🎯 `microbetag` locally¶

Running microbetag locally provides a great range of features and can be used as an interface for several tasks, network annotation related and not.

Due to its many dependencies and the variety of possible input and output configurations, installing and running microbetag across different operating systems and platforms can be challenging. Performance may vary depending on the specific setup too.

If you encounter any issues, please don’t hesitate to reach out to us via our Matrix community.

Bug reports, feature suggestions, and general feedback—especially from the diverse ways in which microbetag may be used are the most welcome too.

✅ Check availability¶

Once installed, microbetag should be available when running:

  (microbetag) u0156635@gbw-l-l0074:~$ microbetag --help
  usage: microbetag [-h] [--config CONFIG] [-v]

  Microbetag CLI

  options:
  -h, --help            show this help message and exit
  --config CONFIG, -c CONFIG
                          Path to the configuration yaml file.
  -v, --version         Show Microbetag version

If not, please follow instructions here on how to get it!

Use `microbetag`’s features as a library¶

You can now use microbetag’s features independently: either general tasks required for the actual annotation steps or annotation steps on their own. For example, you may run individual genome annotation steps, build your own GENREs, as well as the routines allowing you to export pathway and/or seed complementarities.

To go through them, you may have a look at the API Reference but also on the unittests of ours.

Input/output for these tests can be found in the test_data folder where each case is explained further.

In the .. using custom genomes tutorial, we provide an example on how to run a complete microbetag-pipeline, starting from an abundance table and a list of genome sequencing files, and end up with an annotated network.

microbetag and its required environments are also available in containerized versions. If you wish to install it as such, follow instructions here. If already installed, you may jump to the corresponding tutorial on running microbetag on a container.

Important

Remember that microbetag will use all files that have been produced from a previous run, given the output directory stays the same! That means that if you wish to re-calculate a part for any reason, e.g. run FlashWeave again with a different set of parameters, you need to make sure that you first delete the previous output files of this step!

🤖 Use `microbetag` API programmatically¶

One may use the API routes described through Python. For example, to get the microbetagDB genomes related species with NCBI Taxonomy ID 853:

import requests
url = "https://msysbio.gbiomed.kuleuven.be/ncbiTaxId-to-genomeId/853"
r = requests.get(url)
r.status_code
200
r.json()
{"537007": ["GCA_002222595.2"]}

For more about how to use the microbetagDB API you may check here.

🎯 microbetag locally¶

✅ Check availability¶

Use microbetag’s features as a library¶

🤖 Use microbetag API programmatically¶

🎯 `microbetag` locally¶

Use `microbetag`’s features as a library¶

🤖 Use `microbetag` API programmatically¶