exon-test

3 releases

0.3.4-beta.9	Oct 27, 2023

#11 in #proteomics

Apache-2.0

7KB

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

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

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

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_formats`	`true`	Parse VCF FORMAT fields. If False, FORMAT fields will be returned as a single string.

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.

Dependencies

~63MB
~1M SLoC