CLI Reference

Commands

`factorforge optimize`

Optimize a protein sequence into a host-compatible CDS (N. benthamiana by default; --host by2 for Tobacco BY-2).

factorforge optimize input.fasta -o output.fasta

Options:

Option	Default	Description
`--engine`, `-e`	`dp`	Engine: `dp` (feasibility) or `profile` (rule/profile)
`--profile`, `-p`	`balanced`	Optimization profile
`--objective`	`feasibility_best`	DP objective
`--gc-min`	`55`	Minimum GC% target
`--gc-max`	`65`	Maximum GC% target
`--format`	`fasta`	Output format: `fasta` or `genbank`
`--host`	`nbenthamiana`	Expression host: `nbenthamiana` or `by2` (Tobacco BY-2)
`--reference-id`	—	Expert/research codon-reference ID; checksum-validated and not recommended for production defaults
`--compare-profiles`	—	Comma-separated profiles to compare (e.g. `balanced,high_cai,gc_target`)
`--scan-mode`	`full`	Rule scan: `full` or `fast`
`--template`	—	MoClo construct template

--reference-id is an expert/research path for replaying or comparing packaged codon-reference tables from data/reference/reference_policy_manifest.json. Each selected table is checksum-validated before use. Non-production tiers continue after printing a warning that quotes the manifest claim boundary; they are not production recommendations. Public REST API reference overrides remain unsupported.

Profile-engine FASTA files written with --output start with a self-describing metadata header:

>id|engine=profile|profile=<profile>|cai=<value>|gc=<value>|score=<value>

Profile FASTA headers intentionally omit objective; objective is a DP engine field, while profile output is identified by engine=profile and profile=<profile>.

API Endpoints

The web API (https://factorforge.eijex.com) exposes the following endpoints:

Endpoint	Description
`POST /api/optimize`	Single sequence optimization
`POST /api/optimize/compare`	Compare multiple profiles side-by-side
`POST /api/optimize/batch`	Optimize up to 20 sequences in one request

For AI agent access, use Eijex MCP which wraps these endpoints as MCP tools.

`factorforge list-engines`

List all available optimization engines.

factorforge list-engines

Examples

# Default (DP feasibility engine)
factorforge optimize input.fasta -o output.fasta

# Profile engine
factorforge optimize input.fasta -e profile -p balanced -o output.fasta

# GenBank output with MoClo template
factorforge optimize input.fasta -e profile -p balanced \
  --template standard_expression -o output.gb --format genbank

# Custom GC target range
factorforge optimize input.fasta --gc-min 45 --gc-max 60 -o output.fasta

# Fast scan (skip rare codon run detection)
factorforge optimize input.fasta --scan-mode fast -o output.fasta

# Expert/research reference replay or comparison
factorforge optimize input.fasta --reference-id nbenthamiana_qld183_v103