{
 "cells": [
  {
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   "execution_count": 1,
   "id": "b2d7f028",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:23:03.100419Z",
     "iopub.status.busy": "2025-03-25T06:23:03.100249Z",
     "iopub.status.idle": "2025-03-25T06:23:03.267937Z",
     "shell.execute_reply": "2025-03-25T06:23:03.267490Z"
    }
   },
   "outputs": [],
   "source": [
    "import sys\n",
    "import os\n",
    "sys.path.append(os.path.abspath(os.path.join(os.getcwd(), '../..')))\n",
    "\n",
    "# Path Configuration\n",
    "from tools.preprocess import *\n",
    "\n",
    "# Processing context\n",
    "trait = \"Age-Related_Macular_Degeneration\"\n",
    "cohort = \"GSE43176\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Age-Related_Macular_Degeneration\"\n",
    "in_cohort_dir = \"../../input/GEO/Age-Related_Macular_Degeneration/GSE43176\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/GSE43176.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/gene_data/GSE43176.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/clinical_data/GSE43176.csv\"\n",
    "json_path = \"../../output/preprocess/Age-Related_Macular_Degeneration/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b413344c",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7d073588",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "51d91740",
   "metadata": {},
   "source": [
    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e707e3ec",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "56131f70",
   "metadata": {},
   "source": [
    "### Step 3: Gene Data Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ccc6592f",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "8de7fc52",
   "metadata": {},
   "source": [
    "### Step 4: Gene Identifier Review"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "80575a55",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "c7836aca",
   "metadata": {},
   "source": [
    "### Step 5: Gene Annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "450d95ef",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "dcdde944",
   "metadata": {},
   "source": [
    "### Step 6: Gene Identifier Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e5ab43ff",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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