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

Project details

Release history Release notifications | RSS feed

0.4.4

Sep 26, 2024

0.4.3

Sep 25, 2024

0.4.2

Aug 26, 2024

0.4.1

Aug 22, 2024

0.4.0

Aug 21, 2024

0.3.0

Aug 15, 2024

0.2.1 yanked

Aug 14, 2024

Reason this release was yanked:

Included breaking changes even though versioning indicated it was only a patch

0.2.0

Aug 2, 2024

0.1.0

Jul 10, 2024

0.0.30.dev1 pre-release

Sep 25, 2023

0.0.28.dev1 pre-release

Sep 14, 2023

0.0.28.dev0 pre-release

Aug 24, 2023

0.0.27

Jul 21, 2023

0.0.26

Jun 26, 2023

0.0.25

Nov 10, 2022

0.0.24

Nov 9, 2022

0.0.23

Sep 23, 2022

0.0.22

Sep 14, 2022

0.0.21

Jul 26, 2022

0.0.20

Jun 6, 2022

0.0.19

Jun 3, 2022

0.0.18

May 26, 2022

0.0.17

Mar 15, 2022

0.0.16

Jan 26, 2022

0.0.14

Nov 18, 2021

0.0.13

Nov 17, 2021

0.0.12

Oct 30, 2021

0.0.11

Oct 28, 2021

This version

0.0.10

Oct 26, 2021

0.0.9

Sep 30, 2021

0.0.8

Sep 19, 2021

0.0.7

Aug 31, 2021

0.0.6

Aug 31, 2021

0.0.5

Aug 26, 2021

0.0.4

Aug 19, 2021

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