stangene (top-level)

The top-level stangene module provides the main pipeline entry point and re-exports all public functions.

Pipeline

stangene.run(path, species, output_dir=None, dataset_name=None, reference_dir=None)

Run the full harmonization pipeline on a single dataset.

Return type:

HarmonizationResult

Re-exported functions

All public functions are available directly from stangene:

import stangene

stangene.run(...)
stangene.build_reference(...)
stangene.load_reference(...)
stangene.load_features(...)
stangene.classify_features(...)
stangene.harmonize(...)
stangene.merge_features(...)
stangene.summary(...)
stangene.conflict_report(...)
stangene.generate_markdown_report(...)
stangene.write_reports(...)