exon-test
| Crates.io | exon-test |
| lib.rs | exon-test |
| version | 0.3.4-beta.9 |
| source | src |
| created_at | 2023-10-27 16:14:23.052674 |
| updated_at | 2023-10-27 16:21:28.710462 |
| description | Exon test crate |
| homepage | https://www.wheretrue.dev/docs/exon/ |
| repository | https://github.com/wheretrue/exon |
| max_upload_size | |
| id | 1016178 |
| size | 6,240 |
Trent Hauck (tshauck)
documentation
README
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
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 | .mzml1 |
| SAM | - | .sam |
| VCF | gz2 | .vcf |
Related Projects
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.