omataxonomy 0.4.0

Package to work with combined NCBI and GTDB taxonomy

OMA Taxonomy

omataxonomy is a library based on ete's ncbi_taxonomy module that is used internally for the OMA project, but that can also be used in different contexts. Essentially, it combines the NCBI Taxonomy and the GTDB taxonomy (including all their genome as subspecies). For GTDB we generate stable taxon ids by hashing the scientific names.

omataxonomy stores the data in a sqlite database under ${HOME}/.config/omataxonomy/ and therefor uses little resources when being used as not all the data will be loaded into memory.

Install

OMA Taxonomy can be installed directly from pip:

pip install omataxonomy

Usage

from omataxonomy import Taxonomy
tax = Taxonomy()
print(tax.get_name_lineage(['RS_GCF_006228565.1', 'GB_GCA_001515945.1', "f__Leptotrichiaceae", "Homo sapiens", "Gallus"]))

{'f__Leptotrichiaceae': ['root', 'd__Bacteria', 'p__Fusobacteriota', 'o__Fusobacteriales', 'f__Leptotrichiaceae'], 'Gallus': ['root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa', 'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata', 'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi', 'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota', 'Sauropsida', 'Sauria', 'Archelosauria', 'Archosauria', 'Dinosauria', 'Saurischia', 'Theropoda', 'Coelurosauria', 'Aves', 'Neognathae', 'Galloanserae', 'Galliformes', 'Phasianidae', 'Phasianinae', 'Gallus'], 'GB_GCA_001515945.1': ['root', 'd__Bacteria', 'p__Firmicutes_B', 'c__Moorellia', 'o__Desulfitibacterales', 's__Desulfitibacter sp001515945', 'GB_GCA_001515945.1'], 'Homo sapiens': ['root', 'cellular organisms', 'Eukaryota', 'Opisthokonta', 'Metazoa', 'Eumetazoa', 'Bilateria', 'Deuterostomia', 'Chordata', 'Craniata', 'Vertebrata', 'Gnathostomata', 'Teleostomi', 'Euteleostomi', 'Sarcopterygii', 'Dipnotetrapodomorpha', 'Tetrapoda', 'Amniota', 'Mammalia', 'Theria', 'Eutheria', 'Boreoeutheria', 'Euarchontoglires', 'Primates', 'Haplorrhini', 'Simiiformes', 'Catarrhini', 'Hominoidea', 'Hominidae', 'Homininae', 'Homo', 'Homo sapiens'], 'RS_GCF_006228565.1': ['root', 'd__Bacteria', 'p__Firmicutes_B', 'c__Moorellia', 'o__Moorellales', 'f__Moorellaceae', 'g__Moorella', 's__Moorella thermoacetica', 'RS_GCF_006228565.1']}