microbetag.microbetag¶

Aim:

Perform the microbetag () approach annotating user’s bins instead of mapping taxonomies against the microbetagDB representative genomes.

Input:

  • A folder with .fasta files of the corresponding bins

  • The abundance table of the bins across the samples

  • (optional) a co-occurrence network in a three-columns format

Output:

  • An annotated network in .cx2 format

Attributes¶

logger

Functions¶

run_microbetag(config)

Main function for running the microbetag workflow.

main()

Loads and parses a configuration YAML file

Module Contents¶

microbetag.microbetag.logger[source]¶
microbetag.microbetag.run_microbetag(config: microbetag.config.Config)[source]¶

Main function for running the microbetag workflow. Based on the Config provided, it will apply several pre-calculation and/or annotation steps.

Returns:

A microbetag-annotated network in CX2 format. CX2 is a JSON-based format, so it is

easy to use for the response of the on-the-fly version to the query from MGG.

Return type:

mtg_net

Note

The mtg_net returned, is also saved as a .cx2 file in the output_directory using a timestamp on its filename, e.g. mtag_net_2025-05-08_17-47.cx2.

microbetag.microbetag.main()[source]¶

Loads and parses a configuration YAML file and invokes the main function for running the microbetag pipeline.