GreenGenes¶

GreenGenes publishes its reference releases as an open HTTP directory tree at ftp.microbio.me/greengenes_release/. biodbs browses that tree and downloads files. (GreenGenes2 is served by the separate q2-greengenes2 plugin and is not covered here.)

List Releases¶

from biodbs.fetch.GreenGenes import GreenGenes_Fetcher

fetcher = GreenGenes_Fetcher()
releases = fetcher.list_releases()

print(releases.names())  # e.g. gg_13_8_otus, gg_13_5, 2022.10, 2024.09

Browse Files¶

files = fetcher.list_files("gg_13_8_otus/taxonomy")
print(files.names())
fasta = fetcher.list_files("gg_13_8_otus/rep_set").filter("*.fasta")

Download a File¶

path = fetcher.download_file(
    "gg_13_8_otus/taxonomy/99_otu_taxonomy.txt",
    dest="data/greengenes",
)

Existing files are kept by default (overwrite=True to refetch). Files stream to disk.

Convenience Functions¶

from biodbs.fetch import greengenes_list_releases, greengenes_list_files, greengenes_download_file

releases = greengenes_list_releases()
files = greengenes_list_files("gg_13_8_otus/rep_set")
path = greengenes_download_file("gg_13_8_otus/rep_set/99_otus.fasta", dest="data/greengenes")