taxopy 0.4.0

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:

saccharomyces = taxopy.Taxon('4930', taxdb)
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)
print(lagomorpha.rank_name_dictionary)

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']
{'order': 'Lagomorpha', 'clade': 'Opisthokonta', 'superorder': 'Euarchontoglires', 'class': 'Mammalia', 'superclass': 'Sarcopterygii', 'subphylum': 'Craniata', 'phylum': 'Chordata', 'kingdom': 'Metazoa', 'superkingdom': 'Eukaryota'}

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

The find_majority_vote function allows you to control its stringency via the fraction parameter. For instance, if you would set fraction to 0.75 the resulting taxon would be shared by more than 75% of the input lineages. By default, fraction is 0.5.

majority_vote = taxopy.find_majority_vote([human, gorilla, lagomorpha], taxdb, fraction=0.75)
print(majority_vote.name)

Euarchontoglires

You can also assign weights to each input lineage:

majority_vote = taxopy.find_majority_vote([saccharomyces, human, gorilla, lagomorpha], taxdb)
weighted_majority_vote = taxopy.find_majority_vote([saccharomyces, human, gorilla, lagomorpha], taxdb, weights=[3, 1, 1, 1])
print(majority_vote.name)
print(weighted_majority_vote.name)

Euarchontoglires
Opisthokonta

Acknowledgements

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