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De-novo reconstruction

Two independent routes build a draft model for an organism that has no curated GEM yet.

Homology — {mod}raven_toolbox.reconstruction.homology

Transfer reactions from a curated template model to the target organism via an ortholog search.

  1. Run the search (or bring your own table): {func}raven_toolbox.reconstruction.homology.run_blast / {func}raven_toolbox.reconstruction.homology.run_diamond, then {func}raven_toolbox.reconstruction.homology.make_ortholog_hits to get the canonical gene × gene hits DataFrame (bidirectional / best-hits-only policies supported).
  2. Draft the model: {func}raven_toolbox.reconstruction.homology.get_model_from_homology — AST-based GPR rewrite, configurable complex policy, returns a {class}cobra.Model (plus a HomologyResult).

The external aligners are resolved from the pinned binary registry ({mod}raven_toolbox.binaries).

KEGG — {mod}raven_toolbox.reconstruction.kegg

Draft directly from KEGG orthology, either for a KEGG-listed species or from your own protein FASTA via HMM search.

  • KEGG species (no FASTA): {func}raven_toolbox.reconstruction.kegg.get_kegg_model_for_organism.
  • Your sequences (HMM search): {func}raven_toolbox.reconstruction.kegg.assign_kos → {func}raven_toolbox.reconstruction.kegg.get_kegg_model_from_sequences. The HMM cut-off defaults are calibrated in the KEGG HMM cut-off study.

The KEGG artefact bundle (KO tables, reference model, HMM libraries) is fetched by {mod}raven_toolbox.data; building and publishing it is a maintainer task — see Maintaining KEGG data and the KEGG data format.

After drafting, fill connectivity gaps with the gap-filling guide.