pathogen-decision-engine 1.1.0

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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:

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)