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macsylib

Python library that help to detect of macromolecular, systems genetic pathways… in prokaryotes protein datasets

https://github.com/gem-pasteur/macsylib

Science Score: 39.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Python library that help to detect of macromolecular, systems genetic pathways… in prokaryotes protein datasets

Basic Info
  • Host: GitHub
  • Owner: gem-pasteur
  • License: gpl-3.0
  • Language: Python
  • Default Branch: main
  • Size: 22.7 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created 11 months ago · Last pushed 10 months ago
Metadata Files
Readme Contributing License Codemeta

README.md

MacSyLib banner

MacSyLib

MacSyLib is a python package library that allow to model and detect macromolecular systems, genetic pathways… by similarity search in prokaryotes datasets.

Build Status

Doc

PyPI - Python Version

Open Source License: GPL v3

PyPI Conda

SWH SWH

OpenSSF Best Practices FAIR checklist badge

Citations

MacSyFinder v2: Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Peer Community Journal, Volume 3 (2023), article no. e28. doi : 10.24072/pcjournal.250. https://peercommunityjournal.org/articles/10.24072/pcjournal.250/

Licence:

MacSyLib is developed and released under Open Source License: GPL v3

Installation

[!IMPORTANT] MacSyLib requires hmmer >= 3.1 (http://hmmer.org/). You need to install hmmer by yourself (except if you install macsylib via conda/mamba). If you are a modeler, you will need also git The other dependencies are managed by the python package manager pip.

Installation from distribution

We encourage to install macsylib in a virtualenv

After creating a virtualenv dedicated to MacSyLib and activating it

python3 -m venv my_project
cd my_project
source bin/activate

you can install macsylib as described below:

We distinguish 3 kind of MacSyLib users:

  • The end user, who want to analyse it's data with the library
  • The modeler, who want to modelize new macromolecular systems
  • The developer who want to add or fix methods in the macsylib code

By default the installation is for the end user, if you are modeler or developer there is a specific pip target.

For instance for the modelers bash python -m pip install .[model]

For the developpers bash python -m pip install -e .[dev]

For someone who is both developper and modeler

bash python -m pip install -e [dev,model]

For the developers:
Once you have installed macsylib do not forget to install pre-commit hooks

bash pre-commit install

Models installation

Models are no longer shipped along macsyfinder nor macsylib packages. To install Models you can use msl_data (shipped with MacSyLib). msl_data (formely macsydata) allow to manage models stored in macsy-models. Below some most useful commands.

  • available: List Models available on macsy-models.
  • search: Discover new packages.
  • install: Install or upgarde packages.
  • uninstall: Uninstall packages.
  • cite: How to cite a package.
  • ...

For complete documentation see macsydata section on readthedoc

For models not stored in macsy-models the commands available, search, installation from remote or upgrade from remote are NOT available.

For models Not stored in macsy-models, you have to manage them semi-manually. Download the archive (do not unarchive it), then use msl_data for the installation.

Use MacSyLib

import macsylib

Contributing

We encourage contributions, bug report, enhancement ...

But before to do that, we encourage to read the contributing guide.

Contributors

List of all people who participated in the macsylib project.

Owner

  • Name: gem-pasteur
  • Login: gem-pasteur
  • Kind: organization

CodeMeta (codemeta.json) 

{
  "@context": "https://w3id.org/codemeta/3.0",
  "type": "SoftwareSourceCode",
  "applicationCategory": "Biology",
  "author": [
    {
      "id": "https://orcid.org/0000-0002-0220-0482",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Universit Paris Cit, Bioinformatics and Biostatistics HUB, Paris, France "
      },
      "email": "bneron@pasteur.fr",
      "familyName": "Nron",
      "givenName": "Bertrand"
    },
    {
      "id": "https://orcid.org/0000-0002-5231-3346",
      "type": "Person",
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        "type": "Organization",
        "name": " Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France "
      },
      "email": "sophie.abby@univ-grenoble-alpes.fr",
      "familyName": "Abby",
      "givenName": "Sophie"
    },
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        "name": "Institut Pasteur, Universit Paris Cit, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "erocha@pasteur.fr",
      "familyName": "Rocha",
      "givenName": "Eduardo"
    }
  ],
  "codeRepository": "https://github.com/gem-pasteur/macsylib",
  "contributor": [
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      "id": "https://orcid.org/0000-0002-7552-1009",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Universit Paris Cit, Bioinformatics and Biostatistics HUB, Paris, France "
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      "email": "hmenager@pasteur.fr",
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      "givenName": "Herv"
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      "id": "https://github.com/fjossandon",
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      "email": "fco.j.ossandon@gmail.com",
      "familyName": "Ossandon",
      "givenName": "Franscisco J,"
    },
    {
      "id": "https://orcid.org/0000-0003-2277-689X",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "APC Microbiome Institute: Cork, IE "
      },
      "familyName": "Denise",
      "givenName": "Rmi"
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        "name": "Institut Pasteur, Universit Paris Cit, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "mtouchon@pasteur.fr",
      "familyName": "Touchon",
      "givenName": "Marie"
    },
    {
      "id": "https://orcid.org/0000-0003-4797-6185",
      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Universit Paris Cit, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France"
      },
      "email": "aperrin@pasteur.fr",
      "familyName": "Perrin",
      "givenName": "Amandine"
    },
    {
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      "type": "Person",
      "affiliation": {
        "type": "Organization",
        "name": "Institut Pasteur, Universit Paris Cit, SeqBio, Paris, France "
      },
      "email": "yoann.dufresne@pasteur.fr",
      "familyName": "Dufresne",
      "givenName": "Yoann"
    },
    {
      "id": "https://github.com/TrellixVulnTeam",
      "type": "Person",
      "email": "charles.mcfarland@trellix.com",
      "givenName": "TrellixVulnTeam"
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      "type": "Person",
      "email": "crusoe@debian.org",
      "familyName": "Crusoe",
      "givenName": "Michael R."
    }
  ],
  "dateCreated": "2025-07-01",
  "dateModified": "2025-08-01",
  "datePublished": "2025-08-01",
  "description": "MacSyLib is a python library to model and detect macromolecular systems, genetic pathways in prokaryotes protein datasets.",
  "downloadUrl": "https://pypi.org/project/MacSyLib/",
  "funder": {
    "type": "Organization",
    "name": "Institut Pasteur Paris, CNRS"
  },
  "keywords": [
    "bioinformatics",
    "functional genomics",
    "gene functional annotation"
  ],
  "license": "https://spdx.org/licenses/GPL-3.0+",
  "name": "MacSyLib",
  "operatingSystem": [
    "Linux",
    "BSD",
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  "programmingLanguage": "Python",
  "relatedLink": "https://pypi.org/project/MacSyLib",
  "softwareRequirements": [
    "https://www.python.org/downloads/ (>= 3.10)",
    "http://hmmer.org/ (>= 3.1)"
  ],
  "version": "1.0",
  "codemeta:contIntegration": {
    "id": "https://github.com/gem-pasteur/macsylib/actions"
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  "continuousIntegration": "https://github.com/gem-pasteur/macsylib/actions",
  "developmentStatus": "active",
  "isSourceCodeOf": "MacSyFinder",
  "issueTracker": "https://github.com/gem-pasteur/macsylibr/issues",
  "referencePublication": "https://doi.org/10.24072/pcjournal.250"
}

GitHub Events

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Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: macsylib

MacSyLib: Python library that help to detect of macromolecular, systems genetic pathways… in prokaryotes protein datasets using systems modelling and similarity search.

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 8.7%
Average: 28.9%
Dependent repos count: 49.1%
Maintainers (1)
bneron
Last synced: 10 months ago

Dependencies

.github/workflows/ruff.yml actions
  • actions/checkout v4 composite
  • chartboost/ruff-action v1 composite
.github/workflows/testing.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v3 composite
doc/requirements.txt pypi
  • pygraphviz *
  • sphinx-rtd-theme *
  • sphinx_autodoc_typehints *
  • sphinxcontrib-applehelp *
  • sphinxcontrib-devhelp *
  • sphinxcontrib-htmlhelp *
  • sphinxcontrib-jsmath *
  • sphinxcontrib-qthelp *
  • sphinxcontrib-serializinghtml *
  • sphinxcontrib-svg2pdfconverter *
pyproject.toml pypi
  • PyYAML >=5.1.1
  • certifi *
  • colorama >=0.4.4
  • colorlog >=4.0.2
  • networkx >=2.4
  • packaging >=18.0
  • pandas >=1.03