Train ModelP0_AtacSeq-wChromatin.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "f8e937c5",
   "metadata": {},
   "source": [
    "# Train model using Mouse Brain dataset"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "df641d71",
   "metadata": {},
   "source": [
    "In this notebook, we're going to train our model using the Mouse Brain dataset (GSE60361). \n",
    "\n",
    "This assumes that you've made the graph using the ```Infer GRN.ipynb``` code."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "65a9a75a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Torch version: 1.8.0+cu111\n",
      "Cuda available: True\n",
      "Torch geometric version: 2.0.3\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import torch\n",
    "import torch_geometric\n",
    "from torch_geometric.data import Data, Dataset\n",
    "from tqdm import tqdm\n",
    "from datasets.datasetPatacseq import AtacSeqDataset\n",
    "from scipy.special import softmax\n",
    "%matplotlib inline\n",
    "import matplotlib.pyplot as plt\n",
    "from sklearn.manifold import TSNE\n",
    "from tqdm import tqdm\n",
    "from sklearn.metrics import (auc, precision_recall_curve, roc_auc_score,\n",
    "                             roc_curve)\n",
    "from statistics import mean"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "419e7c62",
   "metadata": {},
   "source": [
    "Load up the dataset. Read ```datasetMouseBrain.py``` on how the dataset was built. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "2da40b66",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 96185/96185 [01:24<00:00, 1140.67it/s]\n",
      "Processing...\n",
      "  4%|▎         | 190/5081 [47:19<20:18:07, 14.94s/it]\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_7791/1161080531.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mdataset\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mAtacSeqDataset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"/gpfs/data/rsingh47/hzaki1/atacseqdataP0Chromatin\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0matacseq\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/datasets/datasetPatacseq.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, root, transform, pre_transform, atacseq)\u001b[0m\n\u001b[1;32m    100\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcounts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcounts\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnormalize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    101\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 102\u001b[0;31m         \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mAtacSeqDataset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mroot\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtransform\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mpre_transform\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    103\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    104\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mproperty\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/torch_geometric/data/dataset.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, root, transform, pre_transform, pre_filter)\u001b[0m\n\u001b[1;32m     86\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     87\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;34m'process'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__class__\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__dict__\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 88\u001b[0;31m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_process\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     89\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     90\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mindices\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0mSequence\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/torch_geometric/data/dataset.py\u001b[0m in \u001b[0;36m_process\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    169\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    170\u001b[0m         \u001b[0mmakedirs\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprocessed_dir\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 171\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprocess\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    172\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    173\u001b[0m         \u001b[0mpath\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mosp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprocessed_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'pre_transform.pt'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/datasets/datasetPatacseq.py\u001b[0m in \u001b[0;36mprocess\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    150\u001b[0m                     \u001b[0mval\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    151\u001b[0m                     \u001b[0;32mfor\u001b[0m \u001b[0mregion\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mregionToGene\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mgene\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 152\u001b[0;31m                         \u001b[0mval\u001b[0m \u001b[0;34m+=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcounts\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mregion\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mrow\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    153\u001b[0m                     \u001b[0mnode_feats\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgeneToIndex\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mgene\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mval\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    154\u001b[0m                 \u001b[0mnode_feats\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_numpy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mexmatrix\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvalues\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/core/frame.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m   3422\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mis_hashable\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3423\u001b[0m             \u001b[0;31m# shortcut if the key is in columns\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3424\u001b[0;31m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_unique\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3425\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mMultiIndex\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   3426\u001b[0m                     \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_getitem_multilevel\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/core/indexes/base.py\u001b[0m in \u001b[0;36m__contains__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m   4535\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0mkind\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0minferred_type\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   4536\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4537\u001b[0;31m     \u001b[0;32mdef\u001b[0m \u001b[0m__contains__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mAny\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0mbool\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   4538\u001b[0m         \"\"\"\n\u001b[1;32m   4539\u001b[0m         \u001b[0mReturn\u001b[0m \u001b[0ma\u001b[0m \u001b[0mboolean\u001b[0m \u001b[0mindicating\u001b[0m \u001b[0mwhether\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mprovided\u001b[0m \u001b[0mkey\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "dataset = AtacSeqDataset(\"/gpfs/data/rsingh47/hzaki1/atacseqdataP0Chromatin\", atacseq=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fefcae56",
   "metadata": {},
   "outputs": [],
   "source": [
    "print()\n",
    "print(f'Dataset: {dataset}:')\n",
    "print('====================')\n",
    "print(f'Number of graphs: {len(dataset)}')\n",
    "print(f'Number of features: {dataset.num_features}')\n",
    "\n",
    "data = dataset[0]  # Get the first graph object.\n",
    "\n",
    "print()\n",
    "print(data)\n",
    "print('=============================================================')\n",
    "\n",
    "# Gather some statistics about the first graph.\n",
    "print(f'Number of nodes: {data.num_nodes}')\n",
    "print(f'Number of edges: {data.num_edges}')\n",
    "print(f'Average node degree: {data.num_edges / data.num_nodes:.2f}')\n",
    "print(f'Contains isolated nodes: {data.contains_isolated_nodes()}')\n",
    "print(f'Contains self-loops: {data.contains_self_loops()}')\n",
    "print(f'Is undirected: {data.is_undirected()}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8a66c7cb",
   "metadata": {},
   "outputs": [],
   "source": [
    "torch.manual_seed(12345)\n",
    "dataset = dataset.shuffle()\n",
    "\n",
    "\n",
    "# shuffle_index = np.loadtxt('shuffle_indices/shuffleIndex_MouseBrain.txt')\n",
    "# shuffle_index = shuffle_index.astype(np.int32)\n",
    "# train_size, val_size = int(len(shuffle_index)* 0.8), int(len(shuffle_index)* 0.9)\n",
    "# train_dataset = [dataset[i] for i in shuffle_index[0:train_size]]\n",
    "# val_dataset = [dataset[i] for i in shuffle_index[train_size: val_size]]\n",
    "# test_dataset =  [dataset[i] for i in shuffle_index[val_size:]]\n",
    "\n",
    "# train_dataset = torch.load('trainDataset.pt')\n",
    "# test_dataset = torch.load('testDataset.pt')\n",
    "\n",
    "train_dataset = dataset[:4064]\n",
    "test_dataset = dataset[4064:]\n",
    "\n",
    "# train_dataset = dataset[:40]\n",
    "# test_dataset = dataset[40:60]\n",
    "\n",
    "print(f'Number of training graphs: {len(train_dataset)}')\n",
    "print(f'Number of test graphs: {len(test_dataset)}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5dce17cb",
   "metadata": {},
   "outputs": [],
   "source": [
    "from torch_geometric.data import DataLoader\n",
    "\n",
    "train_loader = DataLoader(train_dataset, batch_size=30, shuffle=True)\n",
    "train_loader_testing = DataLoader(train_dataset, batch_size=1, shuffle=True)\n",
    "test_loader = DataLoader(test_dataset, batch_size=1, shuffle=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ad8a9de2",
   "metadata": {},
   "outputs": [],
   "source": [
    "from gcnmodel import GCN\n",
    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
    "\n",
    "model = GCN(hidden_channels=128, data=dataset, output_size=9).to(device)\n",
    "print(model)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "783ea868",
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "optimizer = torch.optim.Adam(model.parameters(), lr=0.001)\n",
    "criterion = torch.nn.CrossEntropyLoss()\n",
    "    \n",
    "def test(loader, size):\n",
    "    model.eval()\n",
    "    output = np.zeros((len(loader), size))\n",
    "    actual = np.zeros((len(loader), size))\n",
    "    accuracy = 0\n",
    "    for ind, data in enumerate(loader):  # Iterate in batches over the training/test dataset.\n",
    "        data.x = torch.reshape(data.x, (data.x.shape[0], 2))\n",
    "        data.x = data.x.type(torch.FloatTensor)\n",
    "        data = data.to(device)\n",
    "        out = model(data.x, data.edge_index, data.batch)\n",
    "        output[ind] = softmax(out.cpu().detach().numpy())\n",
    "        actual[ind][data.y] = 1\n",
    "        accuracy += int((out.argmax(dim=1) == data.y).sum())\n",
    "    all_labels = list(dataset.cellToIndex.keys())\n",
    "    actual = np.array(actual)\n",
    "    precision = dict()\n",
    "    recall = dict()\n",
    "    averageAUROC = []\n",
    "    averageAUPR = []\n",
    "    for (idx, c_label) in enumerate(all_labels):\n",
    "        \n",
    "        fpr, tpr, thresholds = roc_curve(actual[:,idx].astype(int), output[:,idx])\n",
    "        precision[idx], recall[idx], _ = precision_recall_curve(actual[:, idx],\n",
    "                                                        output[:, idx])\n",
    "        averageAUROC.append(auc(fpr, tpr))\n",
    "        averageAUPR.append(round(auc(recall[idx], precision[idx]),4))\n",
    "\n",
    "    return accuracy/len(loader.dataset), mean(averageAUROC), mean(averageAUPR)\n",
    "\n",
    "\n",
    "def train():\n",
    "    model.train()\n",
    "    avgLoss = 0\n",
    "    for data in tqdm(train_loader, total=136):  # Iterate in batches over the training dataset.\n",
    "        data.x = torch.reshape(data.x, (data.x.shape[0], 2))\n",
    "        data.x = data.x.type(torch.FloatTensor)\n",
    "        data = data.to(device)\n",
    "        out = model(data.x, data.edge_index, data.batch)# Perform a single forward pass.\n",
    "        loss = criterion(out, data.y)  # Compute the loss.\n",
    "        loss.backward()  # Derive gradients.\n",
    "        optimizer.step()  # Update parameters based on gradients.\n",
    "        optimizer.zero_grad()  # Clear gradients.\n",
    "        avgLoss += loss\n",
    "    return avgLoss / 136\n",
    "\n",
    "\n",
    "for epoch in range(1, 150):\n",
    "        loss = train()\n",
    "        train_acc, trainAUC, trainAUPR = test(train_loader_testing, 19)\n",
    "        test_acc,testAUC, testAUPR = test(test_loader, 19)\n",
    "        print(f'Epoch: {epoch:03d}, Train Acc: {train_acc:.4f}, Train AUC: {trainAUC:.4f}, Train AUPR: {trainAUPR:.4f}, Test Acc: {test_acc:.4f}, Test Auc: {testAUC:.4f}, Test AUPR: {testAUPR:.4f},  Loss: {loss:.4f}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "ab926e3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "torch.save(model.state_dict(), 'model_weightsDec24_P0atacseq.pth')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "ab1d7687",
   "metadata": {},
   "outputs": [
    {
     "ename": "RuntimeError",
     "evalue": "Error(s) in loading state_dict for GCN:\n\tsize mismatch for lin.weight: copying a param with shape torch.Size([19, 128]) from checkpoint, the shape in current model is torch.Size([4, 128]).\n\tsize mismatch for lin.bias: copying a param with shape torch.Size([19]) from checkpoint, the shape in current model is torch.Size([4]).",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mRuntimeError\u001b[0m                              Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-f6b14577a03b>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mmodel\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mGCN\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhidden_channels\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m128\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mdataset\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moutput_size\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m4\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mto\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdevice\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mmodel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_state_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtorch\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'model_weightsDec23_atacseq.pth'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      3\u001b[0m \u001b[0mtest_acc\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mtestAUC\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtestAUPR\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtest\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtest_loader\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m4\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34mf'Test Acc: {test_acc:.4f}, Test Auc: {testAUC:.4f}, Test AUPR: {testAUPR:.4f}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env/lib/python3.7/site-packages/torch/nn/modules/module.py\u001b[0m in \u001b[0;36mload_state_dict\u001b[0;34m(self, state_dict, strict)\u001b[0m\n\u001b[1;32m   1481\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merror_msgs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1482\u001b[0m             raise RuntimeError('Error(s) in loading state_dict for {}:\\n\\t{}'.format(\n\u001b[0;32m-> 1483\u001b[0;31m                                self.__class__.__name__, \"\\n\\t\".join(error_msgs)))\n\u001b[0m\u001b[1;32m   1484\u001b[0m         \u001b[0;32mreturn\u001b[0m \u001b[0m_IncompatibleKeys\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmissing_keys\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0munexpected_keys\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1485\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mRuntimeError\u001b[0m: Error(s) in loading state_dict for GCN:\n\tsize mismatch for lin.weight: copying a param with shape torch.Size([19, 128]) from checkpoint, the shape in current model is torch.Size([4, 128]).\n\tsize mismatch for lin.bias: copying a param with shape torch.Size([19]) from checkpoint, the shape in current model is torch.Size([4])."
     ]
    }
   ],
   "source": [
    "model = GCN(hidden_channels=128, data=dataset, output_size=4).to(device)\n",
    "model.load_state_dict(torch.load('model_weightsDec23_atacseq.pth'))\n",
    "test_acc,testAUC, testAUPR = test(test_loader, 4)\n",
    "print(f'Test Acc: {test_acc:.4f}, Test Auc: {testAUC:.4f}, Test AUPR: {testAUPR:.4f}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "7d61cb4e",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "df3f0543",
   "metadata": {
    "scrolled": true
   },
   "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>Unnamed: 0</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TGGAATTTTCTC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CCAACAAACGCG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TGCGCATAGCCG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>CTGTTTCCCACC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ACAGTCTACATG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3048</th>\n",
       "      <td>TACAGGCACATT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3049</th>\n",
       "      <td>AGTTCATTGATC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3050</th>\n",
       "      <td>AAAGATTCCGGA</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3051</th>\n",
       "      <td>CCCAGACCCCGT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3052</th>\n",
       "      <td>ATAGGCAACGTT</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3053 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Unnamed: 0\n",
       "0     TGGAATTTTCTC\n",
       "1     CCAACAAACGCG\n",
       "2     TGCGCATAGCCG\n",
       "3     CTGTTTCCCACC\n",
       "4     ACAGTCTACATG\n",
       "...            ...\n",
       "3048  TACAGGCACATT\n",
       "3049  AGTTCATTGATC\n",
       "3050  AAAGATTCCGGA\n",
       "3051  CCCAGACCCCGT\n",
       "3052  ATAGGCAACGTT\n",
       "\n",
       "[3053 rows x 1 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv('/gpfs/data/rsingh47/hzaki1/atacseqdata_P0Brain/resources/P0_chromatin_counts.tsv', sep='\\t', usecols=['Unnamed: 0']) "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ad22e5cf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Unnamed: 0  chr1:3012650-3012823  chr1:3012853-3013002  \\\n",
      "0   TGGAATTTTCTC                     0                     0   \n",
      "1   CCAACAAACGCG                     0                     0   \n",
      "2   TGCGCATAGCCG                     0                     0   \n",
      "3   CTGTTTCCCACC                     0                     0   \n",
      "4   ACAGTCTACATG                     0                     0   \n",
      "5   CGCACTTGCGAG                     0                     0   \n",
      "6   GCAACCTGAACA                     0                     0   \n",
      "7   TAAAACCCACCA                     0                     0   \n",
      "8   AAGTTGACCAAG                     0                     0   \n",
      "9   CCGTGAGCTGCA                     0                     0   \n",
      "10  CAACAGCTCTCA                     0                     0   \n",
      "11  ATCGGGTACCAA                     0                     0   \n",
      "12  CGTCTCGAGTGG                     0                     0   \n",
      "13  GCGATAATAGCC                     0                     0   \n",
      "14  GCAATTAAGGAA                     0                     0   \n",
      "15  TAGTAATAACAT                     0                     0   \n",
      "16  CGGCGGGCACGG                     0                     0   \n",
      "17  CTAGGGAAACGG                     0                     0   \n",
      "18  AACACACTACGG                     0                     0   \n",
      "19  TTTCTCTGGACG                     0                     0   \n",
      "\n",
      "    chr1:3030589-3030826  chr1:3071552-3071701  chr1:3078770-3078919  \\\n",
      "0                      0                     0                     0   \n",
      "1                      0                     0                     0   \n",
      "2                      0                     0                     0   \n",
      "3                      0                     0                     0   \n",
      "4                      0                     0                     0   \n",
      "5                      0                     0                     0   \n",
      "6                      0                     0                     0   \n",
      "7                      0                     0                     0   \n",
      "8                      0                     0                     0   \n",
      "9                      0                     0                     0   \n",
      "10                     0                     0                     0   \n",
      "11                     0                     0                     0   \n",
      "12                     0                     0                     0   \n",
      "13                     0                     0                     0   \n",
      "14                     0                     0                     0   \n",
      "15                     0                     0                     0   \n",
      "16                     0                     0                     0   \n",
      "17                     0                     0                     0   \n",
      "18                     0                     0                     0   \n",
      "19                     0                     0                     0   \n",
      "\n",
      "    chr1:3094577-3095346  chr1:3113584-3113964  chr1:3119594-3120813  \\\n",
      "0                      0                     0                     0   \n",
      "1                      0                     0                     0   \n",
      "2                      0                     0                     0   \n",
      "3                      0                     0                     0   \n",
      "4                      0                     0                     0   \n",
      "5                      0                     1                     1   \n",
      "6                      0                     0                     0   \n",
      "7                      0                     0                     0   \n",
      "8                      0                     0                     1   \n",
      "9                      0                     0                     0   \n",
      "10                     0                     0                     0   \n",
      "11                     0                     0                     0   \n",
      "12                     0                     0                     0   \n",
      "13                     0                     0                     0   \n",
      "14                     0                     0                     0   \n",
      "15                     0                     0                     0   \n",
      "16                     0                     1                     0   \n",
      "17                     0                     0                     0   \n",
      "18                     0                     0                     0   \n",
      "19                     0                     0                     0   \n",
      "\n",
      "    chr1:3129824-3129996  ...  chrY:1840090-1840287  chrY:4259374-4259575  \\\n",
      "0                      0  ...                     0                     0   \n",
      "1                      0  ...                     0                     0   \n",
      "2                      0  ...                     0                     0   \n",
      "3                      0  ...                     0                     0   \n",
      "4                      0  ...                     0                     0   \n",
      "5                      0  ...                     0                     0   \n",
      "6                      0  ...                     0                     0   \n",
      "7                      0  ...                     0                     0   \n",
      "8                      0  ...                     0                     0   \n",
      "9                      0  ...                     0                     0   \n",
      "10                     0  ...                     0                     0   \n",
      "11                     0  ...                     0                     0   \n",
      "12                     0  ...                     0                     0   \n",
      "13                     0  ...                     0                     0   \n",
      "14                     0  ...                     0                     0   \n",
      "15                     0  ...                     0                     0   \n",
      "16                     0  ...                     0                     0   \n",
      "17                     0  ...                     0                     0   \n",
      "18                     0  ...                     0                     0   \n",
      "19                     0  ...                     0                     0   \n",
      "\n",
      "    chrY:10643915-10644099  chrY:86743531-86743875  chrY:90732135-90732427  \\\n",
      "0                        0                       0                       0   \n",
      "1                        0                       0                       0   \n",
      "2                        0                       0                       0   \n",
      "3                        0                       0                       1   \n",
      "4                        0                       0                       0   \n",
      "5                        0                       0                       0   \n",
      "6                        0                       0                       0   \n",
      "7                        0                       0                       0   \n",
      "8                        0                       0                       0   \n",
      "9                        0                       0                       0   \n",
      "10                       0                       0                       0   \n",
      "11                       0                       0                       0   \n",
      "12                       0                       0                       0   \n",
      "13                       0                       0                       0   \n",
      "14                       0                       0                       0   \n",
      "15                       0                       0                       0   \n",
      "16                       0                       0                       0   \n",
      "17                       0                       0                       0   \n",
      "18                       0                       0                       0   \n",
      "19                       0                       0                       0   \n",
      "\n",
      "    chrY:90739635-90740189  chrY:90740358-90740604  chrY:90740889-90741401  \\\n",
      "0                        0                       0                       0   \n",
      "1                        0                       0                       2   \n",
      "2                        0                       0                       1   \n",
      "3                        0                       0                       0   \n",
      "4                        0                       0                       0   \n",
      "5                        0                       0                       1   \n",
      "6                        1                       0                       0   \n",
      "7                        0                       0                       0   \n",
      "8                        0                       0                       0   \n",
      "9                        1                       1                       0   \n",
      "10                       0                       0                       0   \n",
      "11                       1                       0                       0   \n",
      "12                       0                       1                       0   \n",
      "13                       0                       0                       0   \n",
      "14                       1                       0                       2   \n",
      "15                       0                       0                       0   \n",
      "16                       0                       0                       0   \n",
      "17                       0                       0                       0   \n",
      "18                       0                       0                       0   \n",
      "19                       1                       0                       1   \n",
      "\n",
      "    chrY:90741510-90742418  chrY:90744330-90744663  \n",
      "0                        0                       0  \n",
      "1                        3                       0  \n",
      "2                        0                       0  \n",
      "3                        1                       0  \n",
      "4                        0                       1  \n",
      "5                        0                       0  \n",
      "6                        2                       1  \n",
      "7                        0                       0  \n",
      "8                        2                       0  \n",
      "9                        0                       0  \n",
      "10                       0                       0  \n",
      "11                       0                       1  \n",
      "12                       0                       1  \n",
      "13                       0                       0  \n",
      "14                       0                       0  \n",
      "15                       0                       0  \n",
      "16                       0                       0  \n",
      "17                       0                       0  \n",
      "18                       0                       0  \n",
      "19                       0                       0  \n",
      "\n",
      "[20 rows x 229430 columns]\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "      Unnamed: 0  chr1:3012650-3012823  chr1:3012853-3013002  \\\n",
      "20  GCACCGCTATAA                     0                     0   \n",
      "21  GAACATTACGAT                     0                     0   \n",
      "22  AGTATGGCTGTT                     0                     0   \n",
      "23  TCTCCACTATAG                     0                     0   \n",
      "24  CGGTGGAAGTTC                     0                     0   \n",
      "25  CCTTTAATGAGT                     0                     0   \n",
      "26  GACATCGTTGGG                     0                     0   \n",
      "27  CTTCGCCAAACC                     0                     0   \n",
      "28  GCGAGCGGATTA                     0                     0   \n",
      "29  CGTGCGGTTATT                     0                     0   \n",
      "30  CACTCAAGACCT                     0                     0   \n",
      "31  CAGGCTTACGAT                     0                     0   \n",
      "32  CGCTTTGAGTCC                     0                     0   \n",
      "33  GGCCATCTATAT                     0                     0   \n",
      "34  GAGTAGTAAGAT                     0                     0   \n",
      "35  CGTTTCCTGTAC                     0                     0   \n",
      "36  CGATGTACTAAT                     0                     0   \n",
      "37  AATGTTTGTCAC                     0                     0   \n",
      "38  ATTTTTCAAACC                     0                     0   \n",
      "39  CTCCCTTTTCGG                     0                     0   \n",
      "\n",
      "    chr1:3030589-3030826  chr1:3071552-3071701  chr1:3078770-3078919  \\\n",
      "20                     0                     0                     0   \n",
      "21                     0                     0                     0   \n",
      "22                     0                     0                     0   \n",
      "23                     0                     0                     0   \n",
      "24                     0                     0                     0   \n",
      "25                     0                     0                     0   \n",
      "26                     0                     0                     0   \n",
      "27                     0                     0                     0   \n",
      "28                     0                     0                     0   \n",
      "29                     0                     0                     0   \n",
      "30                     0                     0                     0   \n",
      "31                     0                     0                     0   \n",
      "32                     0                     0                     0   \n",
      "33                     0                     0                     0   \n",
      "34                     0                     0                     0   \n",
      "35                     0                     0                     0   \n",
      "36                     0                     0                     0   \n",
      "37                     0                     0                     0   \n",
      "38                     0                     0                     0   \n",
      "39                     0                     0                     0   \n",
      "\n",
      "    chr1:3094577-3095346  chr1:3113584-3113964  chr1:3119594-3120813  \\\n",
      "20                     0                     0                     0   \n",
      "21                     0                     0                     1   \n",
      "22                     0                     0                     0   \n",
      "23                     0                     0                     0   \n",
      "24                     0                     0                     0   \n",
      "25                     0                     0                     1   \n",
      "26                     0                     0                     0   \n",
      "27                     0                     0                     0   \n",
      "28                     0                     0                     1   \n",
      "29                     0                     0                     0   \n",
      "30                     0                     0                     0   \n",
      "31                     0                     0                     0   \n",
      "32                     0                     0                     1   \n",
      "33                     0                     0                     0   \n",
      "34                     0                     0                     1   \n",
      "35                     0                     0                     0   \n",
      "36                     0                     0                     0   \n",
      "37                     0                     0                     0   \n",
      "38                     0                     0                     0   \n",
      "39                     0                     0                     0   \n",
      "\n",
      "    chr1:3129824-3129996  ...  chrY:1840090-1840287  chrY:4259374-4259575  \\\n",
      "20                     0  ...                     0                     0   \n",
      "21                     0  ...                     0                     0   \n",
      "22                     0  ...                     0                     0   \n",
      "23                     0  ...                     0                     0   \n",
      "24                     0  ...                     0                     0   \n",
      "25                     0  ...                     0                     0   \n",
      "26                     0  ...                     0                     0   \n",
      "27                     0  ...                     0                     0   \n",
      "28                     0  ...                     0                     0   \n",
      "29                     0  ...                     0                     0   \n",
      "30                     0  ...                     0                     0   \n",
      "31                     0  ...                     0                     0   \n",
      "32                     0  ...                     0                     0   \n",
      "33                     0  ...                     0                     0   \n",
      "34                     0  ...                     0                     0   \n",
      "35                     0  ...                     0                     0   \n",
      "36                     0  ...                     0                     0   \n",
      "37                     0  ...                     0                     0   \n",
      "38                     0  ...                     0                     0   \n",
      "39                     0  ...                     0                     0   \n",
      "\n",
      "    chrY:10643915-10644099  chrY:86743531-86743875  chrY:90732135-90732427  \\\n",
      "20                       0                       0                       0   \n",
      "21                       0                       0                       0   \n",
      "22                       0                       0                       0   \n",
      "23                       0                       0                       1   \n",
      "24                       0                       0                       0   \n",
      "25                       0                       0                       0   \n",
      "26                       0                       0                       0   \n",
      "27                       0                       0                       0   \n",
      "28                       0                       0                       0   \n",
      "29                       0                       0                       0   \n",
      "30                       0                       0                       0   \n",
      "31                       0                       0                       0   \n",
      "32                       0                       0                       0   \n",
      "33                       0                       0                       0   \n",
      "34                       0                       0                       0   \n",
      "35                       0                       0                       0   \n",
      "36                       0                       0                       0   \n",
      "37                       0                       0                       0   \n",
      "38                       0                       0                       0   \n",
      "39                       0                       0                       0   \n",
      "\n",
      "    chrY:90739635-90740189  chrY:90740358-90740604  chrY:90740889-90741401  \\\n",
      "20                       0                       0                       0   \n",
      "21                       0                       0                       0   \n",
      "22                       0                       0                       0   \n",
      "23                       0                       0                       0   \n",
      "24                       2                       0                       1   \n",
      "25                       0                       0                       0   \n",
      "26                       0                       0                       0   \n",
      "27                       0                       0                       0   \n",
      "28                       1                       0                       0   \n",
      "29                       0                       0                       1   \n",
      "30                       0                       0                       0   \n",
      "31                       0                       0                       1   \n",
      "32                       0                       0                       0   \n",
      "33                       1                       0                       0   \n",
      "34                       0                       0                       0   \n",
      "35                       0                       0                       0   \n",
      "36                       0                       0                       0   \n",
      "37                       0                       0                       1   \n",
      "38                       0                       0                       0   \n",
      "39                       0                       0                       0   \n",
      "\n",
      "    chrY:90741510-90742418  chrY:90744330-90744663  \n",
      "20                       0                       0  \n",
      "21                       1                       1  \n",
      "22                       0                       0  \n",
      "23                       0                       0  \n",
      "24                       0                       0  \n",
      "25                       0                       0  \n",
      "26                       0                       1  \n",
      "27                       1                       1  \n",
      "28                       0                       0  \n",
      "29                       0                       0  \n",
      "30                       0                       0  \n",
      "31                       0                       0  \n",
      "32                       0                       0  \n",
      "33                       0                       0  \n",
      "34                       1                       0  \n",
      "35                       1                       0  \n",
      "36                       1                       0  \n",
      "37                       0                       0  \n",
      "38                       0                       0  \n",
      "39                       0                       0  \n",
      "\n",
      "[20 rows x 229430 columns]\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_42781/1240027057.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      2\u001b[0m for chunk in pd.read_csv('/gpfs/data/rsingh47/hzaki1/atacseqdata_P0Brain/resources/P0_chromatin_counts.tsv', sep='\\t', \n\u001b[1;32m      3\u001b[0m                          \u001b[0mchunksize\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mchunksize\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m                          iterator=True):\n\u001b[0m\u001b[1;32m      5\u001b[0m     \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mchunk\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/io/parsers/readers.py\u001b[0m in \u001b[0;36m__next__\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m   1022\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m__next__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1023\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1024\u001b[0;31m             \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_chunk\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1025\u001b[0m         \u001b[0;32mexcept\u001b[0m \u001b[0mStopIteration\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1026\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/io/parsers/readers.py\u001b[0m in \u001b[0;36mget_chunk\u001b[0;34m(self, size)\u001b[0m\n\u001b[1;32m   1072\u001b[0m                 \u001b[0;32mraise\u001b[0m \u001b[0mStopIteration\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1073\u001b[0m             \u001b[0msize\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnrows\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_currow\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1074\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnrows\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msize\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1075\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1076\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0m__enter__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/io/parsers/readers.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m   1045\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnrows\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mNone\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1046\u001b[0m         \u001b[0mnrows\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalidate_integer\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"nrows\"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnrows\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1047\u001b[0;31m         \u001b[0mindex\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcolumns\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcol_dict\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnrows\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1048\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1049\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mindex\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/io/parsers/c_parser_wrapper.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m    222\u001b[0m         \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    223\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mlow_memory\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 224\u001b[0;31m                 \u001b[0mchunks\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_reader\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_low_memory\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mnrows\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    225\u001b[0m                 \u001b[0;31m# destructive to chunks\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    226\u001b[0m                 \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_concatenate_chunks\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mchunks\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.read_low_memory\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._read_rows\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._convert_column_data\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._convert_tokens\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._convert_with_dtype\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32m/gpfs/home/hzaki1/celltypefromgrn/env-gpu/lib/python3.7/site-packages/pandas/core/dtypes/common.py\u001b[0m in \u001b[0;36mis_extension_array_dtype\u001b[0;34m(arr_or_dtype)\u001b[0m\n\u001b[1;32m   1418\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1419\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1420\u001b[0;31m \u001b[0;32mdef\u001b[0m \u001b[0mis_extension_array_dtype\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0marr_or_dtype\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m->\u001b[0m \u001b[0mbool\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1421\u001b[0m     \"\"\"\n\u001b[1;32m   1422\u001b[0m     \u001b[0mCheck\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0man\u001b[0m \u001b[0mobject\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0ma\u001b[0m \u001b[0mpandas\u001b[0m \u001b[0mextension\u001b[0m \u001b[0marray\u001b[0m \u001b[0mtype\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "chunksize = 20\n",
    "for chunk in pd.read_csv('/gpfs/data/rsingh47/hzaki1/atacseqdata_P0Brain/resources/P0_chromatin_counts.tsv', sep='\\t', \n",
    "                         chunksize=chunksize, \n",
    "                         iterator=True):\n",
    "    print(chunk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "e004fe26",
   "metadata": {},
   "outputs": [
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       "      <td>-1.464720</td>\n",
       "      <td>-0.137934</td>\n",
       "      <td>-0.715391</td>\n",
       "      <td>...</td>\n",
       "      <td>0.848818</td>\n",
       "      <td>-0.442782</td>\n",
       "      <td>0.166991</td>\n",
       "      <td>0.777194</td>\n",
       "      <td>1.886406</td>\n",
       "      <td>0.818283</td>\n",
       "      <td>0.862078</td>\n",
       "      <td>-0.023490</td>\n",
       "      <td>-0.001514</td>\n",
       "      <td>1.137818</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>-1.364619</td>\n",
       "      <td>9.447015</td>\n",
       "      <td>-2.628073</td>\n",
       "      <td>5.984243</td>\n",
       "      <td>-3.475412</td>\n",
       "      <td>-3.017343</td>\n",
       "      <td>1.073840</td>\n",
       "      <td>1.755634</td>\n",
       "      <td>3.508800</td>\n",
       "      <td>3.074618</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.503803</td>\n",
       "      <td>0.693757</td>\n",
       "      <td>0.698400</td>\n",
       "      <td>-0.613128</td>\n",
       "      <td>1.493784</td>\n",
       "      <td>-0.684394</td>\n",
       "      <td>-0.560127</td>\n",
       "      <td>2.892226</td>\n",
       "      <td>0.795175</td>\n",
       "      <td>-0.063960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-1.724235</td>\n",
       "      <td>1.915687</td>\n",
       "      <td>-7.886971</td>\n",
       "      <td>-9.203425</td>\n",
       "      <td>-0.686722</td>\n",
       "      <td>5.294880</td>\n",
       "      <td>-3.968006</td>\n",
       "      <td>2.248889</td>\n",
       "      <td>0.558640</td>\n",
       "      <td>1.097301</td>\n",
       "      <td>...</td>\n",
       "      <td>-1.585393</td>\n",
       "      <td>4.095959</td>\n",
       "      <td>2.076408</td>\n",
       "      <td>4.458320</td>\n",
       "      <td>1.004148</td>\n",
       "      <td>1.699451</td>\n",
       "      <td>2.238309</td>\n",
       "      <td>0.740241</td>\n",
       "      <td>-1.603753</td>\n",
       "      <td>3.018961</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2.192419</td>\n",
       "      <td>-1.217848</td>\n",
       "      <td>-1.030330</td>\n",
       "      <td>-0.462981</td>\n",
       "      <td>-1.138515</td>\n",
       "      <td>1.105841</td>\n",
       "      <td>3.901958</td>\n",
       "      <td>0.727287</td>\n",
       "      <td>-0.596557</td>\n",
       "      <td>-1.591444</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.787046</td>\n",
       "      <td>1.154933</td>\n",
       "      <td>1.673235</td>\n",
       "      <td>-0.330316</td>\n",
       "      <td>-1.616407</td>\n",
       "      <td>-0.006023</td>\n",
       "      <td>-1.466589</td>\n",
       "      <td>0.241086</td>\n",
       "      <td>-0.650903</td>\n",
       "      <td>-0.448479</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.379982</td>\n",
       "      <td>-0.958338</td>\n",
       "      <td>1.849119</td>\n",
       "      <td>1.334524</td>\n",
       "      <td>0.431960</td>\n",
       "      <td>4.136202</td>\n",
       "      <td>-1.471386</td>\n",
       "      <td>0.486075</td>\n",
       "      <td>0.984332</td>\n",
       "      <td>0.857327</td>\n",
       "      <td>...</td>\n",
       "      <td>0.840397</td>\n",
       "      <td>0.004148</td>\n",
       "      <td>-0.307390</td>\n",
       "      <td>-0.123819</td>\n",
       "      <td>0.378542</td>\n",
       "      <td>-0.307433</td>\n",
       "      <td>0.221493</td>\n",
       "      <td>0.018832</td>\n",
       "      <td>-0.353097</td>\n",
       "      <td>0.493338</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>1.615223</td>\n",
       "      <td>0.799734</td>\n",
       "      <td>1.777042</td>\n",
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       "      <td>-0.899616</td>\n",
       "      <td>0.317689</td>\n",
       "      <td>0.083957</td>\n",
       "      <td>-0.536709</td>\n",
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       "      <th>10304</th>\n",
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       "      <td>0.021923</td>\n",
       "      <td>4.905372</td>\n",
       "      <td>0.966132</td>\n",
       "      <td>0.359771</td>\n",
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       "      <td>1.435619</td>\n",
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       "      <td>0.288949</td>\n",
       "      <td>-0.896097</td>\n",
       "      <td>0.006128</td>\n",
       "      <td>-1.333366</td>\n",
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       "      <td>-0.223355</td>\n",
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       "      <td>-0.048524</td>\n",
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       "      <td>-1.769234</td>\n",
       "      <td>-1.732952</td>\n",
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       "      <td>-0.173519</td>\n",
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       "      <td>0.864748</td>\n",
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       "      <td>0.480407</td>\n",
       "      <td>-0.623204</td>\n",
       "      <td>-0.168816</td>\n",
       "      <td>-1.954851</td>\n",
       "      <td>0.290394</td>\n",
       "      <td>-0.437938</td>\n",
       "      <td>-1.209863</td>\n",
       "      <td>0.423491</td>\n",
       "      <td>0.057374</td>\n",
       "      <td>0.776191</td>\n",
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       "    <tr>\n",
       "      <th>10306</th>\n",
       "      <td>0.643357</td>\n",
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       "      <td>-8.461166</td>\n",
       "      <td>-12.643758</td>\n",
       "      <td>-1.364028</td>\n",
       "      <td>3.115762</td>\n",
       "      <td>-2.159244</td>\n",
       "      <td>3.468491</td>\n",
       "      <td>0.181685</td>\n",
       "      <td>4.016421</td>\n",
       "      <td>...</td>\n",
       "      <td>-1.976758</td>\n",
       "      <td>-0.297906</td>\n",
       "      <td>-2.393352</td>\n",
       "      <td>1.762918</td>\n",
       "      <td>1.239178</td>\n",
       "      <td>0.867720</td>\n",
       "      <td>-1.640475</td>\n",
       "      <td>2.265162</td>\n",
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       "      <th>10307</th>\n",
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       "      <td>1.424154</td>\n",
       "      <td>0.541217</td>\n",
       "      <td>1.207876</td>\n",
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       "      <td>0.932045</td>\n",
       "      <td>-0.110615</td>\n",
       "      <td>-0.142087</td>\n",
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       "      <td>-0.763135</td>\n",
       "      <td>0.473027</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10308 rows × 25 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
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       "3              2.192419          -1.217848           -1.030330   \n",
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       "...                 ...                ...                 ...   \n",
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       "\n",
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       "4                1.334524            0.431960            4.136202   \n",
       "...                   ...                 ...                 ...   \n",
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       "0             -5.038763          -1.464720          -0.137934   \n",
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       "...                 ...                ...                ...   \n",
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       "10307          1.424154           0.541217           1.207876   \n",
       "\n",
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       "...                 ...                ...               ...   \n",
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       "\n",
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       "0               0.818283           0.862078            -0.023490   \n",
       "1              -0.684394          -0.560127             2.892226   \n",
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       "...                  ...                ...                  ...   \n",
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       "10307          -0.110615          -0.142087            -0.629526   \n",
       "\n",
       "       0.865330026382709  0.186055380721716  \n",
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       "...                  ...                ...  \n",
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       "10307          -0.763135           0.473027  \n",
       "\n",
       "[10308 rows x 25 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv('/gpfs/data/rsingh47/hzaki1/scMultiOmics_Datasets/AdBrain_cDNA.tsv', sep='\\t', header=0, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "c748ce79",
   "metadata": {},
   "outputs": [
    {
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       "    <tr>\n",
       "      <th>-0.793059</th>\n",
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       "      <td>1.445810</td>\n",
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       "    <tr>\n",
       "      <th>-0.641849</th>\n",
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       "      <td>2.595201</td>\n",
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       "      <td>-0.281475</td>\n",
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       "      <td>1.578672</td>\n",
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       "    <tr>\n",
       "      <th>-0.597772</th>\n",
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       "      <td>-0.739938</td>\n",
       "      <td>0.550149</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10308 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           -7.228593930630781150e-01  \\\n",
       "-9.503142994098140450e-01                              \n",
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       "...                                              ...   \n",
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       "\n",
       "                           7.559886283838490595e-02  \\\n",
       "-9.503142994098140450e-01                             \n",
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       "...                                             ...   \n",
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       "\n",
       "                           -1.309199109879449985e+00  \\\n",
       "-9.503142994098140450e-01                              \n",
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       "...                                              ...   \n",
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       "\n",
       "                           3.009467457550289993e-01  1.415285809331649824e+00  \\\n",
       "-9.503142994098140450e-01                                                       \n",
       "-0.915965                                  2.914415                  0.982705   \n",
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       " 2.392906                                  0.045678                  0.210309   \n",
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       "...                                             ...                       ...   \n",
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       "\n",
       "                           -1.929257297112769720e-01  \\\n",
       "-9.503142994098140450e-01                              \n",
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       " 2.392906                                  -0.042039   \n",
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       "...                                              ...   \n",
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       "\n",
       "                           1.085243040896859856e+00  6.291242803336670741e-01  \\\n",
       "-9.503142994098140450e-01                                                       \n",
       "-0.915965                                 -0.050112                 -0.080515   \n",
       "-0.227151                                 -0.474545                 -0.837446   \n",
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       " 2.392906                                 -0.778954                 -0.716767   \n",
       "-0.237181                                  0.108862                  1.279064   \n",
       "...                                             ...                       ...   \n",
       "-0.127454                                  0.519592                  1.104672   \n",
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       "-0.524536                                 -0.442760                  0.727317   \n",
       "-0.641849                                  0.419300                 -0.281475   \n",
       "-0.597772                                  1.800166                 -0.394263   \n",
       "\n",
       "                           -7.337399238905991661e-01  \\\n",
       "-9.503142994098140450e-01                              \n",
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       "-0.227151                                  -0.913827   \n",
       "-0.362644                                  -0.553078   \n",
       " 2.392906                                   0.078326   \n",
       "-0.237181                                   0.995772   \n",
       "...                                              ...   \n",
       "-0.127454                                   0.796068   \n",
       "-0.793059                                   1.826531   \n",
       "-0.524536                                  -0.361650   \n",
       "-0.641849                                  -0.534643   \n",
       "-0.597772                                  -0.497128   \n",
       "\n",
       "                           -2.967570810367570200e-01  \\\n",
       "-9.503142994098140450e-01                              \n",
       "-0.915965                                   1.657346   \n",
       "-0.227151                                  -0.591524   \n",
       "-0.362644                                  -0.248308   \n",
       " 2.392906                                  -0.381776   \n",
       "-0.237181                                  -0.014815   \n",
       "...                                              ...   \n",
       "-0.127454                                   0.721811   \n",
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       "-0.641849                                  -0.731757   \n",
       "-0.597772                                  -0.652451   \n",
       "\n",
       "                           9.898743246594541301e-01  \\\n",
       "-9.503142994098140450e-01                             \n",
       "-0.915965                                 -0.885185   \n",
       "-0.227151                                 -1.004256   \n",
       "-0.362644                                 -0.390161   \n",
       " 2.392906                                 -0.600903   \n",
       "-0.237181                                 -0.845140   \n",
       "...                                             ...   \n",
       "-0.127454                                 -1.122662   \n",
       "-0.793059                                 -0.746858   \n",
       "-0.524536                                 -1.370566   \n",
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       "\n",
       "                           -1.093108313508130092e+00  \\\n",
       "-9.503142994098140450e-01                              \n",
       "-0.915965                                  -0.275118   \n",
       "-0.227151                                  -0.383973   \n",
       "-0.362644                                  -0.523569   \n",
       " 2.392906                                   0.123984   \n",
       "-0.237181                                  -1.005080   \n",
       "...                                              ...   \n",
       "-0.127454                                  -0.681432   \n",
       "-0.793059                                  -0.410698   \n",
       "-0.524536                                   0.111363   \n",
       "-0.641849                                  -0.342280   \n",
       "-0.597772                                  -0.408360   \n",
       "\n",
       "                           -7.815797181639820845e-01  \\\n",
       "-9.503142994098140450e-01                              \n",
       "-0.915965                                  -0.346100   \n",
       "-0.227151                                  -0.066880   \n",
       "-0.362644                                  -0.221171   \n",
       " 2.392906                                  -0.093016   \n",
       "-0.237181                                   2.192198   \n",
       "...                                              ...   \n",
       "-0.127454                                   2.034477   \n",
       "-0.793059                                   0.794025   \n",
       "-0.524536                                   1.180930   \n",
       "-0.641849                                  -0.760043   \n",
       "-0.597772                                  -0.753352   \n",
       "\n",
       "                           -1.199772056985540125e+00  \\\n",
       "-9.503142994098140450e-01                              \n",
       "-0.915965                                  -0.821616   \n",
       "-0.227151                                   2.035149   \n",
       "-0.362644                                  -0.294042   \n",
       " 2.392906                                  -0.839177   \n",
       "-0.237181                                  -1.090201   \n",
       "...                                              ...   \n",
       "-0.127454                                  -1.138154   \n",
       "-0.793059                                  -0.788586   \n",
       "-0.524536                                  -1.378162   \n",
       "-0.641849                                  -0.079016   \n",
       "-0.597772                                  -0.736521   \n",
       "\n",
       "                           1.851957779876129973e+00  9.322247819574491778e-01  \n",
       "-9.503142994098140450e-01                                                      \n",
       "-0.915965                                 -0.034660                  0.147004  \n",
       "-0.227151                                 -0.935240                  0.483381  \n",
       "-0.362644                                 -0.673771                  1.246412  \n",
       " 2.392906                                 -1.200270                 -0.218617  \n",
       "-0.237181                                 -1.246105                  0.378808  \n",
       "...                                             ...                       ...  \n",
       "-0.127454                                 -1.235292                 -0.282803  \n",
       "-0.793059                                 -0.188988                 -0.095978  \n",
       "-0.524536                                 -1.234706                  1.445810  \n",
       "-0.641849                                 -0.742002                  1.578672  \n",
       "-0.597772                                 -0.739938                  0.550149  \n",
       "\n",
       "[10308 rows x 16 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv('/gpfs/data/rsingh47/hzaki1/scMultiOmics_Datasets/AdBrain_chromatin.tsv', sep='\\t', header=0, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "b48da12f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Barcode</th>\n",
       "      <th>Ident</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Batch</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>09A</th>\n",
       "      <td>CAGCCCCGCCTT</td>\n",
       "      <td>E3Rorb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09A</th>\n",
       "      <td>CGCCTACCATGA</td>\n",
       "      <td>E5Parm1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09A</th>\n",
       "      <td>GATGCGCGGCTA</td>\n",
       "      <td>Ast</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09A</th>\n",
       "      <td>GGTCCGAGTCCT</td>\n",
       "      <td>E4Il1rapl2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09A</th>\n",
       "      <td>TCTCCCGGCACC</td>\n",
       "      <td>E5Parm1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09L</th>\n",
       "      <td>TACTAGTTCAAG</td>\n",
       "      <td>E3Rorb</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09L</th>\n",
       "      <td>ATGACGGGCCCC</td>\n",
       "      <td>Mis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09L</th>\n",
       "      <td>GAAACACCTCAT</td>\n",
       "      <td>Mis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09L</th>\n",
       "      <td>AACGGTTTATCC</td>\n",
       "      <td>InP</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>09L</th>\n",
       "      <td>GACTGATACAGT</td>\n",
       "      <td>Mis</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10309 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Barcode       Ident\n",
       "Batch                          \n",
       "09A    CAGCCCCGCCTT      E3Rorb\n",
       "09A    CGCCTACCATGA     E5Parm1\n",
       "09A    GATGCGCGGCTA         Ast\n",
       "09A    GGTCCGAGTCCT  E4Il1rapl2\n",
       "09A    TCTCCCGGCACC     E5Parm1\n",
       "...             ...         ...\n",
       "09L    TACTAGTTCAAG      E3Rorb\n",
       "09L    ATGACGGGCCCC         Mis\n",
       "09L    GAAACACCTCAT         Mis\n",
       "09L    AACGGTTTATCC         InP\n",
       "09L    GACTGATACAGT         Mis\n",
       "\n",
       "[10309 rows x 2 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pd.read_csv('/gpfs/data/rsingh47/hzaki1/scMultiOmics_Datasets/AdBrainCortex_metadata.tsv', sep='\\t', header=0, index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ab0753e1",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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