GTDB¶

GTDB provides Genome Taxonomy Database release files, including taxonomy tables, metadata, trees, release notes, checksums, and large genome/protein archives. biodbs supports GTDB as a public release-file catalog and downloader.

List Releases¶

from biodbs.fetch.GTDB import GTDB_Fetcher

fetcher = GTDB_Fetcher()
releases = fetcher.list_releases()

print(releases.names())

List Release Files¶

files = fetcher.list_release_files("latest")
rep_files = fetcher.list_release_files("latest", "genomic_files_reps")

Fetch Small Text Files¶

version = fetcher.get_version()
notes = fetcher.get_release_notes()
descriptions = fetcher.get_file_descriptions()
md5sums = fetcher.get_md5sums()

print(version.text)

Fetch Tables¶

taxonomy = fetcher.get_taxonomy(domain="bac120")
metadata = fetcher.get_metadata(domain="ar53")

df = taxonomy.as_dataframe()

Supported domains are bac120 and ar53.

Download Files¶

path = fetcher.download_taxonomy("bac120", dest="data/gtdb")

Existing files are kept by default. Use overwrite=True to download again. Large files are streamed to disk.

Convenience Functions¶

from biodbs.fetch import gtdb_get_taxonomy, gtdb_list_releases

releases = gtdb_list_releases()
taxonomy = gtdb_get_taxonomy("bac120")

Notes¶

GTDB genome and protein archives can be very large. The normal offline test suite does not download archives.