Microbial association network SQL API.

This API contains drivers for interacting with a PostgreSQL database. Many of these drivers have functions that allow for BIOM files, network files and other microbiome-related files to be ported to the database.

Contact the author at lisa.rottjers (at) kuleuven.be. Your feedback is much appreciated! This version is still in early beta and has been tested for Python 3.6.

First set up a virtual environment and make sure it uses Python 3:

virtualenv venv
# Linux
source venv/bin/activate

# Windows
venv/Scripts/activate

# Once you are done with masq:
deactivate

To install masq, run:

pip install git+https://github.com/ramellose/masq.git

If you have both Python 2.7 and Python 3 installed, you may need to change the command to this:

python3 -m pip install git+https://github.com/ramellose/masq.git

At the moment, the CLI is not very well documented, since masq is in early development. You can run the masq script and read the help docs with the following command.

masq -h

masq requires a running instance of PostgreSQL to connect to. It will first set up a database structure in line with the database model used by mako. Then it can upload BIOM files and network files to the PostgreSQL database. Additionally, the metastats and netstats modules contain scripts with queries that can carry out some operations on the PostgreSQL database. These are currently not supported by the CLI, only by the API.

For viewing PostgreSQL databases, I recommend HeidiSQL.

This software is still in early alpha. Any feedback or bug reports will be much appreciated!

• Lisa Röttjers - ramellose

See also the list of contributors who participated in this project.

This project is licensed under the Apache License - see the LICENSE.txt file for details