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uniprot-taxonomy

Tool for extracting taxonomy information from the Uniprot database.

This can be used on a downloaded tab-separated taxonomy file from Uniprot or by querying the database directly (only recommended for small queries).

Local installation

using pip:

$ git clone git@github.com:zhoulab/uniprot-taxonomy.git
$ cd uniprot-taxonomy
$ pip install -e .

Classes

Taxonomy

Class to allow lookup of organisms by taxon or mnemonic ID.

Organism

Class to store taxonomy information of individual organisms.

Examples

Downloaded file

> tax = Taxonomy('taxonomy-all.tab')
> tax['HUMAN']
Organism(taxon=9606,mnemonic="HUMAN")
> tax[9606]
Organism(taxon=9606,mnemonic="HUMAN")
> tax[9606].lineage
['Eukaryota',
 'Metazoa',
 'Chordata',
 'Craniata',
 'Vertebrata',
 'Euteleostomi',
 'Mammalia',
 'Eutheria',
 'Euarchontoglires',
 'Primates',
 'Haplorrhini',
 'Catarrhini',
 'Hominidae',
 'Homo']

Querying the Uniprot database

> page = get_organisms_page(fmt='tab', mnemonic='HUMAN')
> organisms = get_organisms(page)
> organisms.next()
Organism(taxon=9606,mnemonic="HUMAN")

About

get organism taxonomy information from http://uniprot.org

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