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https://github.com/hrshdhgd/kegg-ingest
https://github.com/hrshdhgd/kegg-ingest
Last synced: 29 days ago
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- Host: GitHub
- URL: https://github.com/hrshdhgd/kegg-ingest
- Owner: hrshdhgd
- License: mit
- Created: 2024-08-16T20:01:49.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-08-27T20:25:11.000Z (5 months ago)
- Last Synced: 2024-11-05T20:05:41.653Z (3 months ago)
- Language: Python
- Size: 2.84 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
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README
# 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. All ingests are saved in a `duckdb` database and also exported as a tsv file.
## Installation
To install `kegg-ingest`, use pip:
```sh
pip install kegg-ingest
```
## Commands
### `get`
Fetch and process data from KEGG. (e.g.: https://rest.kegg.jp/get/map011000)
**Usage:**
```sh
kegg-ingest get --db [--batch-size ] [--use-kegg/--no-use-kegg] [--output ]
```
**Options:**
- `--db`: KEGG Database to ingest (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`](https://github.com/cokelaer/bioservices)
- `--output, -o`: Output file to write to (tsv format).
**Example:**
```sh
kegg-ingest get --db pathway
```
This downloads all KEGG pathways in batches of 5 (e.g.: https://rest.kegg.jp/get/map01100+map01110+map01120+map01200+map01210 so on and so forth.)
### `clear-db`
Clear the entire database.
**Usage:**
```sh
kegg-ingest clear-db
```
### `drop`
Drop a specific table from the database.
**Usage:**
```sh
kegg-ingest drop
```
**Arguments:**
- `table_name`: Name of the table to drop.
**Example:**
```sh
kegg-ingest drop get_pathway
```
### `preview`
Show the contents of a table.
**Usage:**
```sh
kegg-ingest preview [--limit ]
```
**Arguments:**
- `table_name`: Name of the table to preview.
**Options:**
- `--limit`: Number of rows to preview (default: 5).
**Example:**
```sh
kegg-ingest preview get_pathway --limit 10
```
### `overview`
Print an overview of the database.
**Usage:**
```sh
kegg-ingest overview
```
### `query`
Run a query on the database.
**Usage:**
```sh
kegg-ingest query
```
**Arguments:**
- `query_text`: SQL query to run.
**Example:**
```sh
kegg-ingest query "SELECT * FROM get_pathway WHERE description LIKE '%metabolism%'"
```
## License
This project is licensed under the MIT License. See the LICENSE file for details.
---
# Acknowledgements
This [cookiecutter](https://cookiecutter.readthedocs.io/en/stable/README.html) project was developed from the [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) template and will be kept up-to-date using [cruft](https://cruft.github.io/cruft/).