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{
"cells": [
{
"cell_type": "code",
"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": []
}
],
"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
}
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