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rnas.csv: list RNA species per network (deltasignal specs/100) - #125
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…nce entity a ReferenceRNASequence), written for every pathway like drugs.csv and pathogens.csv; changes no edge Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ts that chose an RNA member (the first variant build listed 2,393 RISC variants); test fails on the previous code Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Adds
rnas.csvto every pathway bundle, likedrugs.csvandpathogens.csv: the network nodes that ARE an RNA species (reference entity aReferenceRNASequence). Complex variants that merely chose an RNA member are not listed (by_member=False). It changes no edge.Why: deltasignal specs/100 (
DS_RNA_TWIN). A root copy of an RNA reads the copies transcription produces of it, because one mRNA is one pool however many nodes the network splits it into. Without that, TP53 in PIP3 only raised a transcribed PTEN mRNA copy that feeds 12 miRNA complexes, so TP53's effect on AKT inverted.Measured (variant build
20261023-2341_135af3c_rna2, solver 61cdb8a):DS_RNA_TWIN=onvs control: curator tuning +28 (28 fixed / 0 broken), experimental +4 (4 / 0), held-out 0.Adopted by Adam 2026-10-24. Once this is merged, canonical is rebuilt from main and the solver default flips to
on.Tests:
get_rna_entities,export_rnas, and the bundle file list. The test fails on the previous code, which listed RISC variants.🤖 Generated with Claude Code