MacSyLib 1.0.1

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

MacSyLib

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

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

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

python -m pip install .[model]

For the developpers

python -m pip install -e .[dev]

For someone who is both developper and modeler

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

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

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.