microbetag

microbetag attempts to be a microbial interactions co-occurrence network annotator

In this repository we have:

• the precalculation steps/scripts under the microbetagDB folder; the database of microbetag consists of the outcome of these precalculations and to get those the resources under the ref-dbs folder are used
• the microbetag python library which makes use of the microbetagDB and assumes several other software have been installed properly (see Installation)
• a Dockerfile to run microbetag in a container-based way

Dependencies

microbetag makes use of several 3rd-party software. Thus, it inherits the dependencies of theirs.

• Julia
• FlashWeave
• FAPROTAX
• BugBase

To help you create such an environment, we provide the installation.sh script. However, this will work smoothly in case you are running microbetag on Linux systems. If your OS is MacOs or Windows, you need to set this manually or jump into the containerized version of microbetag.

Installation

How to run

python microbetag.py -conf config.yml 

microbetag expects a 7-level taxonomy in a .csv or .tsv format with:

• no D_1__ or K__,P__ any other similar prefixes befor the taxon name
• the complete species name if that is available on its last column.

Example

If your taxonomy is

Bacteria;Firmicutes;Thermoanaerobacteria;Thermoanaerobacterales;Family III;Thermoanaerobacterium;thermosaccharolyticum,

you need to set it as:

Bacteria;Firmicutes;Thermoanaerobacteria;Thermoanaerobacterales;Family III;Thermoanaerobacterium;Thermoanaerobacterium thermosaccharolyticum

One

Docker

The microbetag annotator will be available as a Docker image....

Graphical User Interphase (GUI)

But it microbetag will come with a GUI too.

A first thought on how to do this is to follow this scheme:

• build a database with the microbetag annotations
• implement microbetag so it asks queries on the db
• output could be a list of files, some of them .html so they could provide interactive visualizations such as having annotations on the nodes or/and edges

Funding

This project is funded by an EMBO Short-Term Fellowship.