{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "91f6a8b9",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2025-03-25T06:23:04.077336Z",
     "iopub.status.busy": "2025-03-25T06:23:04.076941Z",
     "iopub.status.idle": "2025-03-25T06:23:04.242353Z",
     "shell.execute_reply": "2025-03-25T06:23:04.242021Z"
    }
   },
   "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 = \"GSE45485\"\n",
    "\n",
    "# Input paths\n",
    "in_trait_dir = \"../../input/GEO/Age-Related_Macular_Degeneration\"\n",
    "in_cohort_dir = \"../../input/GEO/Age-Related_Macular_Degeneration/GSE45485\"\n",
    "\n",
    "# Output paths\n",
    "out_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/GSE45485.csv\"\n",
    "out_gene_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/gene_data/GSE45485.csv\"\n",
    "out_clinical_data_file = \"../../output/preprocess/Age-Related_Macular_Degeneration/clinical_data/GSE45485.csv\"\n",
    "json_path = \"../../output/preprocess/Age-Related_Macular_Degeneration/cohort_info.json\"\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3754622e",
   "metadata": {},
   "source": [
    "### Step 1: Initial Data Loading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "37b829b6",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "ba7bbf78",
   "metadata": {},
   "source": [
    "### Step 2: Dataset Analysis and Clinical Feature Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "2315d845",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "6b9f3ff8",
   "metadata": {},
   "source": [
    "### Step 3: Gene Data Extraction"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "62ef0b19",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "5f0adeb4",
   "metadata": {},
   "source": [
    "### Step 4: Gene Identifier Review"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d8e9e21e",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "7298260c",
   "metadata": {},
   "source": [
    "### Step 5: Gene Annotation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4b4e2c92",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "eabfd56e",
   "metadata": {},
   "source": [
    "### Step 6: Gene Identifier Mapping"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3a2d67d9",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.16"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}