🐍⏩🧬 pyFastANI

Cython bindings and Python interface to FastANI, a tool for fast whole-genome similarity estimation.

🗺️ Overview

FastANI is a method published in 2018 by Jain et al. for high-throughput computATION of whole-genome Average Nucleotide Identity (ANI). It uses MashMap to compute orthologous mappings without the need for expensive alignments.

pyfastani is a Python module, implemented using the Cython language, that provides bindings to FastANI. It directly interacts with the FastANI internals, which has the following advantages over CLI wrappers:

• single dependency: If your software or your analysis pipeline is distributed as a Python package, you can add pyfastani as a dependency to your project, and stop worrying about the FastANI binaries being properly setup on the end-user machine.
• no intermediate files: Everything happens in memory, in Python objects you have control on, making it easier to pass your sequences to FastANI without needing to write them to a temporary file.
• no input formatting: The memory model of FastANI can be interacted with to add new sequences directly without needing to write them to dedicated files. This is useful if your sequences are already loaded in memory, for instance because you obtained them from another Python library (such as or Biopython).

This library is still a work-in-progress, and in an experimental stage, but it should already pack enough features to run one-to-one computations.

💡 Example

Use pyfastani to compute the ANI between the two sequences, loading them with the Bio.SeqIO module:

import Bio.SeqIO
import pyfastani

s1 = next(Bio.SeqIO.parse("vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna", "fasta"))
s2 = next(Bio.SeqIO.parse("vendor/FastANI/data/Shigella_flexneri_2a_01.fna", "fasta"))

s = pyfastani.Sketch(pyfastani.Parameters())

s.add_sequence(s1.id, str(s1.seq))
s.index()
s.query_sequence(str(s2.seq))

💭 Feedback

⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker 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 for more details.

⚖️ License

This library is provided under the MIT License. The FastANI code was written by Chirag Jain and is distributed under the terms of the Apache License 2.0 license. See vendor/FastANI/LICENSE for more information.

This project is in no way not affiliated, sponsored, or otherwise endorsed by the original FastANI authors. It was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.