# Selected settings example, not an options menu or an approved laboratory SOP.
# design_mode: baseline_1dp | paired_3dp (3DP needs structure_settings and an uploaded file).
# rules: HARD_FAIL | WARNING | INFORMATIONAL | IGNORE
# review_policy: REQUIRED | PREFERRED | IGNORE
# FactorForge Conservative Sequence Policy Example (Default Baseline)
# This is an illustrative in-silico template
# ==============================================================================
# FactorForge's default sequence policy is configured as an intentionally
# conservative pre-synthesis baseline to flag sequence features for computational review.
# These checks do not establish synthesis acceptance or biological safety. We recommend customizing these settings or uploading your lab's own
# SOP (.yaml) to match your specific assembly and expression protocols.
# ==============================================================================
$schema: factorforge-sop-v1
profile_id: example_conservative_plant_expression
sop_name: "FactorForge Conservative Sequence Policy Example"
version: 1.2.0
author: Eijex
status: EXAMPLE_TEMPLATE
derived_from: "FactorForge default conservative pre-synthesis baseline; precautionary plant expression heuristics"
scope_note: "Conservative in-silico pre-synthesis baseline. Custom laboratory SOP configuration is recommended."
default_enforcement: IGNORE
unknown_rule_policy: ERROR

rules:
  assembly.type_iis.bsai.v1: HARD_FAIL
  assembly.type_iis.bpii.v1: HARD_FAIL
  assembly.type_iis.bsmbi.v1: HARD_FAIL
  rna.cryptic_splice.v1: WARNING
  rna.polya_motifs.v1: WARNING
  rna.au_rich_elements.v1: WARNING
  synthesis.gc_extremes.v1: WARNING
  policy.synthesis.homopolymer.v1: WARNING
  policy.initiation_mfe.v1: WARNING

workflow:
  design_method: dp_v2_1_1
  codon_policy: plantform_balanced_codon_v1
  watermark: false
  comparison_methods: [high_cai, gc_target, assembly_friendly]
  sequence_requirements:
    reproducibility_seed: null
    kozak_optimization: false
    suppress_tpa: false
    type_iis_enzymes: [BsaI, BpiI, BsmBI]
    custom_restriction_sites: []
    moclo_template: false
  review_policy:
    cai: PREFERRED
    overall_gc: PREFERRED
    local_gc: PREFERRED
    type_iis: REQUIRED
    repeats: PREFERRED
    homopolymers: PREFERRED
    forbidden_motifs: PREFERRED