packbed

pack a .bed into overlapping components

Features

• pack any number of .bed files into overlapping components through a binary, Rust library or Python module
• write a unique overlapping-component-colorized bed file out of any number of .bed files through a binary, Rust library or Python module
• split components into separate .bed files through a binary, Rust library or Python module
• write serialized components to a binary file through a binary and Rust library
• read serialized components from a binary file through a Rust library or Python module
• write specific components each to a different .bed file through a Rust library or Python module

What's new on packbed v0.0.7!

• Implements a new query range algorithm to pack components
• Reduces time by more than x25 when working with more than 1 million reads

Usage

Binary

``` bash Usage: packbed [OPTIONS] --bed ... --output

Arguments: -b, --bed ... Paths to BED12 files delimited by comma -o, --output Path to output BED12 file [not required if -c flag is set]

Options: -t, --threads Number of threads [default: 8] --type Type of output [default: bed] [possible values: bin, comp, bed] --overlap_type Type of overlap [default: exon] -s, --subdirs Flag to split components into separate BED files in subdirectories --colorize Flag to colorize components in output BED(s) file -h, --help Print help --version: Print version ```

[!TIP] If you want to get components in separate .bed files use: bash packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp in case you want to send each component to a different subdirectory (good to parallelize processes): bash packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --type comp -s if you want to colorize the components but send them all to just 1.bed file [default]: bash packbed -b path/to/b1.bed,path/to/b2.bed -o path/to/output --colorize

Library

``` rust use packbed::packbed;

fn main() {

let bed1 = PathBuf::new("/path/to/b1.bed");
let bed2 = PathBuf::new("/path/to/b2.bed");
let beds = vec![bed1, bed2];

let overlap_type = OverlapType::Exon;
let colorize = true;

let comps: HashMap<String, Vec<Vec<Arc<GenePred>>>> = packbed(
    beds,
    overlap_type,
    colorize)
.unwrap();

} ```

Python

build the port to install it as a pkg: bash git clone https://github.com/alejandrogzi/packbed.git && cd packbed/py-packbed hatch shell maturin develop --release use it: ``` python from packbed import pack

beds = ["path/to/bed1.bed", "path/to/bed2.bed"] comps = pack(beds) ```

crate: https://crates.io/crates/packbed