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+++ b/demo/run_magma.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Run MAGMA on KGWAS Sumstats to get gene-based p-values\n",
+    "Given the local bfile where it stores the genotype data, you can run MAGMA to get gene-based p-values. Here is an example code to run it assuming you have (1) saved a trained model under `./data/model/test` (2) downloaded magma executable from [here](https://cncr.nl/research/magma/) (3) have a genotype file for your cohort"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "All required data files are present.\n",
+      "--loading KG---\n",
+      "--using enformer SNP embedding--\n",
+      "--using random go embedding--\n",
+      "--using ESM gene embedding--\n",
+      "Loading example GWAS file...\n",
+      "Example file already exists locally.\n",
+      "Loading GWAS file from ./data/biochemistry_Creatinine_fastgwa_full_10000_1.fastGWA...\n",
+      "Using ldsc weight...\n",
+      "ldsc_weight mean:  0.9999999999999993\n",
+      "Annotation file already exists locally.\n",
+      "MAGMA command executed successfully.\n",
+      "Output: Welcome to MAGMA v1.10 (linux)\n",
+      "Using flags:\n",
+      "\t--bfile /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1\n",
+      "\t--gene-annot ./data/gene_annotation.genes.annot\n",
+      "\t--pval ./data//model_pred/new_experiments/test_magma_format.csv N=9988\n",
+      "\t--out ./data//model_pred/new_experiments/test_magma_out\n",
+      "\n",
+      "Start time is 21:07:31, Monday 25 Nov 2024\n",
+      "\n",
+      "Loading PLINK-format data...\n",
+      "Reading file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.fam... 48769 individuals read\n",
+      "Reading file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.bim... 784256 SNPs read\n",
+      "Preparing file /dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1.bed... \n",
+      "\n",
+      "Reading SNP p-values from file ./data//model_pred/new_experiments/test_magma_format.csv... \n",
+      "\tdetected 2 variables in file\n",
+      "\tusing variable: SNP (SNP id)\n",
+      "\tusing variable: P (p-value)\n",
+      "\tread 542759 lines from file, containing valid SNP p-values for 542758 SNPs in data (100% of lines, 69.21% of SNPs in data)\n",
+      "Loading gene annotation from file ./data/gene_annotation.genes.annot... \n",
+      "\t17919 gene definitions read from file\n",
+      "\tfound 16637 genes containing valid SNPs in genotype data\n",
+      "\n",
+      "\n",
+      "Starting gene analysis... \n",
+      "\tusing model: SNPwise-mean\n",
+      "\tengaging automatic 'big-data' mode\n",
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+      "\tprocessed genes: 16600 (99.8%)     \n",
+      "\tprocessed genes: 16632 (100%)     \n",
+      "                                                                                                                   \n",
+      "\twriting gene analysis results to file ./data//model_pred/new_experiments/test_magma_out.genes.out\n",
+      "\twriting intermediate output to file ./data//model_pred/new_experiments/test_magma_out.genes.raw\n",
+      "\n",
+      "\n",
+      "End time is 21:34:07, Monday 25 Nov 2024 (elapsed: 00:26:36)\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "import sys\n",
+    "sys.path.append('../')\n",
+    "from kgwas import KGWAS, KGWAS_Data\n",
+    "data = KGWAS_Data(data_path = './data/')\n",
+    "data.load_kg()\n",
+    "\n",
+    "data.load_external_gwas(example_file = True)\n",
+    "data.process_gwas_file()\n",
+    "data.prepare_split()\n",
+    "\n",
+    "run = KGWAS(data, device = 'cuda:7', exp_name = 'test')\n",
+    "run.load_pretrained('./data/model/test')\n",
+    "run.run_magma(path_to_magma = \"/dfs/user/kexinh/ggwas/magma\", bfile = \"/dfs/project/datasets/20220524-ukbiobank/data/genetics/ukb_sample_0.1\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Here is an example output of the MAGMA run:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>GENE</th>\n",
+       "      <th>CHR</th>\n",
+       "      <th>START</th>\n",
+       "      <th>STOP</th>\n",
+       "      <th>NSNPS</th>\n",
+       "      <th>NPARAM</th>\n",
+       "      <th>N</th>\n",
+       "      <th>ZSTAT</th>\n",
+       "      <th>P</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>148398</td>\n",
+       "      <td>1</td>\n",
+       "      <td>859993</td>\n",
+       "      <td>879961</td>\n",
+       "      <td>6</td>\n",
+       "      <td>4</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>-1.10670</td>\n",
+       "      <td>0.865800</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>26155</td>\n",
+       "      <td>1</td>\n",
+       "      <td>879583</td>\n",
+       "      <td>894679</td>\n",
+       "      <td>9</td>\n",
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+       "      <td>9988</td>\n",
+       "      <td>0.36490</td>\n",
+       "      <td>0.357590</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>339451</td>\n",
+       "      <td>1</td>\n",
+       "      <td>895967</td>\n",
+       "      <td>901099</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>1.40540</td>\n",
+       "      <td>0.079955</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>84069</td>\n",
+       "      <td>1</td>\n",
+       "      <td>901872</td>\n",
+       "      <td>910488</td>\n",
+       "      <td>3</td>\n",
+       "      <td>2</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>1.56410</td>\n",
+       "      <td>0.058896</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>84808</td>\n",
+       "      <td>1</td>\n",
+       "      <td>910579</td>\n",
+       "      <td>917473</td>\n",
+       "      <td>2</td>\n",
+       "      <td>1</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>1.25460</td>\n",
+       "      <td>0.104820</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16632</th>\n",
+       "      <td>23542</td>\n",
+       "      <td>22</td>\n",
+       "      <td>51039131</td>\n",
+       "      <td>51049979</td>\n",
+       "      <td>3</td>\n",
+       "      <td>2</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>1.15830</td>\n",
+       "      <td>0.123360</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16633</th>\n",
+       "      <td>410</td>\n",
+       "      <td>22</td>\n",
+       "      <td>51061182</td>\n",
+       "      <td>51066601</td>\n",
+       "      <td>9</td>\n",
+       "      <td>5</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>-0.65834</td>\n",
+       "      <td>0.744840</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16634</th>\n",
+       "      <td>85358</td>\n",
+       "      <td>22</td>\n",
+       "      <td>51113070</td>\n",
+       "      <td>51171640</td>\n",
+       "      <td>41</td>\n",
+       "      <td>15</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>-1.18500</td>\n",
+       "      <td>0.881990</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16635</th>\n",
+       "      <td>101928892</td>\n",
+       "      <td>22</td>\n",
+       "      <td>51123086</td>\n",
+       "      <td>51125473</td>\n",
+       "      <td>2</td>\n",
+       "      <td>1</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>-0.14590</td>\n",
+       "      <td>0.558000</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>16636</th>\n",
+       "      <td>49</td>\n",
+       "      <td>22</td>\n",
+       "      <td>51176652</td>\n",
+       "      <td>51183727</td>\n",
+       "      <td>1</td>\n",
+       "      <td>1</td>\n",
+       "      <td>9988</td>\n",
+       "      <td>-0.42425</td>\n",
+       "      <td>0.664310</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>16637 rows × 9 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "            GENE  CHR     START      STOP  NSNPS  NPARAM     N    ZSTAT  \\\n",
+       "0         148398    1    859993    879961      6       4  9988 -1.10670   \n",
+       "1          26155    1    879583    894679      9       4  9988  0.36490   \n",
+       "2         339451    1    895967    901099      1       1  9988  1.40540   \n",
+       "3          84069    1    901872    910488      3       2  9988  1.56410   \n",
+       "4          84808    1    910579    917473      2       1  9988  1.25460   \n",
+       "...          ...  ...       ...       ...    ...     ...   ...      ...   \n",
+       "16632      23542   22  51039131  51049979      3       2  9988  1.15830   \n",
+       "16633        410   22  51061182  51066601      9       5  9988 -0.65834   \n",
+       "16634      85358   22  51113070  51171640     41      15  9988 -1.18500   \n",
+       "16635  101928892   22  51123086  51125473      2       1  9988 -0.14590   \n",
+       "16636         49   22  51176652  51183727      1       1  9988 -0.42425   \n",
+       "\n",
+       "              P  \n",
+       "0      0.865800  \n",
+       "1      0.357590  \n",
+       "2      0.079955  \n",
+       "3      0.058896  \n",
+       "4      0.104820  \n",
+       "...         ...  \n",
+       "16632  0.123360  \n",
+       "16633  0.744840  \n",
+       "16634  0.881990  \n",
+       "16635  0.558000  \n",
+       "16636  0.664310  \n",
+       "\n",
+       "[16637 rows x 9 columns]"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import pandas as pd\n",
+    "pd.read_csv('./data/model_pred/new_experiments/test_magma_out.genes.out', sep = '\\s+')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "To know which gene this gene id maps to, you can use the following file:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>0</th>\n",
+       "      <th>1</th>\n",
+       "      <th>2</th>\n",
+       "      <th>3</th>\n",
+       "      <th>4</th>\n",
+       "      <th>5</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>79501</td>\n",
+       "      <td>1</td>\n",
+       "      <td>69091</td>\n",
+       "      <td>70008</td>\n",
+       "      <td>+</td>\n",
+       "      <td>OR4F5</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>100996442</td>\n",
+       "      <td>1</td>\n",
+       "      <td>142447</td>\n",
+       "      <td>174392</td>\n",
+       "      <td>-</td>\n",
+       "      <td>LOC100996442</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>729759</td>\n",
+       "      <td>1</td>\n",
+       "      <td>367659</td>\n",
+       "      <td>368597</td>\n",
+       "      <td>+</td>\n",
+       "      <td>OR4F29</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>81399</td>\n",
+       "      <td>1</td>\n",
+       "      <td>621096</td>\n",
+       "      <td>622034</td>\n",
+       "      <td>-</td>\n",
+       "      <td>OR4F16</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>148398</td>\n",
+       "      <td>1</td>\n",
+       "      <td>859993</td>\n",
+       "      <td>879961</td>\n",
+       "      <td>+</td>\n",
+       "      <td>SAMD11</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19422</th>\n",
+       "      <td>442867</td>\n",
+       "      <td>Y</td>\n",
+       "      <td>26764151</td>\n",
+       "      <td>26785354</td>\n",
+       "      <td>+</td>\n",
+       "      <td>BPY2B</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19423</th>\n",
+       "      <td>57054</td>\n",
+       "      <td>Y</td>\n",
+       "      <td>26909216</td>\n",
+       "      <td>26959639</td>\n",
+       "      <td>-</td>\n",
+       "      <td>DAZ3</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19424</th>\n",
+       "      <td>57135</td>\n",
+       "      <td>Y</td>\n",
+       "      <td>26979967</td>\n",
+       "      <td>27053187</td>\n",
+       "      <td>+</td>\n",
+       "      <td>DAZ4</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19425</th>\n",
+       "      <td>442868</td>\n",
+       "      <td>Y</td>\n",
+       "      <td>27177048</td>\n",
+       "      <td>27198251</td>\n",
+       "      <td>-</td>\n",
+       "      <td>BPY2C</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>19426</th>\n",
+       "      <td>9085</td>\n",
+       "      <td>Y</td>\n",
+       "      <td>27768264</td>\n",
+       "      <td>27771049</td>\n",
+       "      <td>+</td>\n",
+       "      <td>CDY1</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>19427 rows × 6 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "               0  1         2         3  4             5\n",
+       "0          79501  1     69091     70008  +         OR4F5\n",
+       "1      100996442  1    142447    174392  -  LOC100996442\n",
+       "2         729759  1    367659    368597  +        OR4F29\n",
+       "3          81399  1    621096    622034  -        OR4F16\n",
+       "4         148398  1    859993    879961  +        SAMD11\n",
+       "...          ... ..       ...       ... ..           ...\n",
+       "19422     442867  Y  26764151  26785354  +         BPY2B\n",
+       "19423      57054  Y  26909216  26959639  -          DAZ3\n",
+       "19424      57135  Y  26979967  27053187  +          DAZ4\n",
+       "19425     442868  Y  27177048  27198251  -         BPY2C\n",
+       "19426       9085  Y  27768264  27771049  +          CDY1\n",
+       "\n",
+       "[19427 rows x 6 columns]"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pd.read_csv('./data/misc_data/NCBI37.3.gene.loc', sep = '\\t', header = None)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "a100_env",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}