taxopy 0.2.1

A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers.

taxopy

A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers.

Installation

There are two ways to install taxopy:

• Using pip:

pip install taxopy

• Using conda:

conda install -c conda-forge -c bioconda taxopy

Usage

import taxopy

First you need to download taxonomic information from NCBI's servers and put this data into a TaxDb object:

taxdb = taxopy.TaxDb()
# You can also use your own set of taxonomy files:
taxdb = taxopy.TaxDb(nodes_dmp="taxdb/nodes.dmp", names_dmp="taxdb/names.dmp", keep_files=True)

The TaxDb object stores the name, rank and parent-child relationships of each taxonomic identifier:

print(taxdb.taxid2name['2'])
print(taxdb.taxid2parent['2'])
print(taxdb.taxid2rank['2'])

Bacteria
131567
superkingdom

To get information of a given taxon you can create a Taxon object using its taxonomic identifier:

human = taxopy.Taxon('9606', taxdb)
gorilla = taxopy.Taxon('9593', taxdb)
lagomorpha = taxopy.Taxon('9975', taxdb)

Each Taxon object stores a variety of information, such as the rank, identifier and name of the input taxon, and the identifiers and names of all the parent taxa:

print(lagomorpha.rank)
print(lagomorpha.name)
print(lagomorpha.name_lineage)

order
Lagomorpha
['Lagomorpha', 'Glires', 'Euarchontoglires', 'Boreoeutheria', 'Eutheria', 'Theria', 'Mammalia', 'Amniota', 'Tetrapoda', 'Dipnotetrapodomorpha', 'Sarcopterygii', 'Euteleostomi', 'Teleostomi', 'Gnathostomata', 'Vertebrata', 'Craniata', 'Chordata', 'Deuterostomia', 'Bilateria', 'Eumetazoa', 'Metazoa', 'Opisthokonta', 'Eukaryota', 'cellular organisms', 'root']

You can get the lowest common ancestor of a list of taxa using the find_lca function:

human_lagomorpha_lca = taxopy.find_lca([human, lagomorpha], taxdb)
print(human_lagomorpha_lca.name)

Euarchontoglires

You may also use the find_majority_vote to discover the most specific taxon that is shared by more than half of the lineages of a list of taxa:

majority_vote = taxopy.find_majority_vote([human, gorilla, lagomorpha], taxdb)
print(majority_vote.name)

Homininae

Acknowledgements

Some of the code used in taxopy was taken from the CAT/BAT tool for taxonomic classification of contigs and metagenome-assembled genomes.