KEGG FASTA/HMM reconstruction: align model output with MATLAB RAVEN - #77
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Bring the protein-FASTA reconstruction (get_kegg_model_from_sequences)
into byte-parity with RAVEN develop3 getKEGGModelForOrganism:
- Prune each gene-backed reaction's kegg.orthology annotation to the KOs
that actually matched a gene, via a new prune_orthology flag on
assemble_model_from_ko_genes (off by default, so the organism-annotation
path keeps the full KO list). The order-preserving intersection also
avoids the rxnMiriams index misalignment in the MATLAB pruning.
- Default model.id to the FASTA stem when no model_id is given, so the
draft never inherits the reference model's id.
- Use a neutral reaction note ("Included by KEGG HMM reconstruction").
Note: the hmmsearch -Z parity item is handled on the MATLAB side (Python's
-Z <nprofiles> matches the hmmscan scale the K15 cut-offs were calibrated
against).
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Brings the protein-FASTA reconstruction path (
get_kegg_model_from_sequences)into byte-parity with RAVEN
develop3getKEGGModelForOrganism(HMM branch), sothe Python and MATLAB pipelines produce identical draft models from the same FASTA
and the shared raven-data artefacts.
Changes
kegg.orthologyto matched KOs.assemble_model_from_ko_genesgains aprune_orthologyflag (default off, so the organism-annotation path keeps the fullreference KO list); the FASTA path passes
True. Each gene-backed reaction'skegg.orthologyis restricted to the KOs that actually matched a gene, order-preserving— which also avoids the
rxnMiriamsindex misalignment in the MATLAB pruning.model.id. When nomodel_idis given, the draft's id defaults to the FASTAstem instead of inheriting the reference model's id (RAVEN always sets
model.id). Passmodel_idexplicitly for byte-identical parity with a specific MATLABorganismID.Included by KEGG HMM reconstruction).No behaviour change to the organism-annotation path or to default
keepSpontaneous=trueruns;
assign_kosscoring/filters are unchanged.MATLAB counterpart
The remaining parity items are applied on RAVEN
develop3(separately): pass-Z <nprofiles>tohmmsearch(E-value scale the cut-offs are calibrated against),keep gene-supported spontaneous reactions under
keepSpontaneous=false, fix thekegg.orthologyprune alignment, sort grRule genes, and use the neutral note.Testing
Full suite: 829 passed, 4 skipped. Adds tests for the orthology prune and the
model.iddefault.