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  {
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   "execution_count": 1,
   "id": "28438480",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:24:13.965460Z",
     "iopub.status.busy": "2025-03-25T06:24:13.965038Z",
     "iopub.status.idle": "2025-03-25T06:24:14.135388Z",
     "shell.execute_reply": "2025-03-25T06:24:14.134944Z"
    }
   },
   "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 = \"Allergies\"\n",
    "cohort = \"GSE84046\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Allergies\"\n",
    "in_cohort_dir = \"../../input/GEO/Allergies/GSE84046\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Allergies/GSE84046.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Allergies/gene_data/GSE84046.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Allergies/clinical_data/GSE84046.csv\"\n",
    "json_path = \"../../output/preprocess/Allergies/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6c07446e",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "1bdb6e07",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "80e2c6e4",
   "metadata": {},
   "source": [
    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "605b6ca5",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "e84179ec",
   "metadata": {},
   "source": [
    "### Step 3: Gene Data Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14e4f3fc",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "54ca2046",
   "metadata": {},
   "source": [
    "### Step 4: Gene Identifier Review"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8bc34a43",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "9099408d",
   "metadata": {},
   "source": [
    "### Step 5: Gene Annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "276f5f90",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "72c2c0b0",
   "metadata": {},
   "source": [
    "### Step 6: Gene Identifier Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5f50276e",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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