Local Flask backend prototype for genomic file handling, exploration, and analysis.
This project is an early-stage backend used to experiment with bioinformatics workflows — specifically, parsing FASTA files, inspecting chromosome sequences, and performing small-scale analyses like substring matches or region extractions.
It’s not production-ready and currently serves as a functional scaffold for future work in genome data pipelines and bioinformatics backend design.
- Upload & parse FASTA files using Biopython utilities
- Store metadata for uploaded files in an SQLite dev database
- Extract regions or summarize sequences
- Run substring / motif matches against genome data
- Compute reverse complements and related sequence utilities
Routes render templates for quick local testing and exploration.
| Layer | Tool |
|---|---|
| Framework | Flask |
| Language | Python 3.10+ |
| DB | SQLite (SQLAlchemy ORM) |
| Utilities | Biopython |
| Templates | Jinja2 |
| Server | Werkzeug (Flask dev server) |
- app/ – main application package
- __init__.py – initializes the app factory
- routes/ – contains all route blueprints
- auth_routes.py – handles upload, parsing, and analysis endpoints
- models/ – defines ORM models such as
FileRecord - utils/ – helper functions for parsing, validation, and sequence operations
- templates/ – HTML templates (
upload.html,summary.html, etc.) - db.py – SQLAlchemy database configuration
- myFlaskApp.py – application factory (
create_app)
- requirements.txt – Python dependencies
- README.md – project documentation
git clone https://github.com/pguardado/genome_server.git
cd genome_server
python3 -m venv env
source env/bin/activate
pip install -U pip setuptools wheel
[ -f requirements.txt ] && pip install -r requirements.txt