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
• Settings
• Benchmarks

Installation

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

bash cargo add exon

Usage

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

```rust 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

| Format | Compression(s) | Inferred Extension(s) | | --------- | -------------- | --------------------- | | BAM | - | .bam | | BCF | - | .bcf | | BED | gz, zstd | .bed | | FASTA | gz, zstd | .fasta, .fa, .fna | | FASTQ | gz, zstd | .fastq, .fq | | GENBANK | gz, zstd | .gbk, .genbank, .gb | | GFF | gz, zstd | .gff | | GTF | gz, zstd | .gtf | | HMMDOMTAB | gz, zstd | .hmmdomtab | | MZML | gz, zstd | .mzml[^2] | | SAM | - | .sam | | VCF | gz[^1] | .vcf |

Settings

Exon using the following settings:

| Setting | Default | Description | | ------- | ------- | ----------- | | exon.vcf_parse_info | true | Parse VCF INFO fields. If False, INFO fields will be returned as a single string. | | exon.vcf_parse_format | true | Parse VCF FORMAT fields. If False, FORMAT fields will be returned as a single string. |

You can update the settings by running:

sql SET <setting> = <value>;

For example, to disable parsing of VCF INFO fields:

sql SET exon.vcf_parse_info = false;

Benchmarks

Please see the benchmarks README for more information.