Provide computable object representation and validation for gene fusions
Project description
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
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