[![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/) [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/) [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io) [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io) [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags) [![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.2.3--pyhdfd78af_0) [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io) [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/) [![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) [![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_io) [![](https://readthedocs.org/projects/biobb-io/badge/?version=latest&label=Docs)](https://biobb-io.readthedocs.io/en/latest/?badge=latest) [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/) [![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb) [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4) [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas) [![](https://docs.bioexcel.eu/biobb_io/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_io/junit/report.html) [![](https://docs.bioexcel.eu/biobb_io/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_io/coverage/) [![](https://docs.bioexcel.eu/biobb_io/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_io/flake8/) [![](https://img.shields.io/github/last-commit/bioexcel/biobb_io?label=Last%20Commit)](https://github.com/bioexcel/biobb_io/commits/master) [![](https://img.shields.io/github/issues/bioexcel/biobb_io.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_io/issues/) [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu) [![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847) [](https://bestpractices.coreinfrastructure.org/projects/8847/badge) [//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL) # biobb_io ### Introduction Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: [latest API documentation](http://biobb-io.readthedocs.io/en/latest/). ### Version v5.2.3 2025.2 ### Installation Using PIP: > **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY. * Installation: pip install "biobb_io==5.2.3" * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) Using ANACONDA: * Installation: conda install -c bioconda "biobb_io==5.2.3" * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html) Using DOCKER: * Installation: docker pull quay.io/biocontainers/biobb_io:5.2.3--pyhdfd78af_0 * Usage: docker run quay.io/biocontainers/biobb_io:5.2.3--pyhdfd78af_0 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html). Using SINGULARITY: **MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system. * Installation: singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.2.3--pyhdfd78af_0 * Usage: singularity exec biobb_io.sif The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html). ### Copyright & Licensing This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU Horizon Europe [101093290](https://cordis.europa.eu/project/id/101093290), EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). * (c) 2015-2026 [Barcelona Supercomputing Center](https://www.bsc.es/) * (c) 2015-2026 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) Licensed under the [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. ![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel")