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, kofam, dbcan, and avg.

Synopsis

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

Supported commands

The database subcommands use a separate Selection panel for --all and a command-specific action panel for preparation or removal options. Run each subcommand with --help to see its current grouped menu.

For example, the rendered menus are:

Usage: phu dbs status [OPTIONS] [databases]...

 Show detailed status for one or more databases.

╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ databases  Database names (default: all)                                     │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Selection ───────────────────────────────────────────────────────────────────╮
│ --all  Show status for all supported databases                               │
╰──────────────────────────────────────────────────────────────────────────────╯

Usage: phu dbs prepare [OPTIONS] [databases]...

╭─ Selection ───────────────────────────────────────────────────────────────────╮
│ --all  Prepare all supported databases                                       │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Preparation ─────────────────────────────────────────────────────────────────╮
│ --force-refresh  Force re-download/rebuild when supported                    │
╰──────────────────────────────────────────────────────────────────────────────╯

• 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.

For dbcan, preparation downloads the dbCAN HMM source and PUL workbook, then builds family-offset and PUL-rule indexes plus a sparse model cache. The workbook column cazymes_predicted_dbcan is the source of PUL rules; the dated substrate-only text file is not used to construct rules.

from the AnantharamanLab repository and stores it locally with a manifest and checksum. The parser requires the columns Accession, Protein Function, V-Score, Normalized VL-score, Log10[Hit Number], and Database Origin. The normalized VL-score column is required by the Phase 4 AVL calculation.

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

Prepare the V-score table:

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