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seqrepo pull -i 2021-01-29 # Replace with latest version using `seqrepo list-remote-instances` if outdated
If you get an error similar to the one below:
PermissionError: [Error 13] Permission denied: '/usr/local/share/seqrepo/2021-01-29._fkuefgd' -> '/usr/local/share/seqrepo/2021-01-29'
You will want to do the following:
(Might not be ._fkuefgd, so replace with your error message path)
sudo mv /usr/local/share/seqrepo/2021-01-29._fkuefgd /usr/local/share/seqrepo/2021-01-29
exit
UTA
FUSOR also uses Common Operations On Lots-of Sequences Tool (cool-seq-tool) which uses UTA as the underlying PostgreSQL database.
The following commands will likely need modification appropriate for the installation environment.
-
Install PostgreSQL
-
Create user and database.
$ createuser -U postgres uta_admin $ createuser -U postgres anonymous $ createdb -U postgres -O uta_admin uta -
To install locally (location does not matter):
export UTA_VERSION=uta_20210129.pgd.gz
curl -O http://dl.biocommons.org/uta/$UTA_VERSION
gzip -cdq ${UTA_VERSION} | grep -v "^REFRESH MATERIALIZED VIEW" | psql -h localhost -U uta_admin --echo-errors --single-transaction -v ON_ERROR_STOP=1 -d uta -p 5433
UTA Installation Issues
If you have trouble installing UTA, you can visit these two READMEs.
Connecting to the UTA database
To connect to the UTA database, you can use the default url (postgresql://uta_admin@localhost:5433/uta/uta_20210129). If you use the default url, you must either set the password using environment variable UTA_PASSWORD or setting the parameter db_pwd in the FUSOR class.
If you do not wish to use the default, you must set the environment variable UTA_DB_URL which has the format of driver://user:pass@host:port/database/schema.
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 Ruff and Black and checked prior to commit.
We use pre-commit to run conformance tests.
This performs checks for:
- Code style
- File endings
- Added large files
- AWS credentials
- Private keys
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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