Crate dabuild 

dabuild

dabuild simplifies the access to genome build metadata, including its accession, version, and contigs.

We list the most common use cases below.

Load genome build

The builds module provides several bundled genome builds. Alternatively, you can load a genome build from a Genome Reference Consortium’s (GRC) assembly report.

See the builds documentation for more info.

Use genome build

GenomeBuild is basically a data container and the usage involves accessing the data.

We show several examples with the GRCh38.p13 genome build.

use dabuild::{GenomeBuild, GenomeBuildIdentifier};
use dabuild::builds::get_grch38_p13;

let build: GenomeBuild = get_grch38_p13();

Check build identifiers

We can check the major assembly and the patch of the build:

assert_eq!(build.id().major_assembly(), "GRCh38");
assert_eq!(build.id().patch(), Some("p13"));

Access contigs

The genome build contains one or more Contigs.

We can iterate over all contigs, e.g. to count them:

let count = build.contigs().count();
assert_eq!(count, 640);

and we can also access a specific Contig (e.g. for chrY) by one of its names:

// Query by name ...
let y = build.contig_by_name("Y");
assert!(y.is_some());

// ... or by the GenBank accession ...
let y = build.contig_by_name("CM000686.2");
assert!(y.is_some());

// ... or by the RefSeq accession ...
let y = build.contig_by_name("NC_000024.10");
assert!(y.is_some());

// ... or by the UCSC identifier.
let y = build.contig_by_name("chrY");
assert!(y.is_some());

Modules

builds

Get the most commonly used genome builds.

Structs

Contig

The contig data, such as identifiers and its length.

GenomeBuild

Genome build includes the contigs and the genome build metadata.

GenomeBuildIdentifier

All information needed to identify a genome build.