pyfastani


Namepyfastani JSON
Version 0.6.0 PyPI version JSON
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SummaryCython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
upload_time2024-10-22 02:38:27
maintainerNone
docs_urlNone
authorNone
requires_python>=3.7
licenseMIT License Copyright (c) 2021-2024 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 genomics average nucleotide identity
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            # 🐍⏩🧬 PyFastANI [![Stars](https://img.shields.io/github/stars/althonos/pyfastani.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyfastani/stargazers)

*[Cython](https://cython.org/) bindings and Python interface to [FastANI](https://github.com/ParBLiSS/FastANI/), a method for fast whole-genome similarity estimation.
**Now with multithreading!***

[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/pyfastani/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/pyfastani/actions)
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## πŸ—ΊοΈ Overview

FastANI is a method published in 2018 by [Chirag Jain](https://github.com/cjain7)
*et al.* for high-throughput computation of whole-genome
[Average Nucleotide Identity (ANI)](https://img.jgi.doe.gov/docs/ANI.pdf).
It uses [MashMap](https://github.com/marbl/MashMap) to compute orthologous mappings
without the need for expensive alignments.


`pyfastani` is a Python module, implemented using the [Cython](https://cython.org/)
language, that provides bindings to FastANI. It directly interacts with the
FastANI internals, which has the following advantages over CLI wrappers:

- **simpler compilation**: FastANI requires several additional libraries,
  which make compilation of the original binary non-trivial. In PyFastANI,
  libraries that were needed for threading or I/O are provided as stubs,
  and `Boost::math` headers are vendored so you can build the package without
  hassle. Or even better, just install from one of the provided wheels!
- **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 binary being present on
  the end-user machine.
- **sans I/O**: Everything happens in memory, in Python objects you control,
  making it easier to pass your sequences to FastANI
  without needing to write them to a temporary file.
- **multi-threading**: Genome query resolves the fragment mapping step in
  parallel, leading to shorter querying times even with a single genome.

*This library is still a work-in-progress, and in an experimental stage,
but it should already pack enough features to be used in a standard pipeline.*


## πŸ”§ Installing

PyFastANI can be installed directly from [PyPI](https://pypi.org/project/pyfastani/),
which hosts some pre-built CPython wheels for x86-64 Unix platforms, as well
as the code required to compile from source with Cython:
```console
$ pip install pyfastani
```

In the event you have to compile the package from source, all the required
libraries are vendored in the source distribution, so you'll only need a
C/C++ compiler.

Otherwise, PyFastANI is also available as a [Bioconda](https://pyfastani.github.io/)
package:
```console
$ conda install -c bioconda pyfastani
```

## πŸ’‘ Example

The following snippets show how to compute the ANI between two genomes,
with the reference being a draft genome. For one-to-many or many-to-many
searches, simply add additional references with `m.add_draft` before indexing.
*Note that any name can be given to the reference sequences, this will just
affect the `name` attribute of the hits returned for a query.*

### πŸ”¬ [Biopython](https://github.com/biopython/biopython)

Biopython does not let us access to the sequence directly, so we need to
convert it to bytes first with the `bytes` builtin function. For older
versions of Biopython (earlier than 1.79), use `record.seq.encode()`
instead of `bytes(record.seq)`.

```python
import pyfastani
import Bio.SeqIO

sketch = pyfastani.Sketch()

# add a single draft genome to the mapper, and index it
ref = list(Bio.SeqIO.parse("vendor/FastANI/data/Shigella_flexneri_2a_01.fna", "fasta"))
sketch.add_draft("S. flexneri", (bytes(record.seq) for record in ref))

# index the sketch and get a mapper
mapper = sketch.index()

# read the query and query the mapper
query = Bio.SeqIO.read("vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna", "fasta")
hits = mapper.query_sequence(bytes(query.seq))

for hit in hits:
    print("E. coli K12 MG1655", hit.name, hit.identity, hit.matches, hit.fragments)
```

### πŸ§ͺ [Scikit-bio](https://github.com/biocore/scikit-bio)

Scikit-bio lets us access to the sequence directly as a `numpy` array, but
shows the values as byte strings by default. To make them readable as
`char` (for compatibility with the C code), they must be cast with
`seq.values.view('B')`.

```python
import pyfastani
import skbio.io

sketch = pyfastani.Sketch()

ref = list(skbio.io.read("vendor/FastANI/data/Shigella_flexneri_2a_01.fna", "fasta"))
sketch.add_draft("Shigella_flexneri_2a_01", (seq.values.view('B') for seq in ref))

mapper = sketch.index()

# read the query and query the mapper
query = next(skbio.io.read("vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna", "fasta"))
hits = mapper.query_genome(query.values.view('B'))

for hit in hits:
    print("E. coli K12 MG1655", hit.name, hit.identity, hit.matches, hit.fragments)
```

## ⏱️ Benchmarks

In the original FastANI tool, multi-threading was only used to improve the
performance of many-to-many searches: each thread would have a chunk of the
reference genomes, and querying would be done in parallel for each reference.
However, with a small set of reference genomes, there may not be enough for
all the threads to work, so it cannot scale with a large number of threads. In
addition, this causes the same query genome to be hashed several times, which
is not optimal. In `pyfastani`, multi-threading is used to compute the hashes and mapping of query genome fragments. This allows parallelism to be useful even
when a only few reference genomes are available.

The benchmarks below show the time for querying a single genome (with
`Mapper.query_draft`) using a variable number of threads. *Benchmarks
were run on a [i7-8550U CPU](https://www.intel.fr/content/www/fr/fr/products/sku/122589/) running @1.80GHz with 4 physical / 8 logical
cores, using 50 bacterial genomes from the [proGenomes](https://progenomes.embl.de/) database.
For clarity, only 5 randomly-selected genomes are shown on the second graph. Each run was repeated 3 times.*

![Benchmarks](https://raw.githubusercontent.com/althonos/pyfastani/main/benches/mapping/v0.4.0.svg)

## πŸ”– Citation

PyFastANI is scientific software; it was presented among other optimized
software at the [European Student Council Symposium (ESCS) 2022](https://www.escs2022.iscbsc.org/) during [ECCB 2022](https://eccb2022.org/). Please
cite both [PyFastANI](https://doi.org/10.7490/f1000research.1119176.1) and [FastANI](https://www.nature.com/articles/s41467-018-07641-9) if you are using it in an academic work,
for instance as:

> PyFastANI (Larralde, 2022), a Python library with optimized bindings to FastANI (Jain *et al.*, 2018).

## πŸ”Ž See Also

Computing ANI for metagenomic sequences? You may be interested in
[`pyskani`, a Python package for computing ANI](https://github.com/althonos/pyskani)
using the [`skani` method](https://www.biorxiv.org/content/10.1101/2023.01.18.524587v1)
developed by [Jim Shaw](https://jim-shaw-bluenote.github.io/)
and [Yun William Yu](https://github.com/yunwilliamyu).

## πŸ’­ Feedback

### ⚠️ Issue Tracker

Found a bug ? Have an enhancement request ? Head over to the [GitHub issue
tracker](https://github.com/althonos/pyfastani/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.

### πŸ—οΈ Contributing

Contributions are more than welcome! See
[`CONTRIBUTING.md`](https://github.com/althonos/pyfastani/blob/master/CONTRIBUTING.md)
for more details.


## βš–οΈ License

This library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).

The FastANI code was written by [Chirag Jain](https://github.com/cjain7)
and is distributed under the terms of the
[Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/),
unless otherwise specified in vendored sources. See `vendor/FastANI/LICENSE`
for more information.
The `cpu_features` code was written by [Guillaume Chatelet](https://github.com/gchatelet)
and is distributed under the terms of the [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/).
See `vendor/cpu_features/LICENSE` for more information.
The `Boost::math` headers were written by [Boost Libraries](https://www.boost.org/) contributors
and is distributed under the terms of the [Boost Software License](https://choosealicense.com/licenses/bsl-1.0/).
See `vendor/boost-math/LICENSE` for more information.

*This project is in no way not affiliated, sponsored, or otherwise endorsed
by the [original FastANI authors](https://github.com/cjain7). It was developed by
[Martin Larralde](https://github.com/althonos/) during his PhD project
at the [European Molecular Biology Laboratory](https://www.embl.de/) in
the [Zeller team](https://github.com/zellerlab).*

            

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    "description": "# \ud83d\udc0d\u23e9\ud83e\uddec PyFastANI [![Stars](https://img.shields.io/github/stars/althonos/pyfastani.svg?style=social&maxAge=3600&label=Star)](https://github.com/althonos/pyfastani/stargazers)\n\n*[Cython](https://cython.org/) bindings and Python interface to [FastANI](https://github.com/ParBLiSS/FastANI/), a method for fast whole-genome similarity estimation.\n**Now with multithreading!***\n\n[![Actions](https://img.shields.io/github/actions/workflow/status/althonos/pyfastani/test.yml?branch=main&logo=github&style=flat-square&maxAge=300)](https://github.com/althonos/pyfastani/actions)\n[![Coverage](https://img.shields.io/codecov/c/gh/althonos/pyfastani/branch/main.svg?style=flat-square&maxAge=3600)](https://codecov.io/gh/althonos/pyfastani/)\n[![License](https://img.shields.io/badge/license-MIT-blue.svg?style=flat-square&maxAge=2678400)](https://choosealicense.com/licenses/mit/)\n[![PyPI](https://img.shields.io/pypi/v/pyfastani.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/pyfastani)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/pyfastani?style=flat-square&maxAge=3600&logo=anaconda)](https://anaconda.org/bioconda/pyfastani)\n[![AUR](https://img.shields.io/aur/version/python-pyfastani?logo=archlinux&style=flat-square&maxAge=3600)](https://aur.archlinux.org/packages/python-pyfastani)\n[![Wheel](https://img.shields.io/pypi/wheel/pyfastani.svg?style=flat-square&maxAge=3600)](https://pypi.org/project/pyfastani/#files)\n[![Python Versions](https://img.shields.io/pypi/pyversions/pyfastani.svg?style=flat-square&maxAge=600)](https://pypi.org/project/pyfastani/#files)\n[![Python Implementations](https://img.shields.io/pypi/implementation/pyfastani.svg?style=flat-square&maxAge=600&label=impl)](https://pypi.org/project/pyfastani/#files)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyfastani/)\n[![Mirror](https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400)](https://git.embl.de/larralde/pyfastani/)\n[![Issues](https://img.shields.io/github/issues/althonos/pyfastani.svg?style=flat-square&maxAge=600)](https://github.com/althonos/pyfastani/issues)\n[![Docs](https://img.shields.io/readthedocs/pyfastani/latest?style=flat-square&maxAge=600)](https://pyfastani.readthedocs.io)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square)](https://github.com/althonos/pyfastani/blob/master/CHANGELOG.md)\n[![Downloads](https://img.shields.io/pypi/dm/pyfastani?style=flat-square&color=303f9f&maxAge=86400&label=downloads)](https://pepy.tech/project/pyfastani)\n[![Talk](https://img.shields.io/badge/talk-10.7490%2Ff1000research.1119176.1-f2673c?style=flat-square&maxAge=86400)](https://doi.org/10.7490/f1000research.1119176.1)\n\n\n## \ud83d\uddfa\ufe0f Overview\n\nFastANI is a method published in 2018 by [Chirag Jain](https://github.com/cjain7)\n*et al.* for high-throughput computation of whole-genome\n[Average Nucleotide Identity (ANI)](https://img.jgi.doe.gov/docs/ANI.pdf).\nIt uses [MashMap](https://github.com/marbl/MashMap) to compute orthologous mappings\nwithout the need for expensive alignments.\n\n\n`pyfastani` is a Python module, implemented using the [Cython](https://cython.org/)\nlanguage, that provides bindings to FastANI. It directly interacts with the\nFastANI internals, which has the following advantages over CLI wrappers:\n\n- **simpler compilation**: FastANI requires several additional libraries,\n  which make compilation of the original binary non-trivial. In PyFastANI,\n  libraries that were needed for threading or I/O are provided as stubs,\n  and `Boost::math` headers are vendored so you can build the package without\n  hassle. Or even better, just install from one of the provided wheels!\n- **single dependency**: If your software or your analysis pipeline is\n  distributed as a Python package, you can add `pyfastani` as a dependency to\n  your project, and stop worrying about the FastANI binary being present on\n  the end-user machine.\n- **sans I/O**: Everything happens in memory, in Python objects you control,\n  making it easier to pass your sequences to FastANI\n  without needing to write them to a temporary file.\n- **multi-threading**: Genome query resolves the fragment mapping step in\n  parallel, leading to shorter querying times even with a single genome.\n\n*This library is still a work-in-progress, and in an experimental stage,\nbut it should already pack enough features to be used in a standard pipeline.*\n\n\n## \ud83d\udd27 Installing\n\nPyFastANI can be installed directly from [PyPI](https://pypi.org/project/pyfastani/),\nwhich hosts some pre-built CPython wheels for x86-64 Unix platforms, as well\nas the code required to compile from source with Cython:\n```console\n$ pip install pyfastani\n```\n\nIn the event you have to compile the package from source, all the required\nlibraries are vendored in the source distribution, so you'll only need a\nC/C++ compiler.\n\nOtherwise, PyFastANI is also available as a [Bioconda](https://pyfastani.github.io/)\npackage:\n```console\n$ conda install -c bioconda pyfastani\n```\n\n## \ud83d\udca1 Example\n\nThe following snippets show how to compute the ANI between two genomes,\nwith the reference being a draft genome. For one-to-many or many-to-many\nsearches, simply add additional references with `m.add_draft` before indexing.\n*Note that any name can be given to the reference sequences, this will just\naffect the `name` attribute of the hits returned for a query.*\n\n### \ud83d\udd2c [Biopython](https://github.com/biopython/biopython)\n\nBiopython does not let us access to the sequence directly, so we need to\nconvert it to bytes first with the `bytes` builtin function. For older\nversions of Biopython (earlier than 1.79), use `record.seq.encode()`\ninstead of `bytes(record.seq)`.\n\n```python\nimport pyfastani\nimport Bio.SeqIO\n\nsketch = pyfastani.Sketch()\n\n# add a single draft genome to the mapper, and index it\nref = list(Bio.SeqIO.parse(\"vendor/FastANI/data/Shigella_flexneri_2a_01.fna\", \"fasta\"))\nsketch.add_draft(\"S. flexneri\", (bytes(record.seq) for record in ref))\n\n# index the sketch and get a mapper\nmapper = sketch.index()\n\n# read the query and query the mapper\nquery = Bio.SeqIO.read(\"vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna\", \"fasta\")\nhits = mapper.query_sequence(bytes(query.seq))\n\nfor hit in hits:\n    print(\"E. coli K12 MG1655\", hit.name, hit.identity, hit.matches, hit.fragments)\n```\n\n### \ud83e\uddea [Scikit-bio](https://github.com/biocore/scikit-bio)\n\nScikit-bio lets us access to the sequence directly as a `numpy` array, but\nshows the values as byte strings by default. To make them readable as\n`char` (for compatibility with the C code), they must be cast with\n`seq.values.view('B')`.\n\n```python\nimport pyfastani\nimport skbio.io\n\nsketch = pyfastani.Sketch()\n\nref = list(skbio.io.read(\"vendor/FastANI/data/Shigella_flexneri_2a_01.fna\", \"fasta\"))\nsketch.add_draft(\"Shigella_flexneri_2a_01\", (seq.values.view('B') for seq in ref))\n\nmapper = sketch.index()\n\n# read the query and query the mapper\nquery = next(skbio.io.read(\"vendor/FastANI/data/Escherichia_coli_str_K12_MG1655.fna\", \"fasta\"))\nhits = mapper.query_genome(query.values.view('B'))\n\nfor hit in hits:\n    print(\"E. coli K12 MG1655\", hit.name, hit.identity, hit.matches, hit.fragments)\n```\n\n## \u23f1\ufe0f Benchmarks\n\nIn the original FastANI tool, multi-threading was only used to improve the\nperformance of many-to-many searches: each thread would have a chunk of the\nreference genomes, and querying would be done in parallel for each reference.\nHowever, with a small set of reference genomes, there may not be enough for\nall the threads to work, so it cannot scale with a large number of threads. In\naddition, this causes the same query genome to be hashed several times, which\nis not optimal. In `pyfastani`, multi-threading is used to compute the hashes and mapping of query genome fragments. This allows parallelism to be useful even\nwhen a only few reference genomes are available.\n\nThe benchmarks below show the time for querying a single genome (with\n`Mapper.query_draft`) using a variable number of threads. *Benchmarks\nwere run on a [i7-8550U CPU](https://www.intel.fr/content/www/fr/fr/products/sku/122589/) running @1.80GHz with 4 physical / 8 logical\ncores, using 50 bacterial genomes from the [proGenomes](https://progenomes.embl.de/) database.\nFor clarity, only 5 randomly-selected genomes are shown on the second graph. Each run was repeated 3 times.*\n\n![Benchmarks](https://raw.githubusercontent.com/althonos/pyfastani/main/benches/mapping/v0.4.0.svg)\n\n## \ud83d\udd16 Citation\n\nPyFastANI is scientific software; it was presented among other optimized\nsoftware at the [European Student Council Symposium (ESCS) 2022](https://www.escs2022.iscbsc.org/) during [ECCB 2022](https://eccb2022.org/). Please\ncite both [PyFastANI](https://doi.org/10.7490/f1000research.1119176.1) and [FastANI](https://www.nature.com/articles/s41467-018-07641-9) if you are using it in an academic work,\nfor instance as:\n\n> PyFastANI (Larralde, 2022), a Python library with optimized bindings to FastANI (Jain *et al.*, 2018).\n\n## \ud83d\udd0e See Also\n\nComputing ANI for metagenomic sequences? You may be interested in\n[`pyskani`, a Python package for computing ANI](https://github.com/althonos/pyskani)\nusing the [`skani` method](https://www.biorxiv.org/content/10.1101/2023.01.18.524587v1)\ndeveloped by [Jim Shaw](https://jim-shaw-bluenote.github.io/)\nand [Yun William Yu](https://github.com/yunwilliamyu).\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\ntracker](https://github.com/althonos/pyfastani/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n### \ud83c\udfd7\ufe0f Contributing\n\nContributions are more than welcome! See\n[`CONTRIBUTING.md`](https://github.com/althonos/pyfastani/blob/master/CONTRIBUTING.md)\nfor more details.\n\n\n## \u2696\ufe0f License\n\nThis library is provided under the [MIT License](https://choosealicense.com/licenses/mit/).\n\nThe FastANI code was written by [Chirag Jain](https://github.com/cjain7)\nand is distributed under the terms of the\n[Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/),\nunless otherwise specified in vendored sources. See `vendor/FastANI/LICENSE`\nfor more information.\nThe `cpu_features` code was written by [Guillaume Chatelet](https://github.com/gchatelet)\nand is distributed under the terms of the [Apache License 2.0](https://choosealicense.com/licenses/apache-2.0/).\nSee `vendor/cpu_features/LICENSE` for more information.\nThe `Boost::math` headers were written by [Boost Libraries](https://www.boost.org/) contributors\nand is distributed under the terms of the [Boost Software License](https://choosealicense.com/licenses/bsl-1.0/).\nSee `vendor/boost-math/LICENSE` for more information.\n\n*This project is in no way not affiliated, sponsored, or otherwise endorsed\nby the [original FastANI authors](https://github.com/cjain7). It was developed by\n[Martin Larralde](https://github.com/althonos/) during his PhD project\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in\nthe [Zeller team](https://github.com/zellerlab).*\n",
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    "license": "MIT License  Copyright (c) 2021-2024 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.",
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