APIs

A monorepo of Python FastAPI projects — from a reusable production starter template to a domain-specific bioinformatics service.

Projects

template/ — FastAPI Starter Template

A production-minded, reusable FastAPI starter kit designed to bootstrap new API services with minimal setup. Copy the folder, rename a few values, and start building.

Highlights:

• Multi-file app architecture following FastAPI's "bigger applications" pattern
• Versioned routing (/api/v1), health & readiness endpoints
• Centralized error handling, structured logging, CORS middleware
• API key security example with X-API-Key dependency injection
• In-memory CRUD example for items (swap in a real DB when ready)
• Pydantic v2 schemas for all request and response shapes
• Docker + Docker Compose setup with proper layer caching
• Full test suite (pytest + httpx) with 89% coverage
• Code quality tooling: ruff, black, mypy
• Render deployment blueprint (render.yaml)
• Helper scripts in scripts/ for dev, test, lint, format, and Docker

📖 Read the template README →

bioAPI/ — Bioinformatics REST API

A production-ready FastAPI service for common bioinformatics workflows. Handles file parsing, sequence manipulation, format conversions, and mutation-aware consensus generation — natively in Python via Biopython.

Highlights:

• Sequence Utilities: reverse complement, transcribe, translate, GC content, k-mers, motif search
• File Statistics: upload FASTA, FASTQ, GenBank, BAM, VCF, GFF/GTF and get rich metadata
• Cross-file Extraction: GFF + FASTA overlay to slice genomic features by coordinates
• VCF Support: extract SNPs/INDELs, or inject variants into a reference FASTA for consensus generation
• Format Conversion: convert between standard bioinformatics file types
• Dockerized with pysam C-binding support, CORS, API key auth
• Auto-generated Swagger UI at /docs and ReDoc at /redoc

📖 Read the bioAPI README →

Tech Stack

Tool	Purpose
FastAPI	Web framework & OpenAPI docs
Pydantic v2	Data validation & settings
Uvicorn	ASGI server
Biopython	Bioinformatics operations (bioAPI)
pytest	Testing
ruff	Linting
black	Formatting
mypy	Static type checking
Docker	Containerization