DatabaseGTDB

class DatabaseGTDB(*args, **kwargs)

Database class for GTDB database Parks et al. [PCC+20]

Parameters

storage_hdf5_fp – File path to hdf5

Attributes

avail_ranks	Available taxonomic ranks in the database.
name	Database name/label.
novel_tids	Array of novel tids produced during database creating.
stamp	Database stamp during creation.
state	State of the storage manager and database.
storage_manager	Working storage manager.
summary	Summary storage element states.
xrid	Feature/Representative/Reference identifiers.
xtid	Unique taxon identifiers.

Methods

build_database_storage(storage_hdf5_fp, …)	Factory method to build new database hdf5
close()	Closes local client by shutting down storage manager.
find_rid_by_tid([ids, subs, iterator, …])	Get rids by target tids.
find_sub_tids_by_tid([ids, ter_rank, …])	Get sub-tids by target tids as ids parameter.
find_tid_by_rid([ids, levels, flatten, …])	Get tids by target rids.
get_accession_by_rid([ids, iterator])	Get accession numbers from the database.
get_accession_by_tid([ids, subs, iterator])	Get accession numbers from the database.
get_alignment_by_rid([ids, iterator, like, …])	Get representative alignments for rids
get_alignment_by_tid([ids, subs, iterator, …])	Get representative alignments for tids
get_lineage_by_rid([ids, missing_rank, …])	Generates lineages for rids.
get_lineage_by_tid([ids, missing_rank, …])	Generates lineages for tids
get_sequence_by_rid([ids, iterator, like, …])	Get representative sequence for rids
get_sequence_by_tid([ids, subs, iterator, …])	Get representative sequence for tids
get_stats_by_rid([ids, include, exclude])	Get pre-generated statistics for target rids
get_stats_by_tid([ids, include, exclude])	Get pre-generated statistics for target tids
get_taxonomy_by_rank(levels)	Make taxonomy dataframe for given taxonomic ranks or levels
get_taxonomy_by_rid([ids, levels, tax_format])	Make taxonomy dataframe for given tids.
get_taxonomy_by_tid([ids, levels])	Make taxonomy dataframe for given tids.
infer_topology_by_rid(ids)	Quickly infers topology from tree node map.
infer_topology_by_tid(ids[, subreps, …])	Quickly infers topology from tree node map.
prune_tree_by_rid(ids)	Prune the reference tree and keep ids
prune_tree_by_tid(ids[, subreps, include_rid])	Prune reference tree and keep tips with ids
take_rids_by_rank([levels, iterator, …])	Get rids for given taxonomic ranks (level)
take_tids_by_rank([levels, iterator, …])	Get tids for given taxonomic ranks (level)