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Getting Started

Requirements

  • Python 3.10+

Installation

pip install factorforge-cds

For development:

git clone https://github.com/eijex/factorforge-cds.git
cd factorforge
pip install -e ".[dev]"

Docker (local web app)

Run the full web interface locally — no data leaves your machine:

docker pull ghcr.io/eijex/factorforge-cds:latest
docker run -p 8080:8080 ghcr.io/eijex/factorforge-cds:latest

Then open http://localhost:8080.

Quick Start

CLI:

factorforge optimize my_protein.fasta -o output.fasta

Python API:

from factorforge.engines.profile.pipeline import OptimizationPipeline

pipeline = OptimizationPipeline(profile="balanced")
result = pipeline.run("MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEG...")
print(result.sequence)   # optimized CDS
print(result.metadata)   # CAI, GC%, scan results, domestication edits

Updating

pip:

pip install --upgrade factorforge-cds

Docker:

docker pull ghcr.io/eijex/factorforge-cds:latest

Git clone:

git pull origin main
pip install -e ".[dev]"

Check your installed version:

pip show factorforge-cds
# or
factorforge --version

Release notes: CHANGELOG