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Architecture

Two diagrams. Open the SVGs directly — they are plain text and render in GitHub.

1. Pipeline — pipeline_DAG.svg

Three input modes (genome, protein, pangenome) converging on one shared spine:

00c pharokka → 01 phold → 02 FoldSeek → 03 compare → 04 curate → 05 output
                                          ↑                    → 06 phynteny → 07 integrate

Step 02 forks: 02d searches local FoldSeek databases, 02w uses the public search.foldseek.com API. Both produce identically shaped best_hit.csv / top3.csv, so everything downstream is unaffected by which one ran.

02w is experimental. The web API accepts structures only, so it needs an ESMFold folding step first (scripts/lib/esmfold_cache.py), and it is subject to server-side rate limits and timeouts. Use 02d for anything you intend to publish.

The FFAL lane (integration in progress)

The purple lane marks FoldFirstAskLater (FFAL), Hannelore Longin's structure-first annotation pipeline. FFAL can replace steps 01–02 entirely: it produces per-CDS structural hits, and an adapter reshapes them into what step 03 expects, so phageFACTor's curation runs on FFAL's evidence.

Status: working, not yet merged. Integration is in progress with the FFAL authors; the branch that carries it is dev-tanais on their repository. Nothing in this repo depends on FFAL — the lane is optional and the adapter lives outside this repo.

2. Scoring and curation — scoring_curation_DAG.svg

Where a FoldSeek hit is filtered, scored, ranked and finally named. The superscript numbers refer to the word-lists catalogued in code_lists.md. Prose version of the same logic: curation_gates.md.

Two things the diagram is meant to make obvious:

  1. The informativeness gate removes most hits, before any scoring happens.
  2. Trusted calls are never re-annotated. Only pharokka-hypothetical genes enter curation at all; a sequence-homology call is passed through untouched.