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.
1 maintainer
Metadata
1 maintainer
Release files for taxopy 0.2.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| taxopy-0.2.1.tar.gz | 17.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| taxopy-0.2.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 36.7 kB
Release files / taxopy-0.2.1.tar.gz
| Download URL | taxopy-0.2.1.tar.gz |
|---|---|
| Size | 17.1 kB |
| Tags | Source |
|
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Release files / taxopy-0.2.1-py3-none-any.whl
| Download URL | taxopy-0.2.1-py3-none-any.whl |
|---|---|
| Size | 19.6 kB |
| Tags | Python 3 |
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twine/3.1.1 pkginfo/1.5.0.1 requests/2.23.0 setuptools/46.0.0.post20200311 requests-toolbelt/0.9.1 tqdm/4.43.0 CPython/3.7.6
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