bigtools

A high-performance BigWig and BigBed library in Rust

https://github.com/jackh726/bigtools

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 5 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (13.7%) to scientific vocabulary

Keywords

bigbed bigwig rust

Keywords from Contributors

mesh interactive

Last synced: 6 months ago · JSON representation ·

Repository

A high-performance BigWig and BigBed library in Rust

Basic Info

Host: GitHub
Owner: jackh726
License: mit
Language: Rust
Default Branch: master
Homepage:
Size: 11.8 MB

Statistics

Stars: 101
Watchers: 3
Forks: 8
Open Issues: 16
Releases: 25

Topics

bigbed bigwig rust

Created almost 7 years ago · Last pushed 9 months ago

Metadata Files

Readme License Citation

Bigtools

Rust, CLI
Python

Bigtools is a library and associated tools for reading and writing bigwig and bigbed files.

The primary goals of the project are to be - Performant - Extensible - Modern

Performant

Bigtools uses async/await internally to allow for efficient, multi-core computation when possible. In addition, tools are optimized for minimal memory usage. See Benchmarks for more details.

Extensible

Bigtools is designed to be as modular as possible. This, in addition to the safety and reliability of Rust, allows both flexibility and correctness as a library. In addition, its extremely easy to quickly create new tools or binaries. A number of binaries are available that parallel related existing binaries from UCSC, with drop-in compatibility for the most common flags.

Modern

Bigtools is written in Rust and published to crates.io, so binaries can be installed with cargo install bigtools or it can be used as a library by simply including it in your cargo.toml.

Library

To use bigtools in your Rust project, add bigtools to your Cargo.toml or run:

sh cargo add bigtools

See the bigtools 🦀 Documentation.

Example

```rust,norun use bigtools::bbiread::BigWigRead;

let mut reader = BigWigRead::open("test.bigWig").unwrap(); let chr1 = reader.get_interval("chr1", 0, 10000).unwrap(); for interval in chr1 { println!("{:?}", interval); } ```

Binaries

The bigtools CLI binaries can be installed through crates.io or conda.

sh cargo install bigtools

sh conda install -c bioconda bigtools

Additionally, pre-built binaries can be downloaded through Github releases.

The following binaries are available:

|binary|description| | ---- | ----- | |bigtools|Provides access to multiple subcommands, including all below| |bedgraphtobigwig|Writes a bigWig from a given bedGraph file| |bedtobigbed|Writes a bigBed from a given bed file| |bigbedinfo|Shows info about a provided bigBed| |bigbedtobed|Writes a bed from the data in a bigBed| |bigwigaverageoverbed|Calculate statistics over the regions of a bed file using values from a bigWig| |bigwiginfo|Shows info about a provided bigWig| |bigwigmerge|Merges multiple bigWigs, outputting to either a new bigWig or a bedGraph| |bigwigtobedgraph|Writes a bedGraph from the data in a bigWig| |bigwigvaluesoverbed|Get the per-base values from a bigWig over the regions of a bed file using values|

Renaming the bigtools binary to any of the subcommands (case-insensitive) allows you to run that subcommand directly.

Python wrapper

The pybigtools package is a Python wrapper written using PyO3. It can be installed or used as a dependency either through PyPI or conda.

sh pip install pybigtools

sh conda install -c bioconda pybigtools

See the pybigtools 🐍 API Documentation.

How to build from source

In order to build the bigtools binaries, you can run

cargo build --release

and the binaries can be found in target/release/.

Otherwise, you can install the binaries from source by running

cargo install --path bigtools/

Building the python wheels for pybigtools requires maturin. To build the pybigtools wheel for installation (and install), you can run

maturin build --release -m pybigtools/Cargo.toml pip install target/wheels/pybigtools*.whl

maturin develop --release -m pybigtools/Cargo.toml

Benchmarks

Benchmarks are included in the ./bench directory. They require python to run.

Multiple tools are compared against the comparable UCSC tools. For completeness, both single-threaded and multi-threaded (when available) benchmarks are included. Multiple different configuration options are benchmarked across multiple replicates, but a summar is available in the table below:

How to cite

This repository contains contains a CITATION.cff file with citation information. Github allows you to get a citation in either APA or BibTeX format; this is available in "Cite this repository" under About.

Owner

Name: Jack Huey
Login: jackh726
Kind: user

Repositories: 23
Profile: https://github.com/jackh726

Citation (CITATION.cff)

cff-version: 1.2.0
type: software
title: Bigtools
license: MIT
repository-code: 'https://github.com/jackh726/bigtools'
message: >-
  If you use this software, please cite it using the
  metadata from this file.
authors:
  - given-names: Jack
    family-names: Huey
    orcid: "https://orcid.org/0000-0003-3463-7192"
abstract: >-
  Bigtools is a performant, extensible, and modern library for reading and writing BigWig and BigBed genomic data files, written in Rust. It also includes executable binaries for the command line as well as Python bindings.
keywords:
  - bigwig
  - bigbed
  - bbi
  - bioinformatics
  - genomics
  - kent
  - ucsc
  - rust
  - python
identifiers:
  - type: doi
    value: 10.5281/zenodo.10606493
    description: Zenodo
  - type: doi
    value: 10.1101/2024.02.06.579187
    description: bioRxiv preprint
  - type: doi
    value: 10.1093/bioinformatics/btae350
    description: Publication
preferred-citation:
  type: article
  title: "Bigtools: a high-performance BigWig and BigBed library in Rust"
  authors:
  - given-names: Jack
    family-names: Huey
    orcid: "https://orcid.org/0000-0003-3463-7192"
  - given-names: Nezar
    family-names: Abdennur
    orcid: "https://orcid.org/0000-0001-5814-0864"
  journal: Bioinformatics
  year: 2024
  doi: "10.1093/bioinformatics/btae350"
  url: https://doi.org/10.1093/bioinformatics/btae350

GitHub Events

Total

Create event: 10
Release event: 10
Issues event: 41
Watch event: 26
Delete event: 2
Issue comment event: 126
Push event: 50
Pull request review comment event: 1
Pull request review event: 4
Pull request event: 17
Fork event: 3

Last Year

Create event: 10
Release event: 10
Issues event: 41
Watch event: 26
Delete event: 2
Issue comment event: 126
Push event: 50
Pull request review comment event: 1
Pull request review event: 4
Pull request event: 17
Fork event: 3

Committers

Last synced: 9 months ago

All Time

Total Commits: 550
Total Committers: 7
Avg Commits per committer: 78.571
Development Distribution Score (DDS): 0.098

Past Year

Commits: 138
Committers: 4
Avg Commits per committer: 34.5
Development Distribution Score (DDS): 0.225

Top Committers

Name	Email	Commits
Jack Huey	3****6	496
Nezar Abdennur	n**r@g**m	39
Gert Hulselmans	g**s@k**e	9
Donald Campbell	1****r	3
dependabot[bot]	4****]	1
Peter Kerpedjiev	p**v@g**m	1
Anders Pitman	t**1@g**m	1

Committer Domains (Top 20 + Academic)

kuleuven.be: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 41
Total pull requests: 43
Average time to close issues: 3 months
Average time to close pull requests: 1 day
Total issue authors: 18
Total pull request authors: 9
Average comments per issue: 2.93
Average comments per pull request: 1.16
Merged pull requests: 36
Bot issues: 0
Bot pull requests: 1

Past Year

Issues: 25
Pull requests: 13
Average time to close issues: 28 days
Average time to close pull requests: about 19 hours
Issue authors: 15
Pull request authors: 4
Average comments per issue: 2.24
Average comments per pull request: 1.0
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ghuls (10)
jackh726 (6)
mrvollger (4)
donaldcampbelljr (3)
nvictus (3)
sergpolly (2)
stela2502 (2)
pkerpedjiev (1)
mtvector (1)
casblaauw (1)
nleroy917 (1)
maxgmarin (1)
dmalzl (1)
ypauling (1)
khoroshevskyi (1)

Pull Request Authors

nvictus (40)
ghuls (16)
jackh726 (4)
nleroy917 (2)
anderspitman (2)
donaldcampbelljr (1)
pkerpedjiev (1)
paul-sud (1)
dependabot[bot] (1)

Top Labels

Issue Labels

Pull Request Labels

dependencies (1)

Packages

Total packages: 2
Total downloads:
- cargo 78,383 total
- pypi 2,197 last-month

Total dependent packages: 5
(may contain duplicates)
Total dependent repositories: 1
(may contain duplicates)
Total versions: 40
Total maintainers: 2

crates.io: bigtools

A library and associated tools for reading and writing bigwigs and bigbeds

Documentation: https://docs.rs/bigtools/
License: MIT
Latest release: 0.5.6
published 11 months ago

Versions: 30
Dependent Packages: 4
Dependent Repositories: 1
Downloads: 78,383 Total

Rankings

Dependent packages count: 9.2%

Downloads: 13.5%

Dependent repos count: 16.5%

Average: 18.1%

Stargazers count: 25.2%

Forks count: 26.3%

Maintainers (1)

jackh726

Last synced: 6 months ago

pypi.org: pybigtools

Python bindings to the Bigtools Rust library for high-performance BigWig and BigBed I/O

Documentation: https://pybigtools.readthedocs.io/
License: MIT
Latest release: 0.2.4
published about 1 year ago

Versions: 10
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 2,197 Last month

Rankings

Dependent packages count: 9.9%

Average: 37.6%

Dependent repos count: 65.3%

Maintainers (1)

jackh726

Last synced: 6 months ago

Dependencies

.github/workflows/ci.yml actions

actions-rs/toolchain v1 composite
actions/checkout v2 composite

.github/workflows/release.yml actions

actions/checkout v2 composite
papeloto/action-zip v1 composite
shogo82148/actions-upload-release-asset v1 composite

Cargo.lock cargo

131 dependencies

Cargo.toml cargo

rand 0.8 development
attohttpc 0.25
bincode 1.3
byteorder 1
byteordered 0.6.0
bytes 1.4.0
clap 3.2.0
crossbeam-channel 0.5
crossbeam-utils 0.8
futures 0.3.28
itertools 0.10
libdeflater 0.13
parking_lot 0.12.1
ryu 1.0
serde 1
tempfile 3
thiserror 1
ufmt 0.2

bigtools/Cargo.toml cargo

rand 0.8 development
attohttpc 0.25
bincode 1.3
byteorder 1
byteordered 0.6.0
bytes 1.4.0
clap 4.3
crossbeam-channel 0.5
crossbeam-utils 0.8
futures 0.3.28
itertools 0.10
libdeflater 0.13
ryu 1.0
serde 1
smallvec 1.11.2
tempfile 3
thiserror 1
tokio 1.34.0
ufmt 0.2

pybigtools/Cargo.lock cargo

151 dependencies

pybigtools/Cargo.toml cargo

bench/Dockerfile docker

python 3.8.6 build
rust buster build

pybigtools/pyproject.toml pypi

numpy *

.github/workflows/release-python.yml actions

PyO3/maturin-action v1 composite
actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-python v4 composite
actions/upload-artifact v3 composite

bigtools

Science Score: 67.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Bigtools

Performant

Extensible

Modern

Library

Example

Binaries

Python wrapper

How to build from source

Benchmarks

How to cite

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

crates.io: bigtools

Rankings

Maintainers (1)

pypi.org: pybigtools

Rankings

Maintainers (1)

Dependencies