dilated_model.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "ed0583cd",
   "metadata": {},
   "outputs": [],
   "source": [
    "import torch\n",
    "import numpy as np \n",
    "import pandas as pd \n",
    "import matplotlib.pyplot as plt\n",
    "from torchvision import datasets \n",
    "from torchvision.transforms import ToTensor\n",
    "from torch.utils.data import DataLoader, Subset\n",
    "from torch import nn\n",
    "from torch import optim\n",
    "import STRDataset\n",
    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
    "import sys\n",
    "import STRDataset as dataset\n",
    "import os\n",
    "import time"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Design CNN model \n",
    "# Use dialted model\n",
    "class dialated_CNN(nn.Module):\n",
    "    def __init__(self, size):\n",
    "        '''size is the total number of positions (around start + end) we have'''\n",
    "        super(dialated_CNN, self).__init__(size)\n",
    "        self.conv1 = nn.Conv1d(5, 320, kernel_size = 6,\n",
    "                               dilation=10) # (batchsize, 320, 945)\n",
    "        self.pool1 = nn.MaxPool1d(5) # (batchsize, 320, 189)\n",
    "        self.conv2 = nn.Conv1d(320,480, kernel_size = 5) # (batchsize, 480, 185)\n",
    "        self.pool2 = nn.MaxPool1d(5) # (batchsize, 480, 37)\n",
    "        \n",
    "        self.fc1 = nn.Linear((480*37)+size, 256) #THE input will be larger based on how big metadata is (we input in forward func)\n",
    "        self.fc2 = nn.Linear(256,128)\n",
    "        self.fc3 = nn.Linear(128,1)\n",
    "            \n",
    "    def forward(self,x,meta): #x should be (batchsize, channels(columns), length). meta should be (batchsize, 78)\n",
    "        out = nn.functional.relu(self.conv1(x))\n",
    "        out = self.pool1(out)\n",
    "        out = nn.functional.relu(self.conv2(out))\n",
    "        out = self.pool2(out)\n",
    " \n",
    "        out = torch.flatten(out, start_dim=1) #Should return (batchsize, 480*39)\n",
    "        #print(out.shape) #(4,9120)\n",
    "        \n",
    "        #Concatenate metadata here!\n",
    "        out = torch.cat((out,meta),1)\n",
    "        out = nn.functional.relu(self.fc1(out))\n",
    "        out = nn.functional.relu(self.fc2(out))\n",
    "        out = nn.functional.relu(self.fc3(out))\n",
    "        \n",
    "        return(out)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "ohe_dir = \"/nfs/turbo/dcmb-class/bioinf593/groups/group_05/STRonvoli/data/ohe/\"\n",
    "meta_file = \"/nfs/turbo/dcmb-class/bioinf593/groups/group_05/STRonvoli/data/metadata.tsv\"\n",
    "\n",
    "meta = pd.read_csv(meta_file, sep = '\\t')\n",
    "# dataset = dataset.STRDataset(ohe_dir, meta) \n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "ename": "ParserError",
     "evalue": "Error tokenizing data. C error: Expected 18 fields in line 6, saw 22\n",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mParserError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-14-6214d911ebdb>\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[0mdataset\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mSTRDataset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mohe_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmeta_file\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~/bioinf593/STRonvoli/STRDataset.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, ohe_dir, metadata_file)\u001b[0m\n\u001b[1;32m      9\u001b[0m     \u001b[0mCustom\u001b[0m \u001b[0mPyTorch\u001b[0m \u001b[0mdataset\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mmapping\u001b[0m \u001b[0mshort\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mread\u001b[0m \u001b[0mSTR\u001b[0m \u001b[0mloci\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mtheir\u001b[0m \u001b[0mcorresponding\u001b[0m \u001b[0mfeatures\u001b[0m \u001b[0mto\u001b[0m \u001b[0mlong\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mread\u001b[0m \u001b[0mSTR\u001b[0m \u001b[0mcounts\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     10\u001b[0m     \"\"\"\n\u001b[0;32m---> 11\u001b[0;31m     \u001b[0;32mdef\u001b[0m \u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mohe_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmetadata_file\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     12\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mohe_dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mohe_dir\u001b[0m \u001b[0;31m# each file is a one-hot encoding of the sequence and depth at a locus\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     13\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmetadata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmetadata_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'\\t'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# contains truth labels and metadata\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread_csv\u001b[0;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)\u001b[0m\n\u001b[1;32m    686\u001b[0m     )\n\u001b[1;32m    687\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 688\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\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    689\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m    458\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    459\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--> 460\u001b[0;31m         \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparser\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    461\u001b[0m     \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    462\u001b[0m         \u001b[0mparser\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~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m   1196\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   1197\u001b[0m         \u001b[0mnrows\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_validate_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-> 1198\u001b[0;31m         \u001b[0mret\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   1199\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1200\u001b[0m         \u001b[0;31m# May alter columns / col_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m   2155\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   2156\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-> 2157\u001b[0;31m             \u001b[0mdata\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\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   2158\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   2159\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_first_chunk\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.read\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._read_low_memory\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._read_rows\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._tokenize_rows\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.raise_parser_error\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mParserError\u001b[0m: Error tokenizing data. C error: Expected 18 fields in line 6, saw 22\n"
     ]
    }
   ],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "ename": "ParserError",
     "evalue": "Error tokenizing data. C error: Expected 18 fields in line 6, saw 22\n",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mParserError\u001b[0m                               Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-5-c189b5cb423c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0mohe_dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'/nfs/turbo/dcmb-class/bioinf593/groups/group_05/output/depth'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0;31m#Custom Dataset class\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSTRDataset\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mohe_dir\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mohe_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmetadata_file\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mmetadata_file\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~/bioinf593/STRonvoli/STRDataset.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, ohe_dir, metadata_file)\u001b[0m\n\u001b[1;32m      9\u001b[0m     \u001b[0mCustom\u001b[0m \u001b[0mPyTorch\u001b[0m \u001b[0mdataset\u001b[0m \u001b[0;32mclass\u001b[0m \u001b[0mmapping\u001b[0m \u001b[0mshort\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mread\u001b[0m \u001b[0mSTR\u001b[0m \u001b[0mloci\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mtheir\u001b[0m \u001b[0mcorresponding\u001b[0m \u001b[0mfeatures\u001b[0m \u001b[0mto\u001b[0m \u001b[0mlong\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0mread\u001b[0m \u001b[0mSTR\u001b[0m \u001b[0mcounts\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     10\u001b[0m     \"\"\"\n\u001b[0;32m---> 11\u001b[0;31m     \u001b[0;32mdef\u001b[0m \u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mohe_dir\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmetadata_file\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     12\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mohe_dir\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mohe_dir\u001b[0m \u001b[0;31m# each file is a one-hot encoding of the sequence and depth at a locus\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     13\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmetadata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_csv\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmetadata_file\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msep\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'\\t'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# contains truth labels and metadata\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread_csv\u001b[0;34m(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision)\u001b[0m\n\u001b[1;32m    686\u001b[0m     )\n\u001b[1;32m    687\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 688\u001b[0;31m     \u001b[0;32mreturn\u001b[0m \u001b[0m_read\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilepath_or_buffer\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkwds\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    689\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    690\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36m_read\u001b[0;34m(filepath_or_buffer, kwds)\u001b[0m\n\u001b[1;32m    458\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    459\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--> 460\u001b[0;31m         \u001b[0mdata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mparser\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    461\u001b[0m     \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    462\u001b[0m         \u001b[0mparser\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~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m   1196\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   1197\u001b[0m         \u001b[0mnrows\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_validate_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-> 1198\u001b[0;31m         \u001b[0mret\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   1199\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1200\u001b[0m         \u001b[0;31m# May alter columns / col_dict\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/bioinf593/STRonvoli/bioinf593proj/lib64/python3.6/site-packages/pandas/io/parsers.py\u001b[0m in \u001b[0;36mread\u001b[0;34m(self, nrows)\u001b[0m\n\u001b[1;32m   2155\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   2156\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-> 2157\u001b[0;31m             \u001b[0mdata\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\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   2158\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   2159\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_first_chunk\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader.read\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._read_low_memory\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._read_rows\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.TextReader._tokenize_rows\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/parsers.pyx\u001b[0m in \u001b[0;36mpandas._libs.parsers.raise_parser_error\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mParserError\u001b[0m: Error tokenizing data. C error: Expected 18 fields in line 6, saw 22\n"
     ]
    }
   ],
   "source": [
    "device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')\n",
    "\n",
    "metadata_file = '/nfs/turbo/dcmb-class/bioinf593/groups/group_05/output/trgt/repeatregion_10_parsedvcf.txt'\n",
    "ohe_dir = '/nfs/turbo/dcmb-class/bioinf593/groups/group_05/output/depth'\n",
    "#Custom Dataset class\n",
    "data = STRDataset(ohe_dir=ohe_dir, metadata_file=metadata_file)\n"
   ]
  }
 ],
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