DatabaseUNITE¶

class DatabaseUNITE(storage_hdf5_fp)[source]¶

Database class for UNITE database Nilsson et al. [NLT+19]

Parameters: storage_hdf5_fp (str) – 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.
`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)