# kegg-ingest CLI

`kegg-ingest` is a command line interface for interacting with the KEGG database. This tool allows you to fetch, process, and manage data from KEGG.

## Installation

To install `kegg-ingest`, use pip:

```sh
pip install kegg-ingest

Commands

get

Fetch and process data from KEGG.

Usage:

kegg-ingest get --db <database> [--batch-size <size>] [--use-kegg/--no-use-kegg] [--output <file>]

Options:

• --db: Database to use (required).
• --batch-size, -b: Batch size for processing (default: 10, max: 10).
• --use-kegg/--no-use-kegg: Use KEGG API to fetch data (default: True). Alternatively uses bioservices
• --output, -o: Output file to write to (tsv format).

Example:

kegg-ingest get --db pathway --batch-size 5 --use-kegg --output output.tsv

clear-db

Clear the entire database.

Usage:

kegg-ingest clear-db

drop

Drop a specific table from the database.

Usage:

kegg-ingest drop <table_name>

Arguments:

• table_name: Name of the table to drop.

Example:

kegg-ingest drop pathway_table

preview

Show the contents of a table.

Usage:

kegg-ingest preview <table_name> [--limit <number>]

Arguments:

• table_name: Name of the table to preview.

Options:

• --limit: Number of rows to preview (default: 5).

Example:

kegg-ingest preview pathway_table --limit 10

overview

Print an overview of the database.

Usage:

kegg-ingest overview

query

Run a query on the database.

Usage:

kegg-ingest query <query_text>

Arguments:

• query_text: SQL query to run.

Example:

kegg-ingest query "SELECT * FROM pathway_table WHERE description LIKE '%metabolism%'"

License

This project is licensed under the MIT License. See the LICENSE file for details.

Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.