Bases: BaseAnnotationCombiner

Combines annotations from GEO-based sources.

All sources in this combiner use GEO accession IDs (GSM or GSE) as their primary sample identifier. No ID mapping is required.

Example >>> combiner = GeoCombiner() >>> combiner.combine().clean().save(GEO_COMBINED_BSON)

combine(overrides=None)

Load and combine all GEO source parquets.

Sources whose parquet file does not exist are skipped with a warning.

Parameters:
  • overrides (dict[str, Path] | None, default: None ) –

    Per-source path overrides. Keys are source names from GEO_SOURCES; values replace the default path for that source.
Returns:
  • GeoCombiner –

    self, for chaining.