3. Use existing GTax database metadata in PythonΒΆ

Download current Python objects in pickle format from GCP

localhost:~> gsutil -u <your-GCP-project-ID> -m cp gs://gtax-database/20211025/fasta/taxonomy.pickle .
localhost:~> gsutil -u <your-GCP-project-ID> -m cp gs://gtax-database/20211025/fasta/taxonomy_groups.pickle .

Loading data in Python

from gtax.taxonomy import Taxonomy
taxonomy = Taxonomy(tax_pickle_file='taxonomy.pickle', group_pickle_file = 'taxonomy_groups.pickle')

Output:

2374509 taxonomies loaded
bacteria Node: 526449 Sequences: 16137
archaea Node: 13927 Sequences: 554
liliopsida Node: 46167 Sequences: 265
eudicotyledons Node: 145896 Sequences: 880
viridiplantae Node: 45954 Sequences: 184
fungi Node: 179151 Sequences: 797
arthropoda Node: 883534 Sequences: 1364
neoteleostei Node: 29373 Sequences: 1437
actinopterygii Node: 20735 Sequences: 1047
glires Node: 5236 Sequences: 2178
primates Node: 1019 Sequences: 433
carnivora Node: 761 Sequences: 286
artiodactyla Node: 1184 Sequences: 447
amphibia Node: 12268 Sequences: 122
sauropsida Node: 31218 Sequences: 1073
sarcopterygii Node: 4759 Sequences: 229
chordata Node: 3975 Sequences: 301
eukaryota Node: 181514 Sequences: 803
viruses Node: 223526 Sequences: 13555