omicverse.alignment.fetch_sintax_ref

omicverse.alignment.fetch_sintax_ref#

omicverse.alignment.fetch_sintax_ref(source='rdp_16s_v18', db_dir=None, overwrite=False, timeout=300)[source]#

Download a SINTAX-formatted 16S reference FASTA.

Parameters:

  • source (str (default: 'rdp_16s_v18')) – One of 'rdp_16s_v18' (small, 6.8 MB) or 'silva_16s_v123' (comprehensive, ~440 MB; but old — see notes below). Both are pre-formatted for vsearch --sintax.

  • db_dir (Optional[str] (default: None)) – Required (or set OMICVERSE_DB_DIR). Target directory under which the reference is saved. No $HOME fallback.

  • overwrite (bool (default: False)) – Re-download even if the file already exists.

  • timeout (int (default: 300)) – Per-connection read timeout in seconds (default 300).

Returns:

Absolute path to the downloaded .fa.gz.

Return type:

str

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