bed_reader

§ bed – reader

Read and write the PLINK BED format,simply and efficiently.

§ is Highlights highlight

• 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.
• support PLINK 1.9 .
• Read data locally or from the cloud,efficiently and directly.

§Install

Full version: Can read local and cloud files

Minimal version: Can read local files,only

cargo add bed-reader --no-default-features

§Examples

Read all genotype data from a .bed file.

usendarray as nd; 
usebed_reader::{Bed ,readoption ,assert_eq_nan ,sample_bed_file } ; 

letfile_name = sample_bed_file ("small.bed")?; 
letmutbed = bed::new(file_name)?; 
letval = readoption::builder().f64().read(&mutbed)?; 

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.

usendarray::s; 

letfile_name = sample_bed_file (" some_missing.bed ")?; 
letmutbed = bed::new(file_name)?; 
letval = readoption::builder()
    .iid_index(s ![..;2])
    .sid_index(20..30)
    .f64()
    .read(&mutbed)?; 

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.

usestd::collections::HashSet; 

letmutbed = bed::new(file_name)?; 
println!(" { : ? } ",bed.iid()?.slice(s ![..5]) ) ; println!(" { : ? } ",bed.sid()?.slice(s ![..5]) ) ; println!(" { : ? } ",bed.chromosome()?.iter().collect::<HashSet<_>>() ) ; 
letval = readoption::builder()
    .sid_index(bed.chromosome()?.map(|elem| elem == " 5 ") ) 
     .f64 ( ) 
     .read (&mutbed)?; 

assert!( val.dim ( ) = = (100,6) ) ;

From the cloud: open a file and read data for one SNP (variant)
at index position 2. (See “Cloud URLs and CloudFile Examples”
for details specifying a file in the cloud.)

usendarray as nd; 
usebed_reader::{assert_eq_nan,BedCloud,readoption}; 
leturl = "https://raw.githubusercontent.com/fastlmm/bed-sample-files/main/small.bed"; 
letmutbed_cloud = BedCloud::new(url).await?; 
letval = readoption::builder().sid_index(2).f64().read_cloud(&mutbed_cloud ) .await?; 
assert_eq_nan(&val,&nd::array![[f64::NAN],[f64::NAN],[2.0]]);

§Project Links

§ Main function

After using bed::new or bed::builder to open a PLINK .bed file for reading,use
these methods to see metadata.

§readoption

When using readoption::builder to read genotype data,usethese options to
specify a desired numeric type,
which individuals (samples) to read,which SNPs (variants) to read,etc.

Select which individuals (samples) and SNPs (variants) to read by using these
iid_index and/or
sid_index expressions.

§Environment Variables

• bed_reader_num_thread
• NUM_THREADS

IfreadoptionBuilder::num_threads
or WriteOptionsBuilder::num_threads is not specified,
the number of threads to useis determined by these environment variable (in order of priority):
Ifneither of these environment variables are set,all processors are used.

Any requested sample file will be downloaded to this directory. Ifthe environment variable is not set,
a cache folder,appropriate to the OS,will be used.