https://github.com/althonos/diced

A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.

Science Score: 46.0%

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

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CITATION.cff file
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codemeta.json file
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DOI references
Found 9 DOI reference(s) in README
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Academic publication links
Links to: pubmed.ncbi, ncbi.nlm.nih.gov
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Committers with academic emails
1 of 1 committers (100.0%) from academic institutions
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Scientific vocabulary similarity
Low similarity (12.5%) to scientific vocabulary

Keywords

bioinformatics crispr genomics python-bindings python-library rust-library

Last synced: 5 months ago · JSON representation

Repository

A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.

Basic Info

Host: GitHub
Owner: althonos
License: gpl-3.0
Language: Rust
Default Branch: main
Homepage: https://diced.readthedocs.io
Size: 1.68 MB

Statistics

Stars: 5
Watchers: 1
Forks: 2
Open Issues: 0
Releases: 3

Topics

bioinformatics crispr genomics python-bindings python-library rust-library

Created over 1 year ago · Last pushed over 1 year ago

Metadata Files

Readme Changelog License

🔪🧅 Diced

A Rust re-implementation of the MinCED algorithm to Detect Instances of CRISPRs in Environmental Data.

🗺️ Overview

MinCED is a method developed by Connor T. Skennerton to identify Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in isolate and metagenomic-assembled genomes. It was derived from the CRISPR Recognition Tool [1]. It uses a fast scanning algorithm to identify candidate repeats, combined with an extension step to find maximally spanning regions of the genome that feature a CRISPR repeat.

Diced is a Rust reimplementation of the MinCED method, using the original Java code as a reference. It produces exactly the same results as MinCED, corrects some bugs (minced#35), and is much faster. The Diced implementation is available as a Rust library for convenience.

This is the Rust version, there is a Python package available as well.

📋 Features

library interface: The Rust implementation is written as library to facilitate reusability in other projects. It is used to implement a Python library using PyO3 to generate a native extension.
zero-copy: The Scanner which iterates over candidate CRISPRs is zero-copy if provided with a simple &str reference, but it also supports data behind smart pointers such as Rc<str> or Arc<str>.
fast string matching: The Java implementation uses a handwritten implementation of the Boyer-Moore algorithm [2], while the Rust implementation uses the str::find method of the standard library, which implements the Two-way algorithm [3]. In addition, the memchr crate can be used as a fast SIMD-capable implementation of the memmem function.

💡 Example

Diced supports any sequence in string format.

```rust let mut reader = std::fs::File::open("tests/data/AquifexaeolicusVF5.fna") .map(std::io::BufReader::new) .map(noodlesfasta::Reader::new) .unwrap(); let record = reader.records().next().unwrap().unwrap(); let seq = std::str::fromutf8(record.sequence().as_ref()).unwrap();

for crispr in diced::Scanner::new(&seq) { println!("{} to {}: {} repeats", crispr.start(), crispr.end(), crispr.len()); for repeat in crispr.repeats() { println!(" - at {}: {}", repeat.start(), repeat.as_str()); } } ```

💭 Feedback

⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

📋 Changelog

This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.

⚖️ License

This library is provided under the open-source GPLv3 license, or later. The code for this implementation was derived from the MinCED source code, which is available under the GPLv3 as well.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original MinCED authors. It was developed by Martin Larralde during his PhD project at the Leiden University Medical Center in the Zeller team.

📚 References

[1] Bland, C., Ramsey, T. L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N. C., & Hugenholtz, P. (2007). 'CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats'. BMC bioinformatics, 8, 209. PMID:17577412 doi:10.1186/1471-2105-8-209.
[2] Boyer, R. S. and & Moore, J. S. (1977). 'A fast string searching algorithm'. Commun. ACM 20, 10 762–772. doi:10.1145/359842.359859
[3] Crochemore, M. & Perrin, D. (1991). 'Two-way string-matching'. J. ACM 38, 3, 650–674. doi:10.1145/116825.116845

Owner

Name: Martin Larralde
Login: althonos
Kind: user
Location: Heidelberg, Germany
Company: EMBL / LUMC, @zellerlab

Twitter: althonos
Repositories: 91
Profile: https://github.com/althonos

PhD candidate in Bioinformatics, passionate about programming, SIMD-enthusiast, Pythonista, Rustacean. I write poems, and sometimes they are executable.

GitHub Events

Total

Release event: 1
Watch event: 3
Push event: 7
Create event: 1

Last Year

Release event: 1
Watch event: 3
Push event: 7
Create event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 74
Total Committers: 1
Avg Commits per committer: 74.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 15
Committers: 1
Avg Commits per committer: 15.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Martin Larralde	m**e@e**e	74

Committer Domains (Top 20 + Academic)

embl.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 0
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 0
Total pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

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Packages

Total packages: 2
Total downloads:
- cargo 3,268 total
- pypi 476 last-month

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 6
Total maintainers: 2

pypi.org: diced

Rust re-implementation of the MinCED algorithm to Detect Instances of CRISPRs in Environmental Data.

Homepage: https://github.com/althonos/lightmotif/tree/main/diced-py
Documentation: https://diced.readthedocs.io
License: GPL-3.0-or-later
Latest release: 0.1.2
published over 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 476 Last month

Rankings

Dependent packages count: 10.8%

Average: 35.8%

Dependent repos count: 60.8%

Maintainers (1)

althonos

Last synced: 6 months ago

crates.io: diced-py

PyO3 bindings and Python interface to the diced crate.

Homepage: https://github.com/althonos/lightmotif/tree/main/diced-py
Documentation: https://docs.rs/diced-py/
License: GPL-3.0-or-later
Latest release: 0.1.2
published over 1 year ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 3,268 Total

Rankings

Dependent repos count: 27.1%

Dependent packages count: 35.9%

Average: 53.2%

Downloads: 96.4%

Maintainers (1)

althonos

Last synced: 7 months ago

Dependencies

Cargo.lock cargo

adler 1.0.2
autocfg 1.3.0
bit-vec 0.6.3
bitflags 2.5.0
bstr 1.9.1
byteorder 1.5.0
bytes 1.6.0
cfg-if 1.0.0
crc32fast 1.4.2
crossbeam-channel 0.5.13
crossbeam-utils 0.8.20
equivalent 1.0.1
flate2 1.0.30
hashbrown 0.14.5
heck 0.4.1
indexmap 2.2.6
indoc 2.0.5
libc 0.2.155
lock_api 0.4.12
memchr 2.7.2
memoffset 0.9.1
miniz_oxide 0.7.3
noodles-bgzf 0.30.0
noodles-core 0.15.0
noodles-csi 0.35.0
noodles-fasta 0.38.0
noodles-gff 0.33.0
once_cell 1.19.0
parking_lot 0.12.3
parking_lot_core 0.9.10
percent-encoding 2.3.1
portable-atomic 1.6.0
proc-macro2 1.0.84
pyo3 0.21.2
pyo3-build-config 0.21.2
pyo3-ffi 0.21.2
pyo3-macros 0.21.2
pyo3-macros-backend 0.21.2
quote 1.0.36
redox_syscall 0.5.1
scopeguard 1.2.0
serde 1.0.203
serde_derive 1.0.203
smallvec 1.13.2
strsim 0.11.1
syn 2.0.66
target-lexicon 0.12.14
unicode-ident 1.0.12
unindent 0.2.3
windows-targets 0.52.5
windows_aarch64_gnullvm 0.52.5
windows_aarch64_msvc 0.52.5
windows_i686_gnu 0.52.5
windows_i686_gnullvm 0.52.5
windows_i686_msvc 0.52.5
windows_x86_64_gnu 0.52.5
windows_x86_64_gnullvm 0.52.5
windows_x86_64_msvc 0.52.5

Cargo.toml cargo

diced/Cargo.toml cargo

noodles-fasta 0.38.0 development
noodles-gff 0.33.0 development
memchr 2.7.2
strsim 0.11

diced-py/Cargo.toml cargo

diced-py/diced/tests/requirements.txt pypi

biopython * test

docs/requirements.txt pypi

ipython *
nbsphinx *
pygments *
pygments-style-monokailight *
recommonmark *
semantic_version *
setuptools >=46.4
setuptools-rust >=1.0
sphinx >=5.0
sphinxcontrib-jquery *

pyproject.toml pypi

.github/workflows/python.yml actions

actions/checkout v3 composite
actions/download-artifact v2 composite
actions/setup-python v2 composite
actions/upload-artifact v3 composite
actions/upload-artifact v2 composite
docker/setup-qemu-action v2 composite
dtolnay/rust-toolchain stable composite
pypa/cibuildwheel v2.19.0 composite
pypa/gh-action-pypi-publish release/v1 composite
rasmus-saks/release-a-changelog-action v1.0.1 composite

.github/workflows/rust.yml actions

actions-rs/cargo v1 composite
actions-rs/install v0.1 composite
actions-rs/toolchain v1 composite
actions/cache v2 composite
actions/checkout v1 composite
codecov/codecov-action v4.0.1 composite
rasmus-saks/release-a-changelog-action v1.0.1 composite

https://github.com/althonos/diced

Science Score: 46.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

🔪🧅 Diced

🗺️ Overview

📋 Features

💡 Example

💭 Feedback

⚠️ Issue Tracker

📋 Changelog

⚖️ License

📚 References

Owner

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

pypi.org: diced

Rankings

Maintainers (1)

crates.io: diced-py

Rankings

Maintainers (1)

Dependencies