Metadata-Version: 2.1
Name: pathogen-decision-engine
Version: 1.0.1
Description-Content-Type: text/markdown

# Pathogen Decision Engine Package

The Decision Engine Package is a Python package for building and using decision engines based on rule sets defined in CSV files.

## Installation

You can install the package via pip:

    pip install pathogen-decision-engine

## Usage

### Command-Line Interface (CLI)

The package provides a command-line interface (CLI) for performing inference using the decision engine. To use the CLI,
you must provide either the path of a rule table path made as a CSV file ...
Example:

    decision_engine_cli --rule_table_path table.csv --input_dict '{"PA":1, "PVS":0, "PS":1, "PM":2, "PP":1, "BA":1, "BS":0, "BP":0}'

... or either through dict expressed as a string
Example

    decision_engine_cli --rule_table_dict "{'PA':{'0':1,'1':0},'PVS':{'0':0,'1':1},'PS':{'0':0,'1':'>=1'},'PM':{'0':0,'1':0},'PP':{'0':0,'1':0},'BA':{'0':0,'1':0},'BS':{'0':0,'1':0},'BP':{'0':0,'1':0},'Output':{'0':'Pathogenic','1':'Pathogenic','2':'Pathogenic'}}" --input_dict '{"PA":1, "PVS":0, "PS":1, "PM":2, "PP":1, "BA":1, "BS":0, "BP":0}'


### Python API

You can also use the package programmatically in your Python code. Here's an example of how to use the DecisionEngine class:

```python
from pathogen_decision_engine import PathogenDecisionEngine

df = None ### ... create a df dataframe as you wish

# Create a DecisionEngine object
decision_engine = PathogenDecisionEngine(df)

# Define input dictionary
input_dict = {"PA":1, "PVS":0, "PS":1, "PM":2, "PP":1, "BA":1, "BS":0, "BP":0}

# Perform inference
result = decision_engine.infer(input_dict)
print(result)
```
