pytaxonkit
Python bindings for the TaxonKit library. Results of queries are returned as pandas data frames, dictionaries, and other convenient data structures.
Install
Installation with Conda is recommended.
(See environment.yaml for details on prerequisites if you want to try a different installation method.)
conda install -c bioconda pytaxonkit
Please follow the taxonkit instructions for downloading the NCBI Taxonomy database dump files.
By default, taxonkit and pytaxonkit search for these files in ~/.taxonkit/, but this directory can be overridden by setting the data_dir appropriately for the functions described below.
Execute help(pytaxonkit.name2taxid) (and so on) from the Python interpreter for more details.
Usage
pytaxonkit provides convenient access to TaxonKit operations from Python for use in the interactive interpreter, IPython, Jupyter notebooks, or custom Python code.
NOTES
- The
reformatoperation is automatically run bypytaxonkit.lineageand cannot be invoked independently.- The
taxid-changelogoperation is not supported.- The
genautocompleteoperation is specific to the shell and is not supported.
name2taxid
>>> import pytaxonkit
>>> names = ['Phyllobolus spinuliferus', 'Alteromonas putrefaciens', 'Rexia erectus']
>>> pytaxonkit.name2taxid(names)
Name TaxID Rank
0 Phyllobolus spinuliferus 359607 species
1 Alteromonas putrefaciens 24 species
2 Rexia erectus 262902 species
>>> pytaxonkit.name2taxid(names, sciname=True)
Name TaxID Rank
0 Phyllobolus spinuliferus <NA> <NA>
1 Alteromonas putrefaciens <NA> <NA>
2 Rexia erectus <NA> <NA>lineage
>>> import pytaxonkit
>>> result = pytaxonkit.lineage([7399, 1973489])
>>> result.columns
Index(['TaxID', 'Code', 'Name', 'Lineage', 'LineageTaxIDs', 'Rank',
'FullLineage', 'FullLineageTaxIDs', 'FullLineageRanks'],
dtype='object')
>>> result[['TaxID', 'Lineage', 'LineageTaxIDs']]
TaxID Lineage LineageTaxIDs
0 7399 Eukaryota;Arthropoda;Insecta;Hymenoptera;;; 2759;6656;50557;7399;;;
1 1973489 Bacteria;Firmicutes;Bacilli;Bacillales;Bacilla... 2;1239;91061;1385;186817;1386;1973489
>>> result = pytaxonkit.lineage(['1382510', '929505', '390333'], formatstr='{f};{g};{s};{S}')
>>> result['Lineage'].iloc[2]
'Lactobacillaceae;Lactobacillus;Lactobacillus delbrueckii;Lactobacillus delbrueckii subsp. bulgaricus'name
>>> import pytaxonkit
>>> pytaxonkit.name(['274127', 511170])
TaxID Name
0 274127 Distathma
1 511170 Delicatulalist
>>> import pytaxonkit
>>> result = pytaxonkit.list([13685, 9903])
>>> for taxon, tree in result:
... subtaxa = [t for t in tree.traverse]
... print(f'Top level result: {taxon.name} ({taxon.taxid}); {len(subtaxa)} related taxa')
...
Top level result: Solenopsis (13685); 293 related taxa
Top level result: Bos (9903); 29 related taxa
>>> subtaxa[0]
BasicTaxon(taxid=9904, rank='species', name='Bos gaurus')
>>> pytaxonkit.list([9605], raw=True)
{'9605 [genus] Homo': {'9606 [species] Homo sapiens': {'63221 [subspecies] Homo sapiens neanderthalensis': {}, "741158 [subspecies] Homo sapiens subsp. 'Denisova'": {}}, '1425170 [species] Homo heidelbergensis': {}, '2665952 [no rank] environmental samples': {'2665953 [species] Homo sapiens environmental sample': {}}}}filter
>>> import pytaxonkit
>>> taxids = [131567, 2759, 33154, 33208, 6072, 33213, 33317, 1206794, 88770, 6656, 197563, 197562, 6960, 50557, 85512, 7496, 33340, 33392, 85604, 7088]
>>> result = pytaxonkit.filter(taxids, equal_to='phylum', higher_than='phylum')
>>> pytaxonkit.name(result)
>>> pytaxonkit.name(result)
TaxID Name
0 2759 Eukaryota
1 33208 Metazoa
2 6656 Arthropoda
>>> taxids = [131567, 2759, 33154, 33208, 6072, 33213, 33317, 1206794, 88770, 6656, 197563, 197562, 6960, 50557, 85512, 7496, 33340, 33342, 7524]
>>> result = pytaxonkit.filter(taxids, lower_than='phylum', discard_norank=True)
>>> pytaxonkit.name(result)
TaxID Name
0 6960 Hexapoda
1 50557 Insecta
2 7496 Pterygota
3 33340 Neoptera
4 33342 Paraneoptera
5 7524 Hemipteralca
>>> import pytaxonkit
>>> taxids = pytaxonkit.name2taxid(['Polistes metricus', 'Nasonia vitripennis'])
>>> taxids
Name TaxID Rank
0 Polistes metricus 91422 species
1 Nasonia vitripennis 7425 species
>>> ancestor = pytaxonkit.lca(taxids.TaxID)
>>> pytaxonkit.name([ancestor])
TaxID Name
0 7400 Apocritaversion
>>> import pytaxonkit
>>> pytaxonkit.__version__
'0.7.2'
>>> pytaxonkit.__taxonkitversion__
'taxonkit v0.7.2'