Metadata-Version: 2.1
Name: orthoani
Version: 0.2.1
Summary: An implementation of the OrthoANI algorithm for nucleotide identity measurement.
Home-page: https://github.com/althonos/orthoani
Author: Martin Larralde
Author-email: martin.larralde@embl.de
License: MIT
Project-URL: Bug Tracker, https://github.com/althonos/orthoani/issues
Project-URL: Changelog, https://github.com/althonos/orthoani/blob/master/CHANGELOG.md
Description: # OrthoANI [![Stars](https://img.shields.io/github/stars/althonos/orthoani.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/orthoani/stargazers)
        
        *A Python implementation of the [OrthoANI](https://doi.org/10.1099/ijsem.0.000760) algorithm for nucleotide identity measurement.*
        
        [![TravisCI](https://img.shields.io/travis/com/althonos/orthoani/master?logo=travis&maxAge=600&style=flat-square)](https://travis-ci.com/althonos/orthoani/branches)
        [![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)
        [![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/orthoani/)
        [![Coverage](https://img.shields.io/codecov/c/gh/althonos/orthoani?style=flat-square&maxAge=3600)](https://codecov.io/gh/althonos/orthoani/)
        [![Sanity](https://img.shields.io/codacy/grade/4a427dadd1864c93ab9a55cb34c389a0.svg?style=flat-square&maxAge=3600)](https://codacy.com/app/althonos/orthoani)
        [![PyPI](https://img.shields.io/pypi/v/orthoani.svg?style=flat-square&maxAge=600)](https://pypi.org/project/orthoani)
        [![Wheel](https://img.shields.io/pypi/wheel/orthoani.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/orthoani/#files)
        [![Python Versions](https://img.shields.io/pypi/pyversions/orthoani.svg?style=flat-square&maxAge=600)](https://pypi.org/project/orthoani/#files)
        [![Python Implementations](https://img.shields.io/pypi/implementation/orthoani.svg?style=flat-square&maxAge=600)](https://pypi.org/project/orthoani/#files)
        [![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/orthoani/blob/master/CHANGELOG.md)
        [![GitHub issues](https://img.shields.io/github/issues/althonos/orthoani.svg?style=flat-square&maxAge=600)](https://github.com/althonos/orthoani/issues)
        [![Downloads](https://img.shields.io/badge/dynamic/json?style=flat-square&color=303f9f&maxAge=86400&label=downloads&query=%24.total_downloads&url=https%3A%2F%2Fapi.pepy.tech%2Fapi%2Fprojects%2Forthoani)](https://pepy.tech/project/orthoani)
        
        ## 🗺️ Overview
        
        OrthoANI is a metric proposed by [Lee *et al.*](https://doi.org/10.1099/ijsem.0.000760)
        in 2016 to improve computation of Average Nucleotide Identity. It uses
        [BLASTn](https://en.wikipedia.org/wiki/BLAST_(biotechnology)) to find orthologous
        blocks in a pair of sequences, and then computes the average identity only
        considering alignments of reciprocal orthologs.
        
        ![Algorithm](https://www.microbiologyresearch.org/docserver/fulltext/ijsem/66/2/000760-f1.gif)
        
        This project is a reimplementation of the closed-source Java implementation
        provided by the authors on [`ezbiocloud.net`](https://www.ezbiocloud.net/sw/oat).
        It relies on [Biopython](https://biopython.org/) to handle the I/O and the
        
        
        ## 🔧 Installing
        
        Installing with `pip` is the easiest:
        ```console
        $ pip install orthoani
        ```
        
        `orthoani` also requires the BLAST+ binaries to be installed on your machine
        and available somewhere in your `$PATH`.
        
        ## 💡 Example
        
        Use Biopython to load two FASTA files, and then `orthoani.orthoani` to compute
        the OrthoANI metric between them:
        ```python
        import orthoani
        from Bio.SeqIO import read
        
        genome_1 = read("sequence1.fa", "fasta")
        genome_2 = read("sequence2.fa", "fasta")
        
        ani = orthoani.orthoani(genome_1, genome_2)
        ```
        
        `orthoani` can also be used from the CLI using a very simple command-line
        interface:
        ```console
        $ orthoani -q sequence1.fa -r sequence2.fa
        0.5725
        ```
        
        ## 🐏 Memory
        
        `orthoani` uses the machine temporary folder to handle BLAST+ input and output
        files, which is configurable through
        [`tempfile.tempdir`](https://docs.python.org/3/library/tempfile.html#tempfile.tempdir).
        On some systems (like ArchLinux), this filesystem can reside in memory, which means
        that your computer could have trouble processing very large files. If this
        happens, try changing the value of the `tempfile.tempdir` to a directory that
        is actually located on physical storage.
        
        
        ## 📜 About
        
        This library is provided under the open-source
        [MIT license](https://choosealicense.com/licenses/mit/).
        
        *This project is in no way not affiliated, sponsored, or otherwise endorsed by
        the [original OrthoANI authors](http://www.chunlab.com/). It was developed by
        [Martin Larralde](https://github.com/althonos/orthoani) during his PhD project
        at the [European Molecular Biology Laboratory](https://www.embl.de/) in
        the [Zeller team](https://github.com/zellerlab).*
        
Keywords: ani,average,nucleotide,identity,genomic,taxonomy
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: !=3.0.*,!=3.1.*,!=3.2.*,>=2.7
Description-Content-Type: text/markdown
