# 🐍🔁 PyTantan [](https://github.com/althonos/pytantan/stargazers)
*[Cython](https://cython.org/) bindings and Python interface to [Tantan](https://gitlab.com/mcfrith/tantan), a fast method for identifying repeats in DNA and protein sequences.*
[](https://github.com/althonos/pytantan/actions)
[](https://codecov.io/gh/althonos/pytantan/)
[](https://choosealicense.com/licenses/gpl-3.0/)
[](https://pypi.org/project/pytantan)
[](https://anaconda.org/bioconda/pytantan)
[](https://aur.archlinux.org/packages/python-pytantan)
[](https://pypi.org/project/pytantan/#files)
[](https://pypi.org/project/pytantan/#files)
[](https://pypi.org/project/pytantan/#files)
[](https://github.com/althonos/pytantan/)
[](https://git.embl.de/larralde/pytantan/)
[](https://github.com/althonos/pytantan/issues)
[](https://pytantan.readthedocs.io)
[](https://github.com/althonos/pytantan/blob/main/CHANGELOG.md)
[](https://pepy.tech/project/pytantan)
## 🗺️ Overview
[Tantan](https://gitlab.com/mcfrith/tantan) is a fast method developed
by Martin Frith[\[1\]](#ref1) to identify simple repeats in DNA or protein
sequences. It can be used to mask repeat regions in reference sequences, and
avoid false homology predictions between repeated regions.
PyTantan is a Python module that provides bindings to [Tantan](https://gitlab.com/mcfrith/tantan)
using [Cython](https://cython.org/). It implements a user-friendly, Pythonic
interface to mask a sequence with various parameters. It interacts with the
Tantan interface rather than with the CLI, which has the following advantages:
- **no binary dependency**: PyTantan is distributed as a Python package, so
you can add it as a dependency to your project, and stop worrying about the
`tantan` binary being present on the end-user machine.
- **no intermediate files**: Everything happens in memory, in a Python object
you control, so you don't have to invoke the Tantan CLI using a sub-process
and temporary files.
- **better portability**: Tantan uses SIMD to accelerate alignment scoring,
but doesn't support dynamic dispatch, so it has to be compiled on the local
machine to be able to use the full capabilities of the local CPU. PyTantan
ships several versions of Tantan instead, each compiled with different
target features, and selects the best one for the local platform at runtime.
## 🔧 Installing
PyTantan is available for all modern versions (3.6+), depending only on the
[`scoring-matrices`](https://pypi.org/project/scoring-matrices) package, and
optionally on the lightweight [`archspec`](https://pypi.org/project/archspec)
package for runtime CPU feature detection.
It can be installed directly from [PyPI](https://pypi.org/project/pytantan/),
which hosts some pre-built wheels for Linux and MacOS, as well as the code
required to compile from source with Cython:
```console
$ pip install pytantan
```
<!-- Otherwise, PyTantan is also available as a [Bioconda](https://bioconda.github.io/)
package:
```console
$ conda install -c bioconda pytantan
``` -->
Check the [*install* page](https://pytantan.readthedocs.io/en/stable/install.html)
of the documentation for other ways to install PyTantan on your machine.
## 💡 Example
The top-level function `pytantan.mask_repeats` can be used to mask a sequence
without having to manage intermediate objects:
```python
import pytantan
masked = pytantan.mask_repeats("ATTATTATTATTATT")
print(masked) # ATTattattattatt
```
The mask symbol (and other parameters) can be given as keyword arguments:
```python
import pytantan
masked = pytantan.mask_repeats("ATTATTATTATTATT", mask='N')
print(masked) # ATTNNNNNNNNNNNN
```
To mask several sequences iteratively with the same parameters, consider
creating a `RepeatFinder` once and calling the `mask_repeats` method for
each sequence to avoid resource re-initialization.
<!-- See the [API documentation](https://pytantan.readthedocs.io/en/stable/api/index.html)
for more examples, including how to use the internal API, and detailed
reference of the parameters and result types. -->
<!-- ## 🧶 Thread-safety -->
<!-- ## ⏱️ Benchmarks -->
## 💭 Feedback
### ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the [GitHub issue tracker](https://github.com/althonos/pytantan/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/pytantan/blob/main/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/pytantan/blob/main/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
## ⚖️ License
This library is provided under the [GNU General Public License v3.0 or later](https://choosealicense.com/licenses/gpl-3.0/).
Tantan is developed by [Martin Frith](https://sites.google.com/site/mcfrith/martin-frith) and is distributed under the
terms of the GPLv3 or later as well. See `vendor/tantan/COPYING.txt` for more information.
*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [Tantan authors](https://github.com/Martinsos). 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> Frith, Martin C. “A new repeat-masking method enables specific detection of homologous sequences.” Nucleic acids research vol. 39,4 (2011): e23. [doi:10.1093/nar/gkq1212](https://doi.org/10.1093/nar/gkq1212)
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"description": "# \ud83d\udc0d\ud83d\udd01 PyTantan [](https://github.com/althonos/pytantan/stargazers)\n\n*[Cython](https://cython.org/) bindings and Python interface to [Tantan](https://gitlab.com/mcfrith/tantan), a fast method for identifying repeats in DNA and protein sequences.*\n\n[](https://github.com/althonos/pytantan/actions)\n[](https://codecov.io/gh/althonos/pytantan/)\n[](https://choosealicense.com/licenses/gpl-3.0/)\n[](https://pypi.org/project/pytantan)\n[](https://anaconda.org/bioconda/pytantan)\n[](https://aur.archlinux.org/packages/python-pytantan)\n[](https://pypi.org/project/pytantan/#files)\n[](https://pypi.org/project/pytantan/#files)\n[](https://pypi.org/project/pytantan/#files)\n[](https://github.com/althonos/pytantan/)\n[](https://git.embl.de/larralde/pytantan/)\n[](https://github.com/althonos/pytantan/issues)\n[](https://pytantan.readthedocs.io)\n[](https://github.com/althonos/pytantan/blob/main/CHANGELOG.md)\n[](https://pepy.tech/project/pytantan)\n\n\n## \ud83d\uddfa\ufe0f Overview\n\n[Tantan](https://gitlab.com/mcfrith/tantan) is a fast method developed\nby Martin Frith[\\[1\\]](#ref1) to identify simple repeats in DNA or protein \nsequences. It can be used to mask repeat regions in reference sequences, and \navoid false homology predictions between repeated regions.\n\nPyTantan is a Python module that provides bindings to [Tantan](https://gitlab.com/mcfrith/tantan)\nusing [Cython](https://cython.org/). It implements a user-friendly, Pythonic\ninterface to mask a sequence with various parameters. It interacts with the \nTantan interface rather than with the CLI, which has the following advantages:\n\n- **no binary dependency**: PyTantan is distributed as a Python package, so\n you can add it as a dependency to your project, and stop worrying about the\n `tantan` binary being present on the end-user machine.\n- **no intermediate files**: Everything happens in memory, in a Python object\n you control, so you don't have to invoke the Tantan CLI using a sub-process\n and temporary files.\n- **better portability**: Tantan uses SIMD to accelerate alignment scoring, \n but doesn't support dynamic dispatch, so it has to be compiled on the local\n machine to be able to use the full capabilities of the local CPU. PyTantan\n ships several versions of Tantan instead, each compiled with different \n target features, and selects the best one for the local platform at runtime.\n\n\n## \ud83d\udd27 Installing\n\nPyTantan is available for all modern versions (3.6+), depending only on the\n[`scoring-matrices`](https://pypi.org/project/scoring-matrices) package, and\noptionally on the lightweight [`archspec`](https://pypi.org/project/archspec)\npackage for runtime CPU feature detection.\n\nIt can be installed directly from [PyPI](https://pypi.org/project/pytantan/),\nwhich hosts some pre-built wheels for Linux and MacOS, as well as the code \nrequired to compile from source with Cython:\n```console\n$ pip install pytantan\n```\n\n<!-- Otherwise, PyTantan is also available as a [Bioconda](https://bioconda.github.io/)\npackage:\n```console\n$ conda install -c bioconda pytantan\n``` -->\n\nCheck the [*install* page](https://pytantan.readthedocs.io/en/stable/install.html)\nof the documentation for other ways to install PyTantan on your machine.\n\n## \ud83d\udca1 Example\n\nThe top-level function `pytantan.mask_repeats` can be used to mask a sequence\nwithout having to manage intermediate objects:\n\n```python\nimport pytantan\nmasked = pytantan.mask_repeats(\"ATTATTATTATTATT\")\nprint(masked) # ATTattattattatt\n```\n\nThe mask symbol (and other parameters) can be given as keyword arguments:\n\n```python\nimport pytantan\nmasked = pytantan.mask_repeats(\"ATTATTATTATTATT\", mask='N')\nprint(masked) # ATTNNNNNNNNNNNN\n```\n\nTo mask several sequences iteratively with the same parameters, consider \ncreating a `RepeatFinder` once and calling the `mask_repeats` method for \neach sequence to avoid resource re-initialization.\n\n<!-- See the [API documentation](https://pytantan.readthedocs.io/en/stable/api/index.html) \nfor more examples, including how to use the internal API, and detailed \nreference of the parameters and result types. -->\n\n<!-- ## \ud83e\uddf6 Thread-safety -->\n\n<!-- ## \u23f1\ufe0f Benchmarks -->\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 tracker](https://github.com/althonos/pytantan/issues)\nif you need to report or ask something. If you are filing in on a bug,\nplease include as much information as you can about the issue, and try to\nrecreate the same bug in a simple, easily reproducible situation.\n\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/pytantan/blob/main/CONTRIBUTING.md)\nfor more details.\n\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/pytantan/blob/main/CHANGELOG.md)\nin the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.\n\n\n## \u2696\ufe0f License\n\nThis library is provided under the [GNU General Public License v3.0 or later](https://choosealicense.com/licenses/gpl-3.0/).\nTantan is developed by [Martin Frith](https://sites.google.com/site/mcfrith/martin-frith) and is distributed under the\nterms of the GPLv3 or later as well. See `vendor/tantan/COPYING.txt` for more information.\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [Tantan authors](https://github.com/Martinsos). 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