build_database_storage

classmethod DatabaseGTDB.build_database_storage(storage_hdf5_fp, taxonomy_map_csv_fp, tree_newick_fp, sequence_fasta_fp, metadata_csv_fp, stamp_dict, force=False, chunksize=500, **kwargs)[source]

Factory method to build new database hdf5

Parameters

  • storage_hdf5_fp (str) – Output path for hdf5 file

  • taxonomy_map_csv_fp (str) – Path to taxonomy file

  • tree_newick_fp (str) – Path to Newick tree file

  • sequence_fasta_fp (str) – Path to FASTA sequences file

  • stamp_dict (dict) – Dictionary with metadata that will be stamped to the database

  • force (bool) – Force output file overwrite

  • chunksize (int) – Sequence/Alignment data processing chunk size. Longer chunks are faster to process but require more memory.

  • **kwargs – Compatibility.

  • metadata_csv_fp (str) –

  • kwargs (Any) –

Returns

Return type

None if file was created successfully.