# 🔪🧅 Diced [](https://github.com/althonos/diced/stargazers)
*A Rust re-implementation of the [MinCED](https://github.com/ctSkennerton/minced) algorithm to Detect Instances of [CRISPRs](https://en.wikipedia.org/wiki/CRISPR) in Environmental Data.*
[](https://github.com/althonos/diced/actions)
[](https://codecov.io/gh/althonos/diced/)
[](https://choosealicense.com/licenses/gpl-3.0/)
[](https://pypi.org/project/diced)
[](https://anaconda.org/bioconda/diced)
[](https://aur.archlinux.org/packages/python-diced)
[](https://pypi.org/project/diced/#files)
[](https://pypi.org/project/diced/#files)
[](https://pypi.org/project/diced/#files)
[](https://github.com/althonos/diced/)
[](https://github.com/althonos/diced/issues)
[](https://diced.readthedocs.io)
[](https://github.com/althonos/diced/blob/main/CHANGELOG.md)
[](https://pepy.tech/project/diced)
## 🗺️ Overview
MinCED is a method developed by [Connor T. Skennerton](https://github.com/ctSkennerton)
to identify [Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)](https://en.wikipedia.org/wiki/CRISPR)
in isolate and metagenomic-assembled genomes. It was derived from the CRISPR
Recognition Tool [\[1\]](#ref1). 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, and is much faster. The Diced implementation is available
as a Rust library for convenience.
*This is the Python version, there is a [Rust crate](https://crates.io/crates/diced) 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.
- **single dependency**: Diced is distributed as a Python package, so you
can add it as a dependency to your project, and stop worrying about the
Java Virtual Machine being present on the end-user machine.
- **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>`. The original Python string and its
substrings are never copied.
- **fast string matching**: The Java implementation uses a handwritten implementation
of the [Boyer-Moore algorithm](https://en.wikipedia.org/wiki/Boyer%E2%80%93Moore_string-search_algorithm)[\[2\]](#ref2), while the Rust
implementation uses the `str::find` method of the standard library, which
implements the [Two-way algorithm](https://en.wikipedia.org/wiki/Two-way_string-matching_algorithm)[\[3\]](#ref3). In addition, the [`memchr`](https://crates.io/crates/memchr) crate can be used as a fast SIMD-capable
implementation of the `memmem` function.
## 💡 Example
Diced supports any sequence in string format.
```python
import Bio.SeqIO
import diced
record = Bio.SeqIO.read("diced/tests/data/Aquifex_aeolicus_VF5.fna", "fasta")
sequence = str(record.seq)
for crispr in diced.scan(sequence):
print(
crispr.start,
crispr.end,
len(crispr.repeats),
crispr.repeats[0],
)
```
## 💭 Feedback
### ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue
tracker](https://github.com/althonos/diced/issues) 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.
<!-- ### 🏗️ Contributing
Contributions are more than welcome! See [`CONTRIBUTING.md`](https://github.com/althonos/diced/blob/master/CONTRIBUTING.md) for more details. -->
## 📋 Changelog
This project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)
and provides a [changelog](https://github.com/althonos/diced/blob/master/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
## ⚖️ License
This library is provided under the open-source
[GPLv3 license](https://choosealicense.com/licenses/gpl-3.0/), or later.
The code for this implementation was derived from the
[MinCED source code](https://github.com/ctSkennerton/minced), 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](https://github.com/ctSkennerton). It was developed
by [Martin Larralde](https://github.com/althonos/) during his PhD project at
the [Leiden University Medical Center](https://www.lumc.nl/en/) in the
[Zeller team](https://github.com/zellerlab).*
## 📚 References
- <a id="ref1">\[1\]</a> 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](https://pubmed.ncbi.nlm.nih.gov/17577412/) [doi:10.1186/1471-2105-8-209](https://doi.org/10.1186/1471-2105-8-209).
- <a id="ref2">\[2\]</a> Boyer, R. S. and & Moore, J. S. (1977). 'A fast string searching algorithm'. Commun. ACM 20, 10 762–772. [doi:10.1145/359842.359859](https://doi.org/10.1145/359842.359859)
- <a id="ref3">\[3\]</a> Crochemore, M. & Perrin, D. (1991). 'Two-way string-matching'. J. ACM 38, 3, 650–674. [doi:10.1145/116825.116845](https://doi.org/10.1145/116825.116845)
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"description": "# \ud83d\udd2a\ud83e\uddc5 Diced [](https://github.com/althonos/diced/stargazers)\n\n*A Rust re-implementation of the [MinCED](https://github.com/ctSkennerton/minced) algorithm to Detect Instances of [CRISPRs](https://en.wikipedia.org/wiki/CRISPR) in Environmental Data.*\n\n[](https://github.com/althonos/diced/actions)\n[](https://codecov.io/gh/althonos/diced/)\n[](https://choosealicense.com/licenses/gpl-3.0/)\n[](https://pypi.org/project/diced)\n[](https://anaconda.org/bioconda/diced)\n[](https://aur.archlinux.org/packages/python-diced)\n[](https://pypi.org/project/diced/#files)\n[](https://pypi.org/project/diced/#files)\n[](https://pypi.org/project/diced/#files)\n[](https://github.com/althonos/diced/)\n[](https://github.com/althonos/diced/issues)\n[](https://diced.readthedocs.io)\n[](https://github.com/althonos/diced/blob/main/CHANGELOG.md)\n[](https://pepy.tech/project/diced)\n\n## \ud83d\uddfa\ufe0f Overview\n\nMinCED is a method developed by [Connor T. Skennerton](https://github.com/ctSkennerton) \nto identify [Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)](https://en.wikipedia.org/wiki/CRISPR) \nin isolate and metagenomic-assembled genomes. It was derived from the CRISPR \nRecognition Tool [\\[1\\]](#ref1). It uses a fast scanning algorithm to identify\ncandidate repeats, combined with an extension step to find maximally spanning\nregions of the genome that feature a CRISPR repeat.\n\nDiced is a Rust reimplementation of the MinCED method, using the original\nJava code as a reference. It produces exactly the same results as MinCED,\ncorrects some bugs, and is much faster. The Diced implementation is available \nas a Rust library for convenience.\n\n*This is the Python version, there is a [Rust crate](https://crates.io/crates/diced) available as well.*\n\n### \ud83d\udccb Features\n\n- **library interface**: The Rust implementation is written as library to facilitate \n reusability in other projects. It is used to implement a Python library using\n PyO3 to generate a native extension.\n- **single dependency**: Diced is distributed as a Python package, so you\n can add it as a dependency to your project, and stop worrying about the\n Java Virtual Machine being present on the end-user machine.\n- **zero-copy**: The `Scanner` which iterates over candidate CRISPRs is zero-copy if \n provided with a simple `&str` reference, but it also supports data behind smart \n pointers such as `Rc<str>` or `Arc<str>`. The original Python string and its\n substrings are never copied.\n- **fast string matching**: The Java implementation uses a handwritten implementation \n of the [Boyer-Moore algorithm](https://en.wikipedia.org/wiki/Boyer%E2%80%93Moore_string-search_algorithm)[\\[2\\]](#ref2), while the Rust \n implementation uses the `str::find` method of the standard library, which \n implements the [Two-way algorithm](https://en.wikipedia.org/wiki/Two-way_string-matching_algorithm)[\\[3\\]](#ref3). In addition, the [`memchr`](https://crates.io/crates/memchr) crate can be used as a fast SIMD-capable \n implementation of the `memmem` function.\n\n## \ud83d\udca1 Example\n\nDiced supports any sequence in string format.\n\n```python\nimport Bio.SeqIO\nimport diced\n\nrecord = Bio.SeqIO.read(\"diced/tests/data/Aquifex_aeolicus_VF5.fna\", \"fasta\")\nsequence = str(record.seq)\n\nfor crispr in diced.scan(sequence):\n print(\n crispr.start,\n crispr.end,\n len(crispr.repeats),\n crispr.repeats[0],\n )\n```\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/althonos/diced/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n<!-- ### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See [`CONTRIBUTING.md`](https://github.com/althonos/diced/blob/master/CONTRIBUTING.md) for more details. -->\n\n## \ud83d\udccb Changelog\n\nThis project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html)\nand provides a [changelog](https://github.com/althonos/diced/blob/master/CHANGELOG.md)\nin the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.\n\n## \u2696\ufe0f License\n\nThis library is provided under the open-source\n[GPLv3 license](https://choosealicense.com/licenses/gpl-3.0/), or later. \nThe code for this implementation was derived from the \n[MinCED source code](https://github.com/ctSkennerton/minced), which is \navailable under the GPLv3 as well.\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [original MinCED authors](https://github.com/ctSkennerton). It was developed \nby [Martin Larralde](https://github.com/althonos/) during his PhD project at \nthe [Leiden University Medical Center](https://www.lumc.nl/en/) in the \n[Zeller team](https://github.com/zellerlab).*\n\n## \ud83d\udcda References\n\n- <a id=\"ref1\">\\[1\\]</a> 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](https://pubmed.ncbi.nlm.nih.gov/17577412/) [doi:10.1186/1471-2105-8-209](https://doi.org/10.1186/1471-2105-8-209).\n- <a id=\"ref2\">\\[2\\]</a> Boyer, R. S. and & Moore, J. S. (1977). 'A fast string searching algorithm'. Commun. ACM 20, 10 762\u2013772. [doi:10.1145/359842.359859](https://doi.org/10.1145/359842.359859)\n- <a id=\"ref3\">\\[3\\]</a> Crochemore, M. & Perrin, D. (1991). 'Two-way string-matching'. J. ACM 38, 3, 650\u2013674. 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