Junior B.
b731478f5d
Set up the project skeleton per PLAN.md §4: - src/ package: identifiers, disease, drugs, scoring, provenance with pydantic schemas and confidence-tier logic (working); data-pull/compute functions stubbed per their build week - 5 starter notebooks (01-05) with PLAN-referenced steps - tests/test_scoring.py: tier-assignment tests pass; scoring reference test xfail until Week 3 - docs/: recovery_test_report, data_sources, known_limitations skeletons - pyproject.toml (requires-python >=3.11,<3.14), .gitignore, README - data/ tree preserved via .gitkeep; raw/processed/results gitignored Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
48 lines
1.3 KiB
Plaintext
48 lines
1.3 KiB
Plaintext
{
|
|
"cells": [
|
|
{
|
|
"cell_type": "markdown",
|
|
"metadata": {},
|
|
"source": [
|
|
"# 04 \u2014 Connectivity scoring\n",
|
|
"\n",
|
|
"Week 3 (PLAN.md \u00a76). CMap-style connectivity scoring of every drug against the sickle cell signature. Strongly negative connectivity = strong reversal = candidate.\n\nOutputs `data/results/ranked_candidates_v1.csv`. Also build the secondary mechanistically-weighted ranking. Document the gene-overlap count; mark signature-less drugs as 'not scored' rather than dropping them."
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"import sys\n",
|
|
"sys.path.insert(0, '..') # import the src package from notebooks/"
|
|
]
|
|
},
|
|
{
|
|
"cell_type": "code",
|
|
"execution_count": null,
|
|
"metadata": {},
|
|
"outputs": [],
|
|
"source": [
|
|
"from src import scoring\n",
|
|
"\n",
|
|
"# Load signature + drug profiles, then:\n",
|
|
"# ranking = scoring.rank_drugs(up, down, drug_profiles)\n",
|
|
"# scoring.persist_ranking(ranking) -> data/results/ranked_candidates_v1.csv"
|
|
]
|
|
}
|
|
],
|
|
"metadata": {
|
|
"kernelspec": {
|
|
"display_name": "Python 3",
|
|
"language": "python",
|
|
"name": "python3"
|
|
},
|
|
"language_info": {
|
|
"name": "python"
|
|
}
|
|
},
|
|
"nbformat": 4,
|
|
"nbformat_minor": 5
|
|
} |