add_database.md

Add new fusion database

1. Implement a new database in fusion_report/data/{database}.py. You have to include a method get_all_fusions() which should return list of all gene fusion in your database in format GENEA--GENEB.

"""Test Database"""
import re
from typing import List

from fusion_report.common.db import Db
from fusion_report.common.singleton import Singleton


class Test(Db, metaclass=Singleton):
    """Implementation of Test Database. All core functionality is handled by parent class."""

    def __init__(self, path: str) -> None:
        super().__init__(path, 'Test', 'Test.sql')

    def get_all_fusions(self) -> List[str]:
        """Returns all fusions from database."""
        query: str = '''SELECT DISTINCT XYZ FROM XYZ'''
        res = self.select(query)

        return res['fusions']

2. Create database schema in fusion_report/schema/{database.sql}. This is a SQL script which defines a structure of your database.
3. Update enrich() function in fusion_report/app.py

local_fusions: Dict[str, List[str]] = {
    FusionGDB2(path).name: FusionGDB2(path).get_all_fusions(),
    MitelmanDB(path).name: MitelmanDB(path).get_all_fusions(),
    CosmicDB(path).name: CosmicDB(path).get_all_fusions(),
    TestDB(path).name: TestDB(path).get_all_fusions() # add your database here
}

4. Give yourself a high five for awesome job! 👍