Module builds 

Get the most commonly used genome builds.

We provide several common genome build out-of-shelf. Other builds can be loaded from a genome assembly report.

Bundled genome builds

These bundled genome builds can be loaded using the respective loader function:

• GRCh37.p13: get_grch37_p13
• GRCh38.p13: get_grch38_p13

Example

Load GRCh38.p13 (Homo sapiens):

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

let build: GenomeBuild = get_grch38_p13();

Load from an assembly report

A genome build can be loaded from the Genome Reference Consortium assembly report using parse_assembly_report function.

For instance, GRCm39 can be loaded from an example assembly report:

use std::{fs::File, io::BufReader, str::FromStr};

let path = "data/GCF_000001635.27_GRCm39_assembly_report.txt";
let build: GenomeBuild = parse_assembly_report(
        GenomeBuildIdentifier::from_str("GRCm39").expect("Infallible"),
        BufReader::new(File::open(path).expect("File should be present and readable")),
).expect("No I/O or format issues");

assert_eq!(build.id().major_assembly(), "GRCm39");

Enums

GenomeAssemblyParseError

Represents the reasons for which parsing of the genome assembly report can fail.

Functions

get_grch37_p13

Get the GRCh37.p13 build.

get_grch38_p13

Get the GRCh38.p13 build.

parse_assembly_report

Parse an assembly report into a GenomeBuild.