API Reference

GFFBase's public surface is intentionally compatible with legacy gffutils. Pages in this section are auto-generated from the live docstrings via mkdocstrings.

Module	What's there
FeatureDB	The query database. The row-by-row legacy methods, the vectorized children_batched / parents_batched / region_batched (with explode_segments= for physical lines), the derived-feature methods, attribute_search, and mode / derived_source.
Feature	The user-facing record type. Backwards-compatible with gffutils.Feature.
create_db	The ingestion entrypoint.
DataIterator & GFFWriter	Streaming I/O.
merge_criteria	Predicates consumed by FeatureDB.merge.
Exceptions	GFFFormatError, FeatureNotFoundError, DuplicateIDError, AttributeStringError, EmptyInputError, SchemaVersionError, MultipartConstraintError, ReadOnlyError, ClosedDatabaseError.
Multipart features	MultipartFeature, FeatureSegment — several GFF3 lines sharing one ID as a single logical feature.
validate	14 post-ingest invariants; db.validate() and gffbase validate.
migrate	Schema v1 → v2 upgrade, and the opt-in multipart coalesce.
Compatibility modules	bins, helpers, constants, attributes, convert, create, inspect, version, and the optional integrations.

If a method name is missing here it lives in the source under python/gffbase/; cross-reference the Migration guide for the legacy-equivalence table.