dbs

What does it do?

The phu dbs command group manages local databases used by phu. It provides a scalable contract so each database can define its own preparation logic while sharing a common user interface.

Current built-in backends are pfam and kofam.

Synopsis

phu dbs [COMMAND] [OPTIONS] [DATABASES...]

Supported commands

• phu dbs list
• phu dbs status [DATABASES...] [--all]
• phu dbs prepare [DATABASES...] [--all] [--force-refresh]
• phu dbs refresh [DATABASES...] [--all]
• phu dbs remove [DATABASES...] [--all] --yes

Behavior contract

For each database, operations are interpreted by that backend:

• prepare: make the database ready for runtime use.
• refresh: validate local state and repair incomplete or stale data.
• remove: delete local data for selected databases.
• status: report readiness and local metadata.

For pfam, preparation includes:

1. Ensuring Pfam-A.hmm is present locally.
2. Building the byte-offset index used for accession lookup.

For kofam, preparation includes:

1. Ensuring kofam.hmm and ko_list are present locally.
2. Building KO metadata index from ko_list (threshold, score_type, etc.).
3. Building the byte-offset index for sparse KO model extraction.

KOfam metadata drives threshold behavior in phu screen; see screen thresholds and decision logic.

KOfam support follows the KofamKOALA method for KO assignment and thresholding:

Aramaki T., Blanc-Mathieu R., Endo H., Ohkubo K., Kanehisa M., Goto S., Ogata H. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2019 Nov 19. pii: btz859. doi: 10.1093/bioinformatics/btz859.

Examples

Prepare only PFAM:

phu dbs prepare pfam

Prepare all supported databases:

phu dbs prepare --all

Prepare only KOfam:

phu dbs prepare kofam

Check status:

phu dbs status pfam kofam

Refresh integrity:

phu dbs refresh pfam kofam

Remove PFAM data:

phu dbs remove pfam --yes

Remove KOfam data:

phu dbs remove kofam --yes

List supported databases:

phu dbs list