https://github.com/shencangsheng/pg_bedtools_rs

A PostgreSQL plugin for bedtools, implemented in Rust.
https://github.com/shencangsheng/pg_bedtools_rs

bed bedtools pgrx plugin position postgresql rust

Last synced: 13 days ago
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A PostgreSQL plugin for bedtools, implemented in Rust.

• Host: GitHub
• URL: https://github.com/shencangsheng/pg_bedtools_rs
• Owner: shencangsheng
• License: mit
• Created: 2024-11-27T03:05:07.000Z (6 months ago)
• Default Branch: main
• Last Pushed: 2025-03-27T14:15:40.000Z (about 2 months ago)
• Last Synced: 2025-03-27T15:27:23.654Z (about 2 months ago)
• Topics: bed, bedtools, pgrx, plugin, position, postgresql, rust
• Language: Rust
• Homepage:
• Size: 12.7 KB
• Stars: 2
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](./LICENSE.md)

# pg_bedtools_rs

A `PostgreSQL` plugin for `bedtools`, implemented in `Rust`.

## 🌟 Features

- [x] `bed_merge`

## 🛠️ Installer

![Local Machine](https://img.shields.io/badge/local%20machine-blue?logo=computer&logoColor=white)

```bash

cargo install cargo-pgrx --version 0.11.4 --locked

cargo pgrx install --pg-config [PATH]

```

### ![Docker](https://img.shields.io/badge/docker-blue?logo=docker&logoColor=white)

```bash

docker run --rm -v $(pwd):/usr/src/app shencangsheng/pgrx:13

cp target/release/pg_bedtools_rs-pg13/root/.pgrx/13.18/pgrx-install/lib/postgresql/pg_bedtools_rs.so ${POSTGRESQL_PATH}/lib/

cp target/release/pg_bedtools_rs-pg13/root/.pgrx/13.18/pgrx-install/share/postgresql/extension/pg_bedtools_rs--0.1.0.sql ${POSTGRESQL_PATH}/extension/

cp target/release/pg_bedtools_rs-pg13/root/.pgrx/13.18/pgrx-install/share/postgresql/extension/pg_bedtools_rs.control ${POSTGRESQL_PATH}/extension/

```

```sql

CREATE EXTENSION pg_bedtools_rs

```

## 📦 Supports

- PostgreSQL 13

## 💡 Trying

Basic example:

```sql

create table tube_probe_bed (

   id SERIAL PRIMARY KEY,

   chromosome varchar NOT NULL,

   pos_start integer NOT NULL,

   pos_end integer NOT NULL

);

INSERT INTO

	TUBE_PROBE_BED (CHROMOSOME, POS_START, POS_END)

VALUES

	('chr1', 5, 10),

	('chr1', 10, 14),

	('chr1', 7, 15),

	('chr1', 22, 30),

	('chr1', 25, 35),

	('chr2', 5, 10),

	('chr2', 7, 15);

	

select * from bed_merge('tube_probe_bed');

```

Returns:

| CHROMOSOME | POS_START | POS_END |

|------------|-----------|---------|

| chr1       | 5         | 15      |

| chr1       | 22        | 35      |

| chr2       | 5         | 15      |

## 👍 Libraries Used

* [noamteyssier/bedrs](https://github.com/noamteyssier/bedrs)

* [shencangsheng/pgrx-docker](https://github.com/shencangsheng/pgrx-docker)

## 📝 License

A short snippet describing the license (MIT)

MIT © Cangsheng Shen