Expand description
Exon is a library to facilitate open-ended analysis of scientific data, ease the application of ML models, and provide a common data interface for science and engineering teams.
Overview
The main interface for users is through datafusion’s SessionContext
plus the ExonSessionExt
extension trait. This has a number of convenience methods for loading data from various sources.
See the read_*
methods on ExonSessionExt
for more information. For example, read_fasta
, or read_gff
. There’s also a read_inferred_exon_table
method that will attempt to infer the data type and compression from the file extension for ease of use.
To facilitate those methods, Exon implements a number of traits for DataFusion that serve as a good base for scientific data work. See the datasources
module for more information.
Examples
Loading a FASTQ file
use exon::ExonSessionExt;
use datafusion::prelude::*;
use datafusion::error::Result;
let ctx = SessionContext::new();
let df = ctx.read_fastq("test-data/datasources/fastq/test.fastq", None).await?;
assert_eq!(df.schema().fields().len(), 4);
assert_eq!(df.schema().field(0).name(), "name");
assert_eq!(df.schema().field(1).name(), "description");
assert_eq!(df.schema().field(2).name(), "sequence");
assert_eq!(df.schema().field(3).name(), "quality_scores");
Loading a ZSTD-compressed FASTA file
use exon::ExonSessionExt;
use datafusion::prelude::*;
use datafusion::error::Result;
use datafusion::common::FileCompressionType;
let ctx = SessionContext::new();
let file_compression = FileCompressionType::ZSTD;
let df = ctx.read_fasta("test-data/datasources/fasta/test.fasta.zstd", Some(file_compression)).await?;
assert_eq!(df.schema().fields().len(), 3);
assert_eq!(df.schema().field(0).name(), "id");
assert_eq!(df.schema().field(1).name(), "description");
assert_eq!(df.schema().field(2).name(), "sequence");
let results = df.collect().await?;
assert_eq!(results.len(), 1); // 1 batch, small dataset
Modules
- Data sources for Exon. Datasources module.
- Error types for Exon.
- Logical plan augmentations for Exon.
- Physical plan augmentations for Exon.
- Physical plan augmentations for Exon.
- Utilities for working with stream bgzf files.
- UDFs for Exon. User-defined functions (UDFs) for Exon.
Traits
- Extension trait for [
RuntimeEnv
] that provides additional methods for Exon use-cases. - Extension trait for
SessionContext
that adds Exon-specific functionality.
Functions
- Create a new [
SessionConfig
] for the exon.