PR2¶

PR2 (Protist Ribosomal Reference) publishes its reference sequence and taxonomy files as assets on GitHub releases. biodbs supports PR2 as a release catalog and downloader over the GitHub API.

List Releases¶

from biodbs.fetch.PR2 import PR2_Fetcher

fetcher = PR2_Fetcher()
releases = fetcher.list_releases()

print(releases.names())  # release tags, newest first

List Release Assets¶

# assets for the latest release
assets = fetcher.list_assets()

# assets for a specific release tag
assets = fetcher.list_assets(tag="v5.0.0")

print(assets.names())
fasta = assets.filter("*.fasta.gz")

Download an Asset¶

path = fetcher.download_asset(
    "pr2_version_5.0.0_SSU_taxo_long.fasta.gz",
    dest="data/pr2",
)

Existing files are kept by default. Use overwrite=True to download again. The latest release is used unless you pass tag=. Files are streamed to disk.

Convenience Functions¶

from biodbs.fetch import pr2_list_releases, pr2_list_assets, pr2_download_asset

releases = pr2_list_releases()
assets = pr2_list_assets()
path = pr2_download_asset("pr2_version_5.0.0_SSU_UTAX.fasta.gz", dest="data/pr2")

Notes¶

Asset names include the version and marker (e.g. SSU), so filter the asset listing rather than hard-coding filenames. The normal offline test suite does not download release assets.