Exon is an analysis toolkit for life-science applications. It features:

• Support for many file formats from bioinformatics, proteomics, and others
• Local filesystem and object storage support
• Arrow FFI primitives for multi-language support
• SQL based access to bioinformatics data -- general DML and some DDL support

Please note Exon was recently excised from a larger library, so please be patient as we work to clean up after that. If you have a comment or question in the meantime, please file an issue.

• Installation
• Usage
• File Formats
• Related Projects
• Settings
• Benchmarks

Installation

Exon is available via crates.io. To install, run:

cargo add exon

Usage

Exon is designed to be used as a library. For example, to read a FASTA file:

use exon::context::ExonSessionExt;

use datafusion::prelude::*;
use datafusion::error::Result;

let ctx = SessionContext::new_exon();

let df = ctx.read_fasta("test-data/datasources/fasta/test.fasta", None).await?;

Please see the rust docs for more information.

File Formats

[^1]: Uses bgzip not gzip. [^2]: mzML also works.

Related Projects

• Exon R Bindings
• BioBear

Settings

Exon using the following settings:

You can update the settings by running:

SET <setting> = <value>;

For example, to disable parsing of VCF INFO fields:

SET exon.vcf_parse_info = false;

Benchmarks

Please see the benchmarks README for more information.