| Name | pyncbitk JSON |
| Version |
0.1.0a1
JSON |
| download |
| home_page | None |
| Summary | Cython bindings and Python interface to the NCBI C++ Toolkit. |
| upload_time | 2024-12-12 16:55:18 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.7 |
| license | MIT License Copyright (c) 2024 Martin Larralde <martin.larralde@embl.de> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
bioinformatics
blast
sequence
alignment
ncbi
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 🧬🧰 PyNCBItk [](https://github.com/althonos/pyncbitk/stargazers)
*(Unofficial) [Cython](https://cython.org/) bindings and Python interface to the [NCBI C++ Toolkit](https://www.ncbi.nlm.nih.gov/toolkit).*
[](https://github.com/althonos/pyncbitk/actions)
[](https://codecov.io/gh/althonos/pyncbitk/)
[](https://choosealicense.com/licenses/mit/)
[](https://pypi.org/project/pyncbitk)
[](https://anaconda.org/bioconda/pyncbitk)
[](https://aur.archlinux.org/packages/python-pyncbitk)
[](https://pypi.org/project/pyncbitk/#files)
[](https://pypi.org/project/pyncbitk/#files)
[](https://pypi.org/project/pyncbitk/#files)
[](https://github.com/althonos/pyncbitk/)
[](https://git.lumc.nl/mflarralde/pyncbitk/)
[](https://github.com/althonos/pyncbitk/issues)
[](https://pyncbitk.readthedocs.io)
[](https://github.com/althonos/pyncbitk/blob/main/CHANGELOG.md)
[](https://pepy.tech/project/pyncbitk)
***⚠️ This package is a work-in-progress and in a very experimental state. Expect segmentation faults, compilation issues, missing features, incomplete documentation.***
## 🗺️ Overview
The [NCBI C++ Toolkit](https://ncbi.github.io/cxx-toolkit/) is a framework of
C++ libraries to work with biological sequence data developed at the
[National Center for Biotechnology Information](https://www.ncbi.nlm.nih.gov/).
It features a flexible object model for representing sequences of various
origin, including composite or virtual sequences; a resource manager
to easily manipulate heterogeneous data sources; and a comprehensive API to the
various BLAST algorithms[\[1\]](#ref1) developed at the NBCI.
PyNCBItk is a Python library that provides bindings to the NCBI C++ Toolkit
data model and BLAST+ interface using [Cython](https://cython.org). It exposes
the internals of the C++ Toolkit, allowing BLAST queries to be run directly
from the Python interpreter without external I/O.
## 📋 Roadmap
The package is in a very experimental state, and only a few core features are
supported at the moment:
- [x] Loading sequences from a FASTA file.
- [x] Creating basic sequences through the Python API.
- [x] Running BLAST searches with default parameters.
- [ ] Thorough BLAST configuration.
- [ ] Error and warning management.
- [ ] Support for all kinds of sequence storage.
- [ ] Multi-threading for database searches using Python threads.
- [ ] Advanced interface for the object manager.
- [ ] Interface for all sequence and alignment types.
## 🔧 Installing
PyNCBItk is available for all modern Python (3.7+). Compilation is done
through [CMake](https://cmake.org) using [Scikit-build-core](https://scikit-build-core.readthedocs.io).
To install the project locally, clone the repository and its submodules,
and install the repository with `pip`:
```
$ git clone --recursive https://github.com/althonos/pyncbitk
$ pip install ./pyncbitk -v
```
The compilation uses the [Conan C/C++ package manager](https://docs.conan.io/2/)
to handle compilation of the NCBI C++ Toolkit: the project will take ages to
compile the first time, but afterwards only the Cython code will have to be
recompiled.
## 💡 Example
```python
from pyncbitk.objects.seqset import BioSeqSet
from pyncbitk.objtools import DatabaseReader, FastaReader
from pyncbitk.algo import BlastN
# read the queries from a FASTA file
queries = BioSeqSet(FastaReader("queries.fna"))
# open a database of subject sequences
db = DatabaseReader("database.fna")
# run `blastn` with default parameters
blastn = BlastN()
results = blastn.run(queries, db)
```
The result is a `SearchResultsSet` which contains one `SearchResults` object
per query/subject pair. The `SearchResults` object summarizes the result
and contains the hit alignments in a `SeqAlignSet`.
## 💭 Feedback
### ⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the
[GitHub issue tracker](https://github.com/althonos/pyncbitk/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/pyncbitk/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/pyncbitk/blob/main/CHANGELOG.md)
in the [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) format.
## ⚖️ License
This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).
The NCBI C++ Toolkit is a "United States Government Work" and therefore lies in
the public domain, but may be subject to copyright by the U.S. in foreign
countries. Some restrictions apply, see the
[NCBI C++ Toolkit license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/doc/public/LICENSE).
*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the NCBI or any associated entity. It was developed
by [Martin Larralde](https://github.com/althonos/) during his PhD
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> Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. *Journal of molecular biology*, 215(3), 403–410. [doi:10.1016/S0022-2836(05)80360-2](https://doi.org/10.1016/S0022-2836(05)80360-2)
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"description": "# \ud83e\uddec\ud83e\uddf0 PyNCBItk [](https://github.com/althonos/pyncbitk/stargazers)\n\n*(Unofficial) [Cython](https://cython.org/) bindings and Python interface to the [NCBI C++ Toolkit](https://www.ncbi.nlm.nih.gov/toolkit).*\n\n[](https://github.com/althonos/pyncbitk/actions)\n[](https://codecov.io/gh/althonos/pyncbitk/)\n[](https://choosealicense.com/licenses/mit/)\n[](https://pypi.org/project/pyncbitk)\n[](https://anaconda.org/bioconda/pyncbitk)\n[](https://aur.archlinux.org/packages/python-pyncbitk)\n[](https://pypi.org/project/pyncbitk/#files)\n[](https://pypi.org/project/pyncbitk/#files)\n[](https://pypi.org/project/pyncbitk/#files)\n[](https://github.com/althonos/pyncbitk/)\n[](https://git.lumc.nl/mflarralde/pyncbitk/)\n[](https://github.com/althonos/pyncbitk/issues)\n[](https://pyncbitk.readthedocs.io)\n[](https://github.com/althonos/pyncbitk/blob/main/CHANGELOG.md)\n[](https://pepy.tech/project/pyncbitk)\n\n***\u26a0\ufe0f This package is a work-in-progress and in a very experimental state. Expect segmentation faults, compilation issues, missing features, incomplete documentation.***\n\n## \ud83d\uddfa\ufe0f Overview\n\nThe [NCBI C++ Toolkit](https://ncbi.github.io/cxx-toolkit/) is a framework of\nC++ libraries to work with biological sequence data developed at the\n[National Center for Biotechnology Information](https://www.ncbi.nlm.nih.gov/).\nIt features a flexible object model for representing sequences of various\norigin, including composite or virtual sequences; a resource manager\nto easily manipulate heterogeneous data sources; and a comprehensive API to the\nvarious BLAST algorithms[\\[1\\]](#ref1) developed at the NBCI.\n\nPyNCBItk is a Python library that provides bindings to the NCBI C++ Toolkit\ndata model and BLAST+ interface using [Cython](https://cython.org). It exposes\nthe internals of the C++ Toolkit, allowing BLAST queries to be run directly\nfrom the Python interpreter without external I/O.\n\n## \ud83d\udccb Roadmap\n\nThe package is in a very experimental state, and only a few core features are\nsupported at the moment:\n\n- [x] Loading sequences from a FASTA file.\n- [x] Creating basic sequences through the Python API.\n- [x] Running BLAST searches with default parameters.\n- [ ] Thorough BLAST configuration.\n- [ ] Error and warning management.\n- [ ] Support for all kinds of sequence storage.\n- [ ] Multi-threading for database searches using Python threads.\n- [ ] Advanced interface for the object manager.\n- [ ] Interface for all sequence and alignment types.\n\n## \ud83d\udd27 Installing\n\nPyNCBItk is available for all modern Python (3.7+). Compilation is done\nthrough [CMake](https://cmake.org) using [Scikit-build-core](https://scikit-build-core.readthedocs.io).\n\nTo install the project locally, clone the repository and its submodules,\nand install the repository with `pip`:\n```\n$ git clone --recursive https://github.com/althonos/pyncbitk\n$ pip install ./pyncbitk -v\n```\n\nThe compilation uses the [Conan C/C++ package manager](https://docs.conan.io/2/)\nto handle compilation of the NCBI C++ Toolkit: the project will take ages to\ncompile the first time, but afterwards only the Cython code will have to be\nrecompiled.\n\n## \ud83d\udca1 Example\n\n```python\nfrom pyncbitk.objects.seqset import BioSeqSet\nfrom pyncbitk.objtools import DatabaseReader, FastaReader\nfrom pyncbitk.algo import BlastN\n\n# read the queries from a FASTA file\nqueries = BioSeqSet(FastaReader(\"queries.fna\"))\n\n# open a database of subject sequences\ndb = DatabaseReader(\"database.fna\")\n\n# run `blastn` with default parameters\nblastn = BlastN()\nresults = blastn.run(queries, db)\n```\n\nThe result is a `SearchResultsSet` which contains one `SearchResults` object\nper query/subject pair. The `SearchResults` object summarizes the result\nand contains the hit alignments in a `SeqAlignSet`.\n\n## \ud83d\udcad Feedback\n\n### \u26a0\ufe0f Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the\n[GitHub issue tracker](https://github.com/althonos/pyncbitk/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/pyncbitk/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/pyncbitk/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 [MIT License](https://choosealicense.com/licenses/mit/).\nThe NCBI C++ Toolkit is a \"United States Government Work\" and therefore lies in\nthe public domain, but may be subject to copyright by the U.S. in foreign\ncountries. Some restrictions apply, see the\n[NCBI C++ Toolkit license](https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/doc/public/LICENSE).\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the NCBI or any associated entity. It was developed\nby [Martin Larralde](https://github.com/althonos/) during his PhD\nat the [Leiden University Medical Center](https://www.lumc.nl/en/) in\nthe [Zeller team](https://github.com/zellerlab).*\n\n## \ud83d\udcda References\n\n- <a id=\"ref1\">\\[1\\]</a> Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. *Journal of molecular biology*, 215(3), 403\u2013410. [doi:10.1016/S0022-2836(05)80360-2](https://doi.org/10.1016/S0022-2836(05)80360-2)\n",
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