https://github.com/dlesl/gb-io

A Rust library for parsing, writing and manipulating Genbank sequence files
https://github.com/dlesl/gb-io

biology genbank rust

Last synced: 2 months ago
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A Rust library for parsing, writing and manipulating Genbank sequence files

• Host: GitHub
• URL: https://github.com/dlesl/gb-io
• Owner: dlesl
• License: mit
• Created: 2018-09-20T19:42:23.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-10-13T18:35:37.000Z (about 1 year ago)
• Last Synced: 2024-10-08T15:19:40.915Z (3 months ago)
• Topics: biology, genbank, rust
• Language: Rust
• Homepage:
• Size: 3.61 MB
• Stars: 14
• Watchers: 2
• Forks: 5
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# gb-io

[![crates.io link](https://img.shields.io/crates/v/gb-io.svg)](https://crates.io/crates/gb-io)

[![docs.rs link](https://docs.rs/gb-io/badge.svg)](https://docs.rs/gb-io/)

This is a library for parsing and working with Genbank (.gb) files written in

Rust. It supports reading, writing, and extracting parts of a sequence while

retaining feature annotations.

It should be able to handle most files out there. Feedback, improvements, and

details of any .gb files it chokes on are welcome!

### Example

Reverse complement a sequence, retaining feature annotations.

```rust

extern crate gb_io;

use std::fs::File;

use std::io;

use gb_io::reader::SeqReader;

fn main() {

    let file = File::open("mg1655.gb").unwrap();

    let stdout = io::stdout();

    for seq in SeqReader::new(file) {

        let seq = seq.unwrap();

        let rc = seq.revcomp();

        rc.write(stdout.lock()).unwrap();

    }

}

```

### Python bindings

[Martin Larralde](https://github.com/althonos) has written [Python

bindings](https://pypi.org/project/gb-io/) for `gb-io`'s parser.