met-annot-unifier 0.0.1

A Python project to combine tabular outputs from GNPS, Sirius and ISDB

met-annot-unifier

A Python project to combine tabular outputs from GNPS, Sirius and ISDB

• Github repository: https://github.com/mapp-metabolomics-unit/met-annot-unifier/
• Documentation https://mapp-metabolomics-unit.github.io/met-annot-unifier/

Quickstart

Installation

met-annot-unifier is available on PyPi and can be installed with pip:

pip install met-annot-unifier

Usage

For now the package is only available as a command line tool. You can run it with the following command:

python -m met_annot_unifier.cli

Get help on the available modes with:

python -m met_annot_unifier.cli --help

Examples

You can align the annotations tables from GNPS, Sirius and ISDB using two modes:

• align-horizontally: This will return a long table with a single row for each unique compound (according to their planar structures or IK2D). This mode can be useful to output a table to be viewed in Datawarrior or similar tools for chemical structures exploration.

python -m met_annot_unifier.cli align-horizontally --gnps-file <path-to-gnps-table> --sirius-file <path-to-sirius-table> --isdb-file <path-to-isdb-table> --output <output-path>

• align-vertically: This will return a wide table with a single row per feature (m/z and retention time) and columns for each of the three sources. This mode can be useful to output a table to be added to a molecular network to be visualized in Cytoscape or similar tools for network visualization.

python -m met_annot_unifier.cli align-vertically --gnps-file <path-to-gnps-table> --sirius-file <path-to-sirius-table> --isdb-file <path-to-isdb-table> --output <output-path>

You can find example tables in the examples/data folder of this repository. So from the root of this repository you can run the following command to align the tables horizontally:

python -m met_annot_unifier.cli align-horizontally --gnps-file examples/data/gnps_output_example.tsv --sirius-file examples/data/sirius_output_example.tsv --isdb-file examples/data/isdb_output_example.tsv --output examples/data/aligned_table_horizontally.csv

Getting started with your project

First, create a repository on GitHub with the same name as this project, and then run the following commands:

git init -b main
git add .
git commit -m "init commit"
git remote add origin [e-mail]:mapp-metabolomics-unit/met-annot-unifier.git
git push -u origin main

Finally, install the environment and the pre-commit hooks with

make install

You are now ready to start development on your project! The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.

To finalize the set-up for publishing to PyPi or Artifactory, see here. For activating the automatic documentation with MkDocs, see here. To enable the code coverage reports, see here.

Releasing a new version

• Create an API Token on Pypi.
• Add the API Token to your projects secrets with the name PYPI_TOKEN by visiting this page.
• Create a new release on Github.
• Create a new tag in the form *.*.*.

For more details, see here.

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