{
 "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
}