"GA4GH Variation Representation (VR) reference implementation (https://github.com/ga4gh/vr-python/)"
1. Install vr-python
The following instructions are for Ubuntu 18.04+ and MacOS. vr-python is unlikely to work on Windows due to dependencies.
git clone --recurse-submodules https://github.com/ga4gh/vr-python.git cd vr-python python3.7 -m venv venv/3.7 source venv/3.7/bin/activate pip install --upgrade pip setuptools pip install -e . pip install -e '.[dev,notebooks]'
(Python 3.5 and 3.6 should also work.)
2. Pull seqrepo data
Sequence data are required to normalize sequences and infer ga4gh sequence identifiers. The notebooks use SeqRepo. VR implementers may use SeqRepo or other data source.
Then, download seqrepo with:
sudo mkdir /usr/local/share/seqrepo sudo chown $USER:$USER /usr/local/share/seqrepo seqrepo pull
NOTE: This will download approximately 10GB of sequence data. See https://github.com/biocommons/biocommons.seqrepo/ for more information.
Running the Notebooks
Once installed as described above, type:
source venv/3.7/bin/activate jupyter notebook --notebook-dir notebooks/
A stand-alone security review has been performed on the specification itself. This implementation is offered as-is, and without any security guarantees. It will need an independent security review before it can be considered ready for use in security-critical applications. If you integrate this code into your application it is AT YOUR OWN RISK AND RESPONSIBILITY to arrange for a security audit.
Release history Release notifications
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size||File type||Python version||Upload date||Hashes|
|Filename, size ga4gh.vr-0.3.0-py2.py3-none-any.whl (17.9 kB)||File type Wheel||Python version py2.py3||Upload date||Hashes View hashes|
|Filename, size ga4gh.vr-0.3.0-py3.7.egg (29.4 kB)||File type Egg||Python version 3.7||Upload date||Hashes View hashes|
|Filename, size ga4gh.vr-0.3.0.tar.gz (16.8 MB)||File type Source||Python version None||Upload date||Hashes View hashes|
Hashes for ga4gh.vr-0.3.0-py2.py3-none-any.whl