fusor 0.0.20

Provide computable object representation and validation for gene fusions

FUSOR

FUSOR (FUSion Object Representation) provides modeling and validation tools for representing gene fusions in a flexible, computable structure.

Installation

To install FUSOR:

pip install fusor

For a development install, we recommend using Pipenv. See the pipenv docs for direction on installing pipenv in your compute environment.

Once installed, from the project root dir, just run:

pipenv shell
pipenv lock && pipenv sync

MacOS Errors

If you encounter errors, try the following:

export SYSTEM_VERSION_COMPAT=1
pipenv lock && pipenv sync

Data Downloads

SeqRepo

FUSOR relies on seqrepo, which you must download yourself.

From the root directory:

pip install seqrepo
sudo mkdir /usr/local/share/seqrepo
sudo chown $USER /usr/local/share/seqrepo
seqrepo pull -i 2021-01-29

Gene Normalizer

FUSOR also relies on data from gene-normalizer's DynamoDB tables, which you must download yourself. See the README for deploying the database.

Init coding style tests

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

• Check code style
• Check for added large files
• Detect AWS Credentials
• Detect Private Key

Before first commit run:

pre-commit install

Running unit tests

Running unit tests is as easy as pytest.

pipenv run pytest