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Merged
Created by Martin Larralde@larraldeMaintainer

Change internal data layer and output clusters as GenBank files

Added

  • Export of cluster sequences with genes and domain annotations in GenBank format.
  • Proper data model to allow retaining more information from input.
  • Dedicated functions to load the KNN training matrix and the CRF model.

Fixed

  • Sorting issue causing ClusterCRF to be passed a feature table with potentially scrambled proteins.

Changed

  • All internal classes but ClusterCRF expect objects from gecco.model instead of pandas.DataFrame.
  • KNN training matrix is now stored as a compressed sparse matrix.
  • Internal data is stored in the relevant module next to the code needing it instead of in a dedicated gecco.data module.
  • gecco.orf.ORFFinder works at the single record level.
  • Reduce code complexity in gecco.hmmer.DomainRow and gecco.refiner.ClusterRefiner.

Removed

  • Export of individual cluster proteins in FASTA files.
  • Unused ProdigalFinder (since PyrodigalFinder is used instead).
Edited by Martin Larralde