https://github.com/Euphrasiologist/nu_plugin_bio

Bioinformatics plugin for nushell.
https://github.com/Euphrasiologist/nu_plugin_bio

Last synced: about 2 months ago
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Bioinformatics plugin for nushell.

• Host: GitHub
• URL: https://github.com/Euphrasiologist/nu_plugin_bio
• Owner: Euphrasiologist
• Created: 2022-10-25T16:30:45.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2023-10-21T12:00:00.000Z (11 months ago)
• Last Synced: 2024-07-07T23:34:13.249Z (3 months ago)
• Language: Rust
• Size: 17.3 MB
• Stars: 22
• Watchers: 1
• Forks: 2
• Open Issues: 5
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-nu - nu_plugin_bio

README

        
# Nushell bio

A bioinformatics plugin for nushell. This plugin parses most common bioinformatics formats into structured data so you can use them with nushell more effectively.

# Quick setup

Go and get nushell, it's great. I'm assuming you have the rust toolchain installed. Then come back!

```nu

# clone this repo

git clone https://github.com/Euphrasiologist/nu_plugin_bio

# change into the repo directory

cd nu_plugin_bio

# build

# it's quite a long compile time...

cargo build --release

# register the plugin

register nu_plugin_bio/target/release/nu_plugin_bio

# see the current file formats currently supported below

# now you can just use open, and the file extension will be auto-detected.

# there are some test files in the tests/ dir.

open ./tests/test.fasta

    | get id

# if you want to add flags you have to explicitly use from 

# e.g. if you want descriptions in fasta files to be parsed.

open --raw ./tests/test.fasta 

    | from fasta -d

    | first

```

The backend is a `noodles` wrapper, an excellent, all-Rust bioinformatics I/O library.

## Aims

Aim to support the following:

- [x] BAM 1.6

- [x] BCF 2.2

  - [x] bcf.gz 

- [x] VCF 4.3

  - [x] vcf.gz

- [x] BED(3 only right now)

- [x] CRAM 3.0

- [x] FASTA

  - [x] fa.gz 

- [x] FASTQ

  - [x] fq.gz

- [x] GFF3

- [ ] GTF 2.2

- [x] SAM 1.6

- [x] GFA 1.0

  - [x] gfa.gz

Note that performance will not be optimal with the current state of `nu_plugin`, as we cannot access the engine state of nushell, and therefore need to load entire data structures into memory. Testing still needs to be done on large files.

## More?

If there's a bioinformatics format you want to add, let me know, or add a PR.