Biobroker

This repository contains the source code for the Biobroker python package. This package contains multiple utilities, but the overall philosophy/goal can be described in a phrase:

Given an input file of any type containing metadata about entities, broker it to any archive and return a human-readable result.

I understand that this is a very ambitious project; for starters, the variety of existing archives is way too high. For now, this package is being developed by extending my knowledge on the european genomics/bio archives hosted by EMBL-EBI. It may be that some archives can't just be adapted, but I will be very happy if this library can be extended to just work with enough archives to ensure a biology laboratory can set up an automatic brokering process that works for them.

Install

pip3 install biobroker

Usage

This library does not support CLI access at the moment (Maybe in the future I could think of a CLI; although I would much rather have a simple GUI). As such, you will have to install and write scripts using the objects provided.

For usage, please see the examples/ folder in the repository.

For extensive documentation about the overall infrastructure and each class, please see the ReadTheDocs page