04 Project Structure

This project consists of several key directories and files, organized as follows:

1. docker/: Contains Docker-related files, including the Dockerfile, docker-compose.yml and snakemake related files.
   • snakemake/: Contains Snakefile, snakemake config file, and environment files for snakemake rules.
2. src/guidescanpy/: Contains the main source code for Guidescan.
   • commands/: Contains various command-line utilities for the project.
   • flask/: Contains the Flask application components.
     • core/: Class GenomeStructure is defined in genome.py, which contains the core code for the implementation of the query functionality.
     • blueprints/: Contains the blueprints for the Flask app.
     • templates/: Contains HTML templates.
     • db.py: The functions related to database operations and querying.
   • tasks/: Contains Celery tasks definitions.
   • config.json: The main configuration file for the project.
3. tests/: Contains pytest unit test files and test data files. @patch decorators helps prevent actual database communication.
4. pyproject.toml: The TOML configuration file for project metadata and dependencies.