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🧬🧰 PyNCBItk [![Stars](https://img.shields.io/github/stars/althonos/pyncbitk.svg?style=social\u0026maxAge=3600\u0026label=Star)](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[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/pyncbitk/test.yml?branch=main\u0026logo=github\u0026style=flat-square\u0026maxAge=300)](https://github.com/althonos/pyncbitk/actions)\n[![Coverage](https://img.shields.io/codecov/c/gh/althonos/pyncbitk?style=flat-square\u0026maxAge=3600\u0026logo=codecov)](https://codecov.io/gh/althonos/pyncbitk/)\n[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square\u0026maxAge=2678400)](https://choosealicense.com/licenses/mit/)\n[![PyPI](https://img.shields.io/pypi/v/pyncbitk.svg?style=flat-square\u0026maxAge=3600\u0026logo=PyPI)](https://pypi.org/project/pyncbitk)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/pyncbitk?style=flat-square\u0026maxAge=3600\u0026logo=anaconda)](https://anaconda.org/bioconda/pyncbitk)\n[![AUR](https://img.shields.io/aur/version/python-pyncbitk?logo=archlinux\u0026style=flat-square\u0026maxAge=3600)](https://aur.archlinux.org/packages/python-pyncbitk)\n[![Wheel](https://img.shields.io/pypi/wheel/pyncbitk.svg?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/pyncbitk/#files)\n[![Python Versions](https://img.shields.io/pypi/pyversions/pyncbitk.svg?style=flat-square\u0026maxAge=600\u0026logo=python)](https://pypi.org/project/pyncbitk/#files)\n[![Python Implementations](https://img.shields.io/pypi/implementation/pyncbitk.svg?style=flat-square\u0026maxAge=600\u0026label=impl)](https://pypi.org/project/pyncbitk/#files)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/althonos/pyncbitk/)\n[![Mirror](https://img.shields.io/badge/mirror-LUMC-003EAA.svg?maxAge=2678400\u0026style=flat-square)](https://git.lumc.nl/mflarralde/pyncbitk/)\n[![Issues](https://img.shields.io/github/issues/althonos/pyncbitk.svg?style=flat-square\u0026maxAge=600)](https://github.com/althonos/pyncbitk/issues)\n[![Docs](https://img.shields.io/readthedocs/pyncbitk/latest?style=flat-square\u0026maxAge=600)](https://pyncbitk.readthedocs.io)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/althonos/pyncbitk/blob/main/CHANGELOG.md)\n[![Downloads](https://img.shields.io/pypi/dm/pyncbitk?style=flat-square\u0026color=303f9f\u0026maxAge=86400\u0026label=downloads)](https://pepy.tech/project/pyncbitk)\n\n***⚠️ This package is a work-in-progress and in a very experimental state. Expect segmentation faults, compilation issues, missing features, incomplete documentation.***\n\n## 🗺️ 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## 📋 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## 🔧 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 an alpha release, use `pip` with the `--pre` flag:\n```console\n$ pip install pyncbitk --pre\n```\n\nThe `pyncbitk` package requires additional runtime libraries that are distributed\nin the `pyncbitk-runtime` package. These libraries should be available in a pre-compiled\nwheel for Linux and MacOS platforms. Otherwise, they can be compiled on setup \nwith 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## 💡 Example\n\n```python\nfrom pyncbitk.objects.seqset import BioSeqSet\nfrom pyncbitk.objtools import DatabaseReader, FastaReader\nfrom pyncbitk.algo.blast import BlastN\n\n# read the sequences from FASTA-formatted files\nqueries = BioSeqSet(FastaReader(\"queries.fna\", split=False))\nsubjects = BioSeqSet(FastaReader(\"subjects.fna\", split=False))\n\n# run `blastn` with default parameters\nblastn = BlastN()\nresults = blastn.run(queries, subjects)\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\nSee the [Examples section](https://pyncbitk.readthedocs.io/en/latest/examples/index.html) \nin the [online documentation](https://pyncbitk.readthedocs.io/en/latest/examples/index.html)\nfor more information.\n\n## 💭 Feedback\n\n### ⚠️ 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### 🏗️ 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## 📋 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## ⚖️ 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/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## 📚 References\n\n- \u003ca id=\"ref1\"\u003e\\[1\\]\u003c/a\u003e Altschul, S. F., Gish, W., Miller, W., Myers, E. W., \u0026 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)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falthonos%2Fpyncbitk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falthonos%2Fpyncbitk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falthonos%2Fpyncbitk/lists"}