Requirements and setup
The supplied scripts use Python 3 standard-library imports. This is not a self-contained rerunnable bundle: original relative or absolute paths, saved inputs and writable output locations need setup. Fetch scripts use live APIs, whose later responses may differ. Several scripts perform work at top level when run or imported. No raw API payloads or credentials are included.
Pharmacogenomics
Attention–coverage subset checks
Reads a gene-reference table and saved publication counts, then writes robustness findings and JSON.
Requires the original relative data/processed/gene_reference.csv and hypotheses/raw_pubmed.json inputs; writes beside the script.
Download original robustness.py · Related published note/results
hypotheses/robustness.py · 3511 bytes
SHA-256 9f44b32b948104766348bb82d18efab844b23d3cf1e0006464a7022c843f36d1
Curation and publication association script
Fetches CPIC change-log records and combines them with gene coverage and saved publication counts.
Needs the original gene-reference CSV, raw_pubmed.json, network access to the CPIC API, and a writable output directory.
Download original mediation.py · Related published note/results
hypotheses/mediation.py · 4080 bytes
SHA-256 8926315ed405ec1a43fbdfee251182d5b3c872b61aae7b204f32bb9ac66cb800
Screening
Indicator deduplication and screening output
Reads the saved World Bank object and writes the supplied deduplicated result table and findings.
Requires raw_worldbank.json beside the script; produces results_deduped.csv and FINDINGS_DEDUPED.md. The raw input is not in this supplement.
Download original dedupe.py · Related published note/results
screening/dedupe.py · 3145 bytes
SHA-256 212628c8a83935c94756d06ba0857a01ca1d3a1db5e0e16abbfb2b6042713582
World Bank note
World Bank context-data fetcher
Retrieves the note’s three health indicators for the specified countries and writes raw JSON and a tidy CSV.
Uses live World Bank API v2 and an absolute OUT_DIR from the original workspace; adjust the output path before any local use.
Download original fetch.py · Related published note/results
notes/_repro/worldbank-health/fetch.py · 6844 bytes
SHA-256 5f9f2d334ca3046f5abc4cbbe3ef6b9668dfcbd7ad19ffe555e2e5befa0c2077
FAERS note
FAERS reaction-term fetcher
Retrieves the original top-five reaction-term responses for the note’s named drugs.
Uses the live openFDA API and an absolute OUT path. The source contains top-level fetch/write operations.
Download original fetch.py · Related published note/results
notes/_scripts/faers-adverse-events/fetch.py · 3295 bytes
SHA-256 1e3c4e1022678c03c16637daf365d40b748ce3590b67e6ca1e1a74df73f33fa0
FAERS saved-response derivation
Reads the note’s saved raw responses and writes its CSV and descriptive output.
Requires raw.json at the source’s absolute OUT location and writes data.csv there; this supplement does not include the raw payload.
Download original derive.py · Related published note/results
notes/_scripts/faers-adverse-events/derive.py · 2609 bytes
SHA-256 83b12f6e80a0f87dfead389726405dc34a956c9fcea210a5195b01346211de3d
Already available source code
These five candidates match previously published files exactly and are linked here without duplicate upload.