22 releases
0.2.34 | May 2, 2023 |
---|---|
0.2.33 | May 1, 2023 |
0.2.29 | Nov 1, 2022 |
0.2.28 | Oct 20, 2022 |
0.2.14 | May 28, 2022 |
#42 in Biology
112 downloads per month
2.5MB
6K
SLoC
Contains (Zip file, 13KB) some_missing.properties.npz
bed-reader
Read and write the PLINK BED format, simply and efficiently.
Features
- Fast and multi-threaded
- Supports many indexing methods. Slice data by individuals (samples) and/or SNPs (variants).
- The Python-facing APIs for this library is used by PySnpTools, FaST-LMM, and PyStatGen.
- Supports PLINK 1.9.
Examples
Read all genotype data from a .bed file.
use ndarray as nd;
use bed_reader::{Bed, ReadOptions, assert_eq_nan, sample_bed_file};
let file_name = sample_bed_file("small.bed")?;
let mut bed = Bed::new(file_name)?;
let val = ReadOptions::builder().f64().read(&mut bed)?;
assert_eq_nan(
&val,
&nd::array![
[1.0, 0.0, f64::NAN, 0.0],
[2.0, 0.0, f64::NAN, 2.0],
[0.0, 1.0, 2.0, 0.0]
],
);
Read every second individual (samples) and SNPs (variants) 20 to 30.
use ndarray::s;
let file_name = sample_bed_file("some_missing.bed")?;
let mut bed = Bed::new(file_name)?;
let val = ReadOptions::builder()
.iid_index(s![..;2])
.sid_index(20..30)
.f64()
.read(&mut bed)?;
assert!(val.dim() == (50, 10));
List the first 5 individual (sample) ids, the first 5 SNP (variant) ids, and every unique chromosome. Then, read every genomic value in chromosome 5.
use std::collections::HashSet;
let mut bed = Bed::new(file_name)?;
println!("{:?}", bed.iid()?.slice(s![..5])); // Outputs ndarray: ["iid_0", "iid_1", "iid_2", "iid_3", "iid_4"]
println!("{:?}", bed.sid()?.slice(s![..5])); // Outputs ndarray: ["sid_0", "sid_1", "sid_2", "sid_3", "sid_4"]
println!("{:?}", bed.chromosome()?.iter().collect::<HashSet<_>>());
// Outputs: {"12", "10", "4", "8", "19", "21", "9", "15", "6", "16", "13", "7", "17", "18", "1", "22", "11", "2", "20", "3", "5", "14"}
let val = ReadOptions::builder()
.sid_index(bed.chromosome()?.map(|elem| elem == "5"))
.f64()
.read(&mut bed)?;
assert!(val.dim() == (100, 6));
Project Links
Dependencies
~20–30MB
~422K SLoC