taxopy

• Allow download of a remote custom taxdump via the taxdump_url parameter of the TaxDb class.
• Allow fuzzy string matching in taxid_from_name through the fuzzy parameter. The degree of similarity between the query and the matches can be controlled using the score_cutoff parameter.

• Add the rank_lineage, ranked_name_lineage, and ranked_taxid_lineage attributes to Taxon.

• Allow taxid_from_name to take a list of names as input.

• Strip whitespace when parsing string fields in nodes.dmp and names.dmp. By @Midnighter (https://github.com/apcamargo/taxopy/pull/13).

• Add an __hash__ dunder method to Taxon to make it hashable. By @maxibor (https://github.com/apcamargo/taxopy/pull/11).

• Add a __eq__ dunder method to Taxon.

• Migrated from setup.py to flit.
• Class attributes are now exposed using getters (via the @property decorator).
• Added a __str__ dunder method to the Taxon class.
• Modified Taxon's __repr__ dunder method to make it display a string that resembles GTDB's lineage strings:

taxon = taxopy.Taxon(9673, taxdb)
repr(taxon)

r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes;o__Timlovirales

• Added a parent method to the Taxon class:

taxon = taxopy.Taxon(9673, taxdb)
parent_taxon = taxon.parent(taxdb)
print(taxon)
print(parent_taxon)

r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes;o__Timlovirales
r__Riboviria;k__Orthornavirae;p__Lenarviricota;c__Leviviricetes

• Fixes a bug where the taxdb.oldtaxid2newtaxid dictionary was being accessed to create a legacy_taxid even when a merged.dmp file was not supplied.

• Fixes a bug where taxopy tried to read the _merged_dmp and oldtaxid2newtaxid attributes from the TaxDb class itself rather than an instance.

• Add support to merged.dmp and legacy taxids.

• The rank_taxid_dictionary attribute was added to Taxon objects.

• The find_lca and find_majority_vote functions return objects of the _AggregatedTaxon class. _AggregatedTaxon is a subclass of Taxon with two additional attributes: agreement and aggregated_taxa.

• Taxids are now encoded as integers instead of strings. This reduced the memory usage and made taxopy faster.

• Add the new function taxid_from_name, which takes a taxon name and returns a list containing the taxonomic identifiers associated with it.
• Avoid redownloading the database if nodes.dmp and names.dmp are already in the directory.

• Allow the fraction parameter of the find_majority_vote function to assume values less than 0.5.

• Add the weights parameter to the find_majority_vote function.

• Add the fraction parameter to the find_majority_vote function.

• Fix a bug where find_majority_vote tried to create a Taxon object using None as input.
• Allow a list containing two Taxon objects as input to find_majority_vote.

• Added the find_majority_vote function to find the most specific taxon that is shared by more than half of the lineages of a list of taxa.

Initial release.