txdb

Behavior:

• Initializes the taxonomy database from taxdump.tar.gz.
• Creates a SQLite database at ~/.nwr/taxonomy.sqlite.
• Loads data from division.dmp, names.dmp, and nodes.dmp.
• Creates indexes for efficient querying.

Database Location:

~/.nwr/taxonomy.sqlite

The DDL:

DROP TABLE IF EXISTS division;
DROP TABLE IF EXISTS node;
DROP TABLE IF EXISTS name;

CREATE TABLE IF NOT EXISTS division (
    id       INTEGER      NOT NULL
                          PRIMARY KEY,
    division VARCHAR (50) NOT NULL
);

CREATE TABLE IF NOT EXISTS node (
    tax_id        INTEGER      NOT NULL
                               PRIMARY KEY,
    parent_tax_id INTEGER,
    rank          VARCHAR (25) NOT NULL,
    division_id   INTEGER      NOT NULL,
    comment       TEXT,
    FOREIGN KEY (
        division_id
    )
    REFERENCES division (id)
);

CREATE TABLE IF NOT EXISTS name (
    id         INTEGER      NOT NULL
                            PRIMARY KEY,
    tax_id     INTEGER      NOT NULL,
    name       VARCHAR (50) NOT NULL,
    name_class VARCHAR (50) NOT NULL
);

Query the database:

echo "
    SELECT sql
    FROM sqlite_master
    WHERE type='table'
    ORDER BY name;
    " |
    sqlite3 -tabs ~/.nwr/taxonomy.sqlite

Examples:

1. Initialize the taxonomy database nwr txdb

2. Use a custom directory nwr txdb --dir /path/to/nwr