database (db)

usage: kaptive database [options]
                        [subcommand] ...

📦 Manage local and remote Kaptive databases.

Aggregates subcommands for listing, installing, updating, resetting, adding,
extracting, and displaying metadata for Kaptive databases.

Aliases:
    db

🌎 Global options:
  -h, --help            show this help message and exit
  -V, --verbose         Enable verbose output/progress

'database' subcommands:
    list (ls)           📋 List all currently installed local databases.
    available (avail)   🌐 List all available official databases for installation.
    add                 🔗 Add a custom reference database from a GitHub repository.
    install             📦 Install known reference databases via keyword.
    update              🔄 Update installed local databases from remote repositories.
    reset               🧹 Uninstall all local databases and reset local cache.
    extract             📤 Extract database records in FASTA format.
    metadata (info)     📊 Print detailed metadata of a Kaptive database.

usage: kaptive database list [options]

📋 List all currently installed local databases.

Displays the keywords of all compiled `.pkl` databases found in the user's
local Kaptive directory (`~/.kaptive`).

Aliases:
    ls

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress

usage: kaptive database available [options]

🌐 List all available official databases for installation.

Displays the keywords of all officially supported databases curated in GitHub repositories
that can be installed via `kaptive db install <keyword>`.

Aliases:
    avail

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress

usage: kaptive database add [options] database owner repo_name

🔗 Add a custom reference database from a GitHub repository.

Fetches GenBank and TOML metadata files from any specified GitHub owner/repo/branch,
compiles the database, and registers it in the local cache.

📥 Inputs:
  database              Name for the new database

🌐 GitHub Details:
  owner                 GitHub repository owner
  repo_name             GitHub repository name
  -b, --branch [BRANCH]
                        GitHub repository branch (default: main)

🌎 Global options:
  -h, --help            show this help message and exit
  -V, --verbose         Enable verbose output/progress

usage: kaptive database install [options] database

📦 Install known reference databases via keyword.

Downloads GenBank and TOML definition files from official repositories, compiles
them into vectorized [`Database`][kaptive.db.core.Database] objects, and caches
them locally.

📥 Inputs:
  database       Database keyword (see: `kaptive db avail`) or 'all'

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress

usage: kaptive database update [options] [database]

🔄 Update installed local databases from remote repositories.

Checks installed databases against their source GitHub repositories for newer
versions defined in TOML metadata and re-compiles modified databases.

📥 Inputs:
  database       Database keyword (see: `kaptive db list`) or 'all' (default: all)

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress

usage: kaptive database reset [options]

🧹 Uninstall all local databases and reset local cache.

Deletes all compiled `.pkl` and metadata `.json` files from the local Kaptive cache directory.

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress

usage: kaptive database extract [options] [subcommand] ...

📤 Extract database records in FASTA format.

Aggregates subcommands for extracting locus nucleotide sequences (`loci`), gene
coding sequences (`genes`), and translated amino acid sequences (`proteins`).

🌎 Global options:
  -h, --help            show this help message and exit
  -V, --verbose         Enable verbose output/progress

'extract' subcommands:
    loci                🧬 Extract locus nucleotide sequences in FASTA format.
    genes               🧩 Extract gene coding sequences in FASTA format.
    proteins            🧶 Extract translated protein sequences in FASTA format.

usage: kaptive database metadata [options] database

📊 Print detailed metadata of a Kaptive database.

Displays summary information including organism, taxon ID, antigen type, synthesis pathway,
version, identity threshold, GenBank filename, DOIs, repository URL, and curator contacts.

Aliases:
    info

📥 Inputs:
  database       Database path or keyword (see: `kaptive db list`)

🌎 Global options:
  -h, --help     show this help message and exit
  -V, --verbose  Enable verbose output/progress