socialgene 0.1.2

Creating and interacting with graph databases of protein domains and their genome coordinates

Note: All releases may intorduce breaking changes until the release of v1.0.0

Both user and developer documentation can be found at: https://socialgene.github.io

Installation with pip

pip install socialgene

Create conda environment and install python package inside

git clone https://github.com/socialgene/sgpy.git
cd sgpy
make create_conda

Build Python package from source

git clone https://github.com/socialgene/sgpy.git
cd sgpy
make install_python

Run all tests

git clone https://github.com/socialgene/sgpy.git
cd sgpy
make run_ci

User-facing classes

SocialGene()

This is the main class that most other user-facing classes should/do inherit from

FindMyBGC()

SingleProteinSearch()

Common example use cases

Starting with a single input protein and

• want to compare it against all other proteins in the Neo4j database

Starting with a set of proteins (BGC) and

• want to compare against all other proteins in the Neo4j database

Other

Most of the the classes that describe the structure of SocialGene() (e.g. proteins, domains, loci) live in socialgene/src/socialgene/classes/molbio.py