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v1.0.6: validate on the export's inputs, results for bugphyzzExports v1.1.0 - #7
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…k run_all.sh export_inputs.R drops what bugphyzzExports drops before ASR: the 2020 Bergey's scrape (ADR 0002) and sources/sheet_overrides.tsv (ADR 0005). Co-authored-by: Claude Code <noreply@anthropic.com>
Co-authored-by: Claude Code <noreply@anthropic.com>
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I found nothing worth raising. This repo is a validation-scripts repo, not an R package: it has no DESCRIPTION, NAMESPACE or man/, so the Bioconductor export-documentation checks don't apply. The new |
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export_inputs.R, called by the three prediction scripts afterphysiologies(), drops the rows the bugphyzzExports export drops: the 2020 Bergey's scrape (bugphyzzExports ADR 0002) andsources/sheet_overrides.tsv(ADR 0005). It reads the rules from a bugphyzzExports clone (BUGPHYZZEXPORTS_DIR, default~/git/bugphyzzExports).02_validation_binary.shlooked forbiofilm_forming; the prediction step writesbiofilm_formation.run_all.shwas only on supermicro; now tracked.all: 11 physiology/value pairs pass the export thresholds (10 in v1.0.5); COGEM 3 crosses 0.7; coding genes, genome size and G+C content improve. host-associated (only TRUE values now) and biofilm formation (too little of the tree) are not validated.Before running, refresh the cache with
bugphyzz::physiologies("all", forceDownload = TRUE); otherwisephysiologies()reuses older downloaded sources.Drafted with Claude Code.