API Reference

The full API documentation is auto-generated from the Hoodini source code.

For the complete Python API reference, see the auto-generated API documentation.

Quick Links

CLI Reference — Command-line usage
Tutorial — Getting started guide
Outputs — Output file formats

Main Modules

`hoodini.pipeline`

The main pipeline module for running Hoodini analyses.


from hoodini.pipeline import Pipeline
 
# Create and run a pipeline
pipeline = Pipeline(
    input="WP_012345678.1",
    output="results/"
)
pipeline.run()

`hoodini.config`

Configuration management for Hoodini runs.


from hoodini.config import Config
 
# Load configuration from file
config = Config.from_yaml("my_config.yml")
 
# Or create programmatically
config = Config(
    blast_limit=100,
    neighborhood_size=20000,
    padloc=True
)

`hoodini.utils`

Utility functions for working with genomic data.


from hoodini.utils import (
    parse_protein_ids,
    fetch_assembly,
    extract_neighborhood
)

Full Reference

For detailed documentation of all modules, classes, and functions, see: