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Releases: apcamargo/taxopy

v0.13.0

03 Aug 02:11
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  • 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.

v0.12.0

04 Sep 22:36
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  • Add the rank_lineage, ranked_name_lineage, and ranked_taxid_lineage attributes to Taxon.

v0.11.0

23 Jan 19:44
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  • Allow taxid_from_name to take a list of names as input.

v0.10.3

23 Jan 17:32
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  • Strip whitespace when parsing string fields in nodes.dmp and names.dmp. By @Midnighter (#13).

v0.10.2

19 Aug 14:23
b97263c
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  • Add an __hash__ dunder method to Taxon to make it hashable. By @maxibor (#11).

v0.10.1

15 Aug 16:56
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  • Add a __eq__ dunder method to Taxon.

v0.10.0

29 Jul 20:11
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  • 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

v0.9.2

30 Dec 20:39
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  • 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.

v0.9.1

15 Dec 12:49
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  • Fixes a bug where taxopy tried to read the _merged_dmp and oldtaxid2newtaxid attributes from the TaxDb class itself rather than an instance.

v0.9.0

16 Sep 01:16
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  • Add support to merged.dmp and legacy taxids.