vmc-python

VMC is the Variation Modelling Collaboration. The VMC's mission is to standardize the exchange of biological sequence variants among computer systems. The primary "products" of this effort are:

1. A terminology document defining core elements of the data model.
2. Machine-readable specifications for the data model.

This repository contains code to demonstrate the use fo the VMC data model.

NOTE: This project is in-progress.

git clone --recurse-submodules https://github.com/ga4gh/vmc-python.git
python3.6 -m venv venv/3.6
source venv/3.6/bin/activate
pip install --upgrade pip setuptools
pip install -e .
pip install -e '.[notebooks]'

git clone --recurse-submodules https://github.com/ga4gh/vmc-python.git
python3.7 -m venv venv/3.7
pip3 install --upgrade pip setuptools
cd vmc-python
pip3 install -e .
pip3 install -e '.[notebooks]'

You need a different kind of help.

seqrepo pull

Sequence data are required to normalize sequences and infer VMC sequence identifiers. The notebooks use SeqRepo. VMC implementers may use SeqRepo or other data source.

Once installed as described above, type:

source venv/3.6/bin/activate
jupyter notebook --notebook-dir notebooks/