules**
After installation, you can import and use the package in your Python scripts or interactive sessions:
```python
from GO2HPO import DataManager, LogManager
# Example usage
data_manager = DataManager()
#....
#....
dataset = data_manager.get_dataset(hpo_list=["HP:0004322"], go_list=["GO:0008150"])
print(dataset)
```
---
## Repository Structure
```
GO2HPO/
├── src/
│ ├── GO2HPO/
│ │ ├── __init__.py
│ │ ├── dataManager.py
│ │ ├── LogManager.py
│ │ ├── dataImportExport.py
│ │ ├── StatisticalAnalyzer.py
├── setup.py
├── requirements.txt
├── README.md
├── LICENSE
```
---
## Dependencies
- `numpy`
- `pandas`
- `joblib`
- Others, like the ones for the generitic algorithm (TO DO)
---
**Lorenzo Modica**
Email: [lorenzomod@hotmail.it](mailto:lorenzomod@hotmail.it)