full_project_skeleton.ipynb

{
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  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
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   "source": [
    "def parse_blosum(path):\n",
    "    \"\"\"\n",
    "        Reads BLOSUM62 matrix file and stores in a 2-dimensional dictionary.\n",
    "        :param path: a str with the BLOSUM62 substitution matrix file path\n",
    "        :return: a 2-dimensional dict with amino acid (AA) substitution scores\n",
    "    \"\"\"\n",
    "\n",
    "    aas = []\n",
    "    aa_scores = []\n",
    "    with open(path, \"rb\") as f:\n",
    "        for line in f:\n",
    "            # Convert bytes to str\n",
    "            line = line.decode('UTF-8')\n",
    "            # Skip headers\n",
    "            if line.startswith('#') or line.startswith('x'):\n",
    "                continue\n",
    "            # Store AAs and scores (matrix is symmetric)\n",
    "            else:\n",
    "                aas.append(line.strip('\\n').split()[0])\n",
    "                aa_scores.append(line.strip('\\n').split()[1:len(line)])\n",
    "\n",
    "    # Create a 2-dimensional dictionary with AAs as keys and empty dictionaries as values\n",
    "    blosum_dict = {}\n",
    "    for aa in aas:\n",
    "        blosum_dict[aa] = {}\n",
    "\n",
    "    #########################\n",
    "    ### START CODING HERE ###\n",
    "    #########################\n",
    "    for i in range(len(aas)):\n",
    "        for j in range(len(aas)):\n",
    "            blosum_dict[aas[i]][aas[j]] = aa_scores[i][j]\n",
    "    #########################\n",
    "    ###  END CODING HERE  ###\n",
    "    #########################\n",
    "\n",
    "    return blosum_dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "outputs": [
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     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "blosum_path = r'E:\\FoB\\FoB2021Project_3h\\data\\BLOSUM62.txt'\n",
    "parse_blosum(blosum_path)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "outputs": [],
   "source": [
    "def parse_vep(path):\n",
    "    \"\"\"\n",
    "        Reads VEP file and parses HGVS IDs and corresponding AA reference-mutation pairs.\n",
    "        :param path: a str with the VEP input file path\n",
    "        :return: three lists with HGVS IDs, reference AAs, and corresponding mutation AAs, respectively\n",
    "    \"\"\"\n",
    "\n",
    "    hgvs_ids = []\n",
    "    ref_aas = []\n",
    "    mut_aas = []\n",
    "    with open(path, \"rb\") as f:\n",
    "        # Read lines\n",
    "        for line in f:\n",
    "            # Convert bytes to str\n",
    "            line = line.decode('UTF-8').strip('\\n')\n",
    "            # Skip header\n",
    "            if line.startswith('#'):\n",
    "                continue\n",
    "            else:\n",
    "                # Get HGVS ID from the first column and append to the list\n",
    "                hgvs_ids.append(line.split('\\t')[0])\n",
    "                # Get amino acid mutation which is in the second column in the file\n",
    "                vars = line.split('\\t')[1]\n",
    "                #########################\n",
    "                ### START CODING HERE ###\n",
    "                #########################\n",
    "                # vars contains ref and mut aas separated by /\n",
    "                ref_aa, mut_aa = vars.split('/')\n",
    "                ref_aas.append(ref_aa)\n",
    "                mut_aas.append(mut_aa)\n",
    "                #########################\n",
    "                ###  END CODING HERE  ###\n",
    "                #########################\n",
    "    return hgvs_ids, ref_aas, mut_aas"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
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  {
   "cell_type": "code",
   "execution_count": 9,
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     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vep_path = r'E:\\FoB\\FoB2021Project_3h\\data\\vep\\HGVS_2020_big_VEP_baseline.tsv'\n",
    "parse_vep(vep_path)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "outputs": [],
   "source": [
    "import numbers\n",
    "import os\n",
    "import sys\n",
    "import matplotlib.collections\n",
    "import matplotlib.pyplot\n",
    "import argparse\n",
    "import numpy\n",
    "\n",
    "matplotlib.use('AGG')\n",
    "\n",
    "def parse_predictor(filename):\n",
    "    \"\"\"\n",
    "        Parses scores of every HGVS ID out of the predictor input file.\n",
    "        :param filename: a str with the predictor input file\n",
    "        :return: a dict with HGVS IDs (keys), and the corresponding predictor scores (values)\n",
    "    \"\"\"\n",
    "\n",
    "    global type_predictor\n",
    "    if 'sift' in filename:\n",
    "        type_predictor = 'sift'\n",
    "    elif 'polyphen' in filename:\n",
    "        type_predictor = 'polyphen'\n",
    "    elif 'baseline' in filename:\n",
    "        type_predictor = 'BLOSUM'\n",
    "    else:\n",
    "        type_predictor = ''\n",
    "\n",
    "    predictor_dict = {}\n",
    "\n",
    "    with open(filename, 'r') as f:\n",
    "        # Total bytes in the file (end of file)\n",
    "        eof = f.seek(0, 2)\n",
    "        # Go to the beginning of the file again\n",
    "        f.seek(0)\n",
    "        # Read the first line (should be the header)\n",
    "        f.readline()\n",
    "        # Get the current position of the file pointer\n",
    "        cur = f.tell()\n",
    "        # If the file doesn't contain predictor results (the header excluded), exit\n",
    "        if cur == eof:\n",
    "            sys.exit('ERROR: input predictor file does not contain predictor results!')\n",
    "\n",
    "        for line in f:\n",
    "            line = line.rstrip()\n",
    "            arr = line.split(\"\\t\")\n",
    "\n",
    "            if len(arr) != 2:\n",
    "                print(\"Warning: the following line does not have two elements separated by a tab:\\n\", line)\n",
    "\n",
    "            key = (arr[0])\n",
    "            value = float(arr[1])\n",
    "            predictor_dict[key] = value\n",
    "\n",
    "    f.close()\n",
    "    return predictor_dict\n",
    "\n",
    "\n",
    "def parse_benchmark(filename):\n",
    "    \"\"\"\n",
    "        Parses every HGVS classification out of the benchmark file.\n",
    "        :param filename: a str with the benchmark input file\n",
    "        :return: a dict with HGVS IDs (keys), and corresponding benchmark classifications (values)\n",
    "    \"\"\"\n",
    "\n",
    "    benchmark_dict = {}\n",
    "\n",
    "    with open(filename,'r') as f:\n",
    "        # Total bytes in the file (end of file)\n",
    "        eof = f.seek(0, 2)\n",
    "        # Go to the beginning of the file again\n",
    "        f.seek(0)\n",
    "        # Read the first line (should be the header)\n",
    "        f.readline()\n",
    "        # Get the current position of the file pointer\n",
    "        cur = f.tell()\n",
    "        # If the file doesn't contain predictor results (the header excluded), exit\n",
    "        if cur == eof:\n",
    "            sys.exit('ERROR: input benchmark file does not contain benchmark results!')\n",
    "\n",
    "        for line in f:\n",
    "            line = line.rstrip()\n",
    "            arr = line.split(\"\\t\")\n",
    "\n",
    "            if len(arr) < 2:\n",
    "                print(\"Warning: the following line does not have three elements separated by a tab:\\n\", line)\n",
    "\n",
    "            key = arr[0]\n",
    "            value = arr[1]\n",
    "            benchmark_dict[key] = value\n",
    "\n",
    "    return benchmark_dict\n",
    "\n",
    "def count_total_results(predictor_score_dict, benchmark_dict):\n",
    "    \"\"\"\n",
    "        Calculates the total number of positives (P), or benign results, and negatives (N), or pathogenic results.\n",
    "        :param predictor_score_dict: a dict of all predictor scores\n",
    "        :param benchmark_dict: a dict of benchmark classifications\n",
    "        :return: a list of ints for the total number of benign and pathogenic results\n",
    "    \"\"\"\n",
    "\n",
    "    pathogenic = 0\n",
    "    benign = 0\n",
    "    for key, value in predictor_score_dict.items():\n",
    "        result = benchmark_dict[key]\n",
    "        if result == 'Pathogenic':\n",
    "            pathogenic += 1\n",
    "        elif result == 'Benign':\n",
    "            benign += 1\n",
    "    return [benign, pathogenic]"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "outputs": [],
   "source": [
    "pred_baseline = r'E:\\FoB\\FoB2021Project_3h\\output\\HGVS_2020_big_baseline_scores.tsv'\n",
    "pred_polyphen = r'E:\\FoB\\FoB2021Project_3h\\data\\vep\\HGVS_2020_big_polyphen_scores.tsv'\n",
    "pred_sift = r'E:\\FoB\\FoB2021Project_3h\\data\\vep\\HGVS_2020_big_sift_scores.tsv'\n",
    "bench = r'E:\\FoB\\FoB2021Project_3h\\data\\HGVS_2020_big_benchmark.tsv'"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "outputs": [
    {
     "data": {
      "text/plain": "{'NC_000016.10:g.89748658C>T': 'Pathogenic',\n 'NC_000008.11:g.143818378G>A': 'Pathogenic',\n 'NC_000023.11:g.32644238T>A': 'Benign',\n 'NC_000002.12:g.39022779A>G': 'Pathogenic',\n 'NC_000001.11:g.154926384G>A': 'Pathogenic',\n 'NC_000001.11:g.215674313G>C': 'Pathogenic',\n 'NC_000002.12:g.112756449T>C': 'Benign',\n 'NC_000012.12:g.32643663G>A': 'Benign',\n 'NC_000001.11:g.215675336C>T': 'Benign',\n 'NC_000002.12:g.159882292G>A': 'Benign',\n 'NC_000003.12:g.184165474C>T': 'Benign',\n 'NC_000001.11:g.92475800A>G': 'Benign',\n 'NC_000014.9:g.91969063T>G': 'Benign',\n 'NC_000012.12:g.49185198G>A': 'Pathogenic',\n 'NC_000009.12:g.95467285G>T': 'Pathogenic',\n 'NC_000012.12:g.49034915C>A': 'Pathogenic',\n 'NC_000001.11:g.11012634G>A': 'Benign',\n 'NC_000016.10:g.8768220C>T': 'Pathogenic',\n 'NC_000015.10:g.92998538C>T': 'Pathogenic',\n 'NC_000007.14:g.4788228G>A': 'Benign',\n 'NC_000018.10:g.62095902C>T': 'Pathogenic',\n 'NC_000005.10:g.122074012C>T': 'Pathogenic',\n 'NC_000002.12:g.25244154C>G': 'Pathogenic',\n 'NC_000017.11:g.42322445G>C': 'Pathogenic',\n 'NC_000003.12:g.4361853C>T': 'Benign',\n 'NC_000009.12:g.136674753T>A': 'Pathogenic',\n 'NC_000016.10:g.74628505A>T': 'Pathogenic',\n 'NC_000003.12:g.190388374C>G': 'Benign',\n 'NC_000009.12:g.126693528G>C': 'Pathogenic',\n 'NC_000011.10:g.47410315G>A': 'Pathogenic',\n 'NC_000019.10:g.17766667A>C': 'Pathogenic',\n 'NC_000023.11:g.38367392C>T': 'Pathogenic',\n 'NC_000021.9:g.34449113T>C': 'Benign',\n 'NC_000016.10:g.53652604C>G': 'Pathogenic',\n 'NC_000003.12:g.87255410C>T': 'Benign',\n 'NC_000015.10:g.48470757C>T': 'Pathogenic',\n 'NC_000019.10:g.39507099G>A': 'Pathogenic',\n 'NC_000004.12:g.10077754G>A': 'Benign',\n 'NC_000017.11:g.31260496C>T': 'Pathogenic',\n 'NC_000010.11:g.46461918A>G': 'Benign',\n 'NC_000011.10:g.111857622C>T': 'Pathogenic',\n 'NC_000003.12:g.186617201G>T': 'Benign',\n 'NC_000007.14:g.16406129C>T': 'Pathogenic',\n 'NC_000013.11:g.101292058C>T': 'Pathogenic',\n 'NC_000016.10:g.2111314G>A': 'Benign',\n 'NC_000015.10:g.74180171C>G': 'Pathogenic',\n 'NC_000006.12:g.150389354G>A': 'Benign',\n 'NC_000003.12:g.64096160G>A': 'Benign',\n 'NC_000002.12:g.219566932G>A': 'Pathogenic',\n 'NC_000001.11:g.241497922G>C': 'Pathogenic',\n 'NC_000002.12:g.85658845G>A': 'Benign',\n 'NC_000012.12:g.109556654A>T': 'Benign',\n 'NC_000002.12:g.178608199T>A': 'Pathogenic',\n 'NC_000023.11:g.153725267A>G': 'Pathogenic',\n 'NC_000001.11:g.18871570T>G': 'Benign',\n 'NC_000013.11:g.32336948G>T': 'Pathogenic',\n 'NC_000012.12:g.48966479C>T': 'Pathogenic',\n 'NC_000012.12:g.52552810C>T': 'Benign',\n 'NC_000017.11:g.63941939C>T': 'Pathogenic',\n 'NC_000021.9:g.34370656T>C': 'Pathogenic',\n 'NC_000017.11:g.41612477C>G': 'Benign',\n 'NC_000005.10:g.58969539G>A': 'Benign',\n 'NC_000002.12:g.218814408C>T': 'Pathogenic',\n 'NC_000003.12:g.43080099G>A': 'Pathogenic',\n 'NC_000017.11:g.10421663C>T': 'Benign',\n 'NC_000007.14:g.107920333C>G': 'Benign',\n 'NC_000012.12:g.10118456T>C': 'Benign',\n 'NC_000012.12:g.47842603T>A': 'Benign',\n 'NC_000002.12:g.71665298G>T': 'Pathogenic',\n 'NC_000001.11:g.209796477G>A': 'Pathogenic',\n 'NC_000017.11:g.39665462G>T': 'Pathogenic',\n 'NC_000001.11:g.34761461C>G': 'Benign',\n 'NC_000018.10:g.26285904A>G': 'Benign',\n 'NC_000023.11:g.14844578G>A': 'Benign',\n 'NC_000019.10:g.49182756C>G': 'Benign',\n 'NC_000004.12:g.148436758C>G': 'Benign',\n 'NC_000020.11:g.62327985G>A': 'Benign',\n 'NC_000010.11:g.104132169G>C': 'Benign',\n 'NC_000004.12:g.47403613T>C': 'Pathogenic',\n 'NC_000013.11:g.26682932A>G': 'Benign',\n 'NC_000011.10:g.121310582C>T': 'Benign',\n 'NC_000005.10:g.53075070A>C': 'Benign',\n 'NC_000009.12:g.3826445A>C': 'Benign',\n 'NC_000017.11:g.46030734C>T': 'Benign',\n 'NC_000001.11:g.204166247A>C': 'Pathogenic',\n 'NC_000019.10:g.33401825A>G': 'Benign',\n 'NC_000005.10:g.40841660G>A': 'Benign',\n 'NC_000003.12:g.37042272G>T': 'Pathogenic',\n 'NC_000018.10:g.49792313A>T': 'Benign',\n 'NC_000002.12:g.29064361T>C': 'Benign',\n 'NC_000022.11:g.41127532C>G': 'Benign',\n 'NC_000001.11:g.186078130C>T': 'Benign',\n 'NC_000011.10:g.121187849A>G': 'Pathogenic',\n 'NC_000015.10:g.63121917G>A': 'Benign',\n 'NC_000005.10:g.157252831A>C': 'Benign',\n 'NC_000005.10:g.53096020T>G': 'Benign',\n 'NC_000019.10:g.11116214T>C': 'Pathogenic',\n 'NC_000006.12:g.2833880G>A': 'Benign',\n 'NC_000017.11:g.75836662A>G': 'Pathogenic',\n 'NC_000023.11:g.25010262G>A': 'Pathogenic',\n 'NC_000009.12:g.132903728G>A': 'Pathogenic',\n 'NC_000017.11:g.50189430C>A': 'Pathogenic',\n 'NC_000001.11:g.212885292G>A': 'Pathogenic',\n 'NC_000002.12:g.202467559T>G': 'Pathogenic',\n 'NC_000008.11:g.56993710G>A': 'Benign',\n 'NC_000009.12:g.132892283T>C': 'Benign',\n 'NC_000016.10:g.70127360T>C': 'Benign',\n 'NC_000016.10:g.8781360T>C': 'Pathogenic',\n 'NC_000002.12:g.113246775C>T': 'Pathogenic',\n 'NC_000009.12:g.744585C>G': 'Benign',\n 'NC_000017.11:g.43041407A>T': 'Benign',\n 'NC_000012.12:g.101764236C>T': 'Pathogenic',\n 'NC_000016.10:g.2083810C>A': 'Pathogenic',\n 'NC_000008.11:g.1885635G>C': 'Benign',\n 'NC_000002.12:g.33188841T>C': 'Benign',\n 'NC_000004.12:g.1841548G>T': 'Benign',\n 'NC_000015.10:g.74754996G>A': 'Benign',\n 'NC_000017.11:g.43071077T>C': 'Benign',\n 'NC_000008.11:g.71198635C>A': 'Benign',\n 'NC_000003.12:g.81705581A>G': 'Benign',\n 'NC_000023.11:g.74421996C>T': 'Pathogenic',\n 'NC_000013.11:g.31148034G>C': 'Benign',\n 'NC_000014.9:g.67724568C>T': 'Pathogenic',\n 'NC_000001.11:g.173825249T>A': 'Pathogenic',\n 'NC_000015.10:g.72355562G>A': 'Pathogenic',\n 'NC_000023.11:g.154462248G>A': 'Benign',\n 'NC_000012.12:g.6342395T>C': 'Benign',\n 'NC_000019.10:g.38510566G>T': 'Pathogenic',\n 'NC_000008.11:g.144360408G>A': 'Pathogenic',\n 'NC_000008.11:g.104379514A>T': 'Benign',\n 'NC_000011.10:g.125960664A>G': 'Benign',\n 'NC_000019.10:g.15122724G>A': 'Benign',\n 'NC_000016.10:g.2108321G>T': 'Pathogenic',\n 'NC_000008.11:g.132882609C>T': 'Pathogenic',\n 'NC_000015.10:g.48487384T>A': 'Pathogenic',\n 'NC_000024.10:g.2787316G>C': 'Pathogenic',\n 'NC_000023.11:g.3029271G>A': 'Benign',\n 'NC_000002.12:g.219637644G>C': 'Benign',\n 'NC_000017.11:g.81535192G>A': 'Benign',\n 'NC_000008.11:g.143922290G>A': 'Pathogenic',\n 'NC_000017.11:g.43063332C>G': 'Pathogenic',\n 'NC_000012.12:g.114354431T>C': 'Benign',\n 'NC_000010.11:g.43113628G>T': 'Pathogenic',\n 'NC_000013.11:g.110492070G>A': 'Pathogenic',\n 'NC_000019.10:g.54131451G>A': 'Benign',\n 'NC_000023.11:g.154379485A>G': 'Pathogenic',\n 'NC_000009.12:g.104819706G>C': 'Benign',\n 'NC_000006.12:g.116627775G>A': 'Pathogenic',\n 'NC_000019.10:g.11116168C>A': 'Pathogenic',\n 'NC_000004.12:g.158706277C>A': 'Pathogenic',\n 'NC_000015.10:g.40936647C>T': 'Pathogenic',\n 'NC_000018.10:g.55228993C>G': 'Pathogenic',\n 'NC_000010.11:g.66379229G>A': 'Benign',\n 'NC_000006.12:g.56553601T>C': 'Benign',\n 'NC_000023.11:g.13753411C>T': 'Pathogenic',\n 'NC_000008.11:g.132124280T>A': 'Benign',\n 'NC_000011.10:g.20654773G>A': 'Benign',\n 'NC_000012.12:g.47989799G>A': 'Pathogenic',\n 'NC_000006.12:g.135497680C>T': 'Benign',\n 'NC_000020.11:g.22581969G>T': 'Benign',\n 'NC_000004.12:g.86016435G>C': 'Benign',\n 'NC_000007.14:g.123134504T>C': 'Benign',\n 'NC_000017.11:g.50195646C>T': 'Pathogenic',\n 'NC_000020.11:g.63413582C>T': 'Pathogenic',\n 'NC_000020.11:g.44432198G>A': 'Benign',\n 'NC_000011.10:g.108510391C>T': 'Benign',\n 'NC_000005.10:g.35694352A>G': 'Benign',\n 'NC_000006.12:g.24520416G>A': 'Benign',\n 'NC_000012.12:g.6566156G>A': 'Benign',\n 'NC_000013.11:g.32327930A>G': 'Benign',\n 'NC_000006.12:g.169769592A>G': 'Benign',\n 'NC_000012.12:g.109783135A>G': 'Benign',\n 'NC_000001.11:g.102876914G>A': 'Benign',\n 'NC_000007.14:g.94430998A>G': 'Benign',\n 'NC_000001.11:g.230704350T>C': 'Benign',\n 'NC_000023.11:g.32464642C>A': 'Pathogenic',\n 'NC_000012.12:g.63624124C>T': 'Pathogenic',\n 'NC_000023.11:g.124372254T>A': 'Benign',\n 'NC_000002.12:g.96810999C>T': 'Benign',\n 'NC_000020.11:g.62881941T>A': 'Benign',\n 'NC_000013.11:g.32340524G>T': 'Pathogenic',\n 'NC_000023.11:g.32365049G>A': 'Pathogenic',\n 'NC_000003.12:g.10153568C>T': 'Benign',\n 'NC_000002.12:g.203956772G>A': 'Benign',\n 'NC_000016.10:g.23641121C>A': 'Pathogenic',\n 'NC_000010.11:g.29550781G>A': 'Benign',\n 'NC_000019.10:g.35746735T>G': 'Pathogenic',\n 'NC_000015.10:g.99972983C>T': 'Benign',\n 'NC_000008.11:g.86668170T>A': 'Pathogenic',\n 'NC_000023.11:g.64921894G>A': 'Pathogenic',\n 'NC_000002.12:g.188993452G>A': 'Pathogenic',\n 'NC_000005.10:g.55956082T>A': 'Pathogenic',\n 'NC_000021.9:g.14965938A>G': 'Benign',\n 'NC_000011.10:g.44262009C>T': 'Benign',\n 'NC_000001.11:g.209792360C>T': 'Pathogenic',\n 'NC_000014.9:g.88437553C>T': 'Pathogenic',\n 'NC_000013.11:g.21703312G>A': 'Benign',\n 'NC_000012.12:g.13564263T>C': 'Benign',\n 'NC_000006.12:g.3104279G>A': 'Pathogenic',\n 'NC_000002.12:g.166041432C>T': 'Pathogenic',\n 'NC_000013.11:g.28018504T>G': 'Pathogenic',\n 'NC_000010.11:g.12097966G>A': 'Benign',\n 'NC_000020.11:g.63408538T>C': 'Pathogenic',\n 'NC_000023.11:g.70259585G>A': 'Benign',\n 'NC_000019.10:g.7170561T>C': 'Pathogenic',\n 'NC_000016.10:g.23215623G>T': 'Benign',\n 'NC_000009.12:g.137782392G>C': 'Benign',\n 'NC_000019.10:g.7267659C>G': 'Pathogenic',\n 'NC_000011.10:g.73395462C>T': 'Pathogenic',\n 'NC_000023.11:g.108573572A>G': 'Pathogenic',\n 'NC_000017.11:g.37739506T>C': 'Pathogenic',\n 'NC_000001.11:g.151406034G>A': 'Pathogenic',\n 'NC_000011.10:g.17145862C>A': 'Pathogenic',\n 'NC_000009.12:g.13183465C>T': 'Benign',\n 'NC_000005.10:g.179837132T>G': 'Benign',\n 'NC_000010.11:g.97601884C>A': 'Pathogenic',\n 'NC_000010.11:g.133626712G>A': 'Benign',\n 'NC_000007.14:g.114690133T>C': 'Benign',\n 'NC_000011.10:g.128838777G>A': 'Benign',\n 'NC_000001.11:g.63411333T>G': 'Pathogenic',\n 'NC_000014.9:g.81144784T>C': 'Benign',\n 'NC_000012.12:g.27963514T>A': 'Pathogenic',\n 'NC_000020.11:g.62821532T>C': 'Pathogenic',\n 'NC_000005.10:g.112842090C>T': 'Pathogenic',\n 'NC_000006.12:g.160130185G>T': 'Benign',\n 'NC_000003.12:g.108162535T>C': 'Benign',\n 'NC_000013.11:g.108207707T>A': 'Benign',\n 'NC_000008.11:g.11494428G>T': 'Benign',\n 'NC_000001.11:g.89269398T>A': 'Benign',\n 'NC_000017.11:g.15999807G>T': 'Pathogenic',\n 'NC_000016.10:g.11553546G>C': 'Pathogenic',\n 'NC_000007.14:g.94411120G>A': 'Pathogenic',\n 'NC_000001.11:g.170719794A>G': 'Benign',\n 'NC_000021.9:g.31663682T>A': 'Benign',\n 'NC_000012.12:g.105142460A>T': 'Benign',\n 'NC_000023.11:g.74421538C>T': 'Benign',\n 'NC_000012.12:g.115983258G>C': 'Pathogenic',\n 'NC_000005.10:g.80654962A>G': 'Benign',\n 'NC_000011.10:g.18408001C>G': 'Benign',\n 'NC_000023.11:g.102938093A>G': 'Benign',\n 'NC_000017.11:g.2373413G>A': 'Benign',\n 'NC_000010.11:g.89015215T>C': 'Benign',\n 'NC_000023.11:g.17724370C>T': 'Pathogenic',\n 'NC_000010.11:g.125767581G>A': 'Benign',\n 'NC_000011.10:g.32392032G>A': 'Pathogenic',\n 'NC_000001.11:g.218442560A>G': 'Benign',\n 'NC_000011.10:g.45914138C>G': 'Benign',\n 'NC_000007.14:g.94426442G>C': 'Pathogenic',\n 'NC_000015.10:g.52135746G>A': 'Benign',\n 'NC_000017.11:g.2672750C>T': 'Pathogenic',\n 'NC_000019.10:g.18069603C>T': 'Benign',\n 'NC_000019.10:g.3121122C>G': 'Pathogenic',\n 'NC_000005.10:g.179112281T>C': 'Benign',\n 'NC_000003.12:g.43080921C>T': 'Pathogenic',\n 'NC_000002.12:g.166054753C>A': 'Pathogenic',\n 'NC_000013.11:g.51937561G>A': 'Pathogenic',\n 'NC_000007.14:g.117540189T>A': 'Pathogenic',\n 'NC_000007.14:g.108573088G>A': 'Benign',\n 'NC_000017.11:g.31330373C>A': 'Pathogenic',\n 'NC_000012.12:g.88507114C>A': 'Benign',\n 'NC_000007.14:g.129209348G>C': 'Pathogenic',\n 'NC_000001.11:g.21577774A>G': 'Benign',\n 'NC_000016.10:g.2094122G>A': 'Pathogenic',\n 'NC_000008.11:g.143817699T>A': 'Pathogenic',\n 'NC_000009.12:g.21207001C>G': 'Benign',\n 'NC_000005.10:g.13823268T>A': 'Pathogenic',\n 'NC_000011.10:g.2572053G>A': 'Pathogenic',\n 'NC_000006.12:g.161785820G>A': 'Pathogenic',\n 'NC_000022.11:g.19963580G>A': 'Benign',\n 'NC_000013.11:g.32319119C>A': 'Pathogenic',\n 'NC_000015.10:g.27989601C>T': 'Pathogenic',\n 'NC_000002.12:g.240045930G>A': 'Benign',\n 'NC_000008.11:g.10606382C>G': 'Benign',\n 'NC_000017.11:g.745039A>G': 'Benign',\n 'NC_000001.11:g.94007741C>A': 'Pathogenic',\n 'NC_000023.11:g.15845965C>A': 'Pathogenic',\n 'NC_000019.10:g.54128339G>T': 'Pathogenic',\n 'NC_000014.9:g.28768479C>A': 'Pathogenic',\n 'NC_000012.12:g.57044168G>C': 'Benign',\n 'NC_000001.11:g.92832073A>C': 'Benign',\n 'NC_000011.10:g.6391976T>C': 'Pathogenic',\n 'NC_000005.10:g.68293835G>C': 'Pathogenic',\n 'NC_000016.10:g.68828302C>T': 'Pathogenic',\n 'NC_000005.10:g.139050960G>A': 'Pathogenic',\n 'NC_000003.12:g.121790166C>A': 'Pathogenic',\n 'NC_000014.9:g.94769802C>T': 'Benign',\n 'NC_000015.10:g.48537615A>T': 'Pathogenic',\n 'NC_000013.11:g.110205399G>A': 'Benign',\n 'NC_000013.11:g.32338225C>A': 'Pathogenic',\n 'NC_000003.12:g.4847072G>A': 'Benign',\n 'NC_000003.12:g.45796521G>T': 'Benign',\n 'NC_000011.10:g.17387595C>T': 'Pathogenic',\n 'NC_000003.12:g.111567528G>C': 'Benign',\n 'NC_000007.14:g.100893967C>T': 'Benign',\n 'NC_000001.11:g.231422424G>A': 'Benign',\n 'NC_000006.12:g.79537307G>A': 'Benign',\n 'NC_000013.11:g.32318748G>A': 'Benign',\n 'NC_000012.12:g.49030958G>A': 'Pathogenic',\n 'NC_000006.12:g.111591806C>T': 'Benign',\n 'NC_000021.9:g.45504470G>C': 'Benign',\n 'NC_000009.12:g.104822520T>C': 'Pathogenic',\n 'NC_000021.9:g.46000812C>T': 'Benign',\n 'NC_000003.12:g.4847421T>C': 'Benign',\n 'NC_000011.10:g.47342744C>T': 'Pathogenic',\n 'NC_000007.14:g.21683834G>A': 'Benign',\n 'NC_000005.10:g.177292005C>T': 'Pathogenic',\n 'NC_000023.11:g.139551260G>A': 'Pathogenic',\n 'NC_000009.12:g.92032275T>G': 'Benign',\n 'NC_000023.11:g.38403681C>T': 'Pathogenic',\n 'NC_000017.11:g.63917337C>T': 'Pathogenic',\n 'NC_000023.11:g.8731961C>G': 'Benign',\n 'NC_000013.11:g.32353757C>T': 'Benign',\n 'NC_000023.11:g.111401175T>C': 'Pathogenic',\n 'NC_000017.11:g.37686568A>G': 'Benign',\n 'NC_000017.11:g.3656727G>A': 'Pathogenic',\n 'NC_000011.10:g.134158027T>G': 'Benign',\n 'NC_000003.12:g.52224303G>A': 'Benign',\n 'NC_000002.12:g.15167232C>T': 'Benign',\n 'NC_000002.12:g.10054288T>C': 'Benign',\n 'NC_000016.10:g.16163118C>T': 'Pathogenic',\n 'NC_000014.9:g.104718929C>T': 'Benign',\n 'NC_000009.12:g.127829767C>A': 'Pathogenic',\n 'NC_000017.11:g.43067655A>C': 'Pathogenic',\n 'NC_000016.10:g.67930456C>G': 'Benign',\n 'NC_000017.11:g.31327751C>T': 'Pathogenic',\n 'NC_000022.11:g.26466246T>C': 'Benign',\n 'NC_000015.10:g.88857646T>A': 'Pathogenic',\n 'NC_000012.12:g.47983410C>T': 'Pathogenic',\n 'NC_000012.12:g.109792704T>C': 'Pathogenic',\n 'NC_000008.11:g.105802291A>G': 'Pathogenic',\n 'NC_000003.12:g.129061545T>C': 'Benign',\n 'NC_000022.11:g.17115076C>T': 'Benign',\n 'NC_000009.12:g.78304842A>C': 'Pathogenic',\n 'NC_000001.11:g.201317635C>T': 'Pathogenic',\n 'NC_000004.12:g.6054100C>G': 'Pathogenic',\n 'NC_000004.12:g.6303072G>C': 'Benign',\n 'NC_000011.10:g.6618809G>A': 'Pathogenic',\n 'NC_000001.11:g.244864001G>A': 'Pathogenic',\n 'NC_000013.11:g.48345087A>T': 'Pathogenic',\n 'NC_000010.11:g.87957867G>A': 'Pathogenic',\n 'NC_000011.10:g.93796509T>C': 'Pathogenic',\n 'NC_000011.10:g.5227096C>A': 'Pathogenic',\n 'NC_000001.11:g.1242601C>T': 'Benign',\n 'NC_000017.11:g.41817149G>A': 'Pathogenic',\n 'NC_000015.10:g.48487375C>A': 'Pathogenic',\n 'NC_000005.10:g.112838778C>T': 'Pathogenic',\n 'NC_000013.11:g.32383740T>C': 'Benign',\n 'NC_000007.14:g.70790771C>G': 'Benign',\n 'NC_000023.11:g.18575428G>T': 'Pathogenic',\n 'NC_000023.11:g.32595855G>A': 'Pathogenic',\n 'NC_000008.11:g.71198987G>A': 'Benign',\n 'NC_000002.12:g.47471041G>T': 'Pathogenic',\n 'NC_000008.11:g.38414892G>C': 'Pathogenic',\n 'NC_000001.11:g.237614782G>A': 'Benign',\n 'NC_000008.11:g.31141456T>A': 'Pathogenic',\n 'NC_000004.12:g.5813454T>C': 'Benign',\n 'NC_000004.12:g.2834901C>T': 'Benign',\n 'NC_000013.11:g.108209928C>A': 'Pathogenic',\n 'NC_000023.11:g.20234771A>C': 'Benign',\n 'NC_000002.12:g.178613870C>T': 'Pathogenic',\n 'NC_000001.11:g.154597125G>A': 'Pathogenic',\n 'NC_000011.10:g.108140127T>G': 'Pathogenic',\n 'NC_000023.11:g.31679373A>T': 'Pathogenic',\n 'NC_000023.11:g.38381360G>A': 'Pathogenic',\n 'NC_000012.12:g.51005436A>G': 'Benign',\n 'NC_000018.10:g.51076674C>T': 'Pathogenic',\n 'NC_000012.12:g.52488365C>G': 'Pathogenic',\n 'NC_000004.12:g.25662726T>C': 'Benign',\n 'NC_000007.14:g.114692179A>T': 'Benign',\n 'NC_000011.10:g.77181392C>T': 'Pathogenic',\n 'NC_000020.11:g.50892557G>T': 'Pathogenic',\n 'NC_000001.11:g.42929712G>A': 'Pathogenic',\n 'NC_000017.11:g.50185605G>A': 'Pathogenic',\n 'NC_000014.9:g.91988289C>T': 'Benign',\n 'NC_000017.11:g.17216380C>A': 'Pathogenic',\n 'NC_000004.12:g.95148783G>T': 'Benign',\n 'NC_000004.12:g.15994028G>A': 'Pathogenic',\n 'NC_000012.12:g.63780027G>A': 'Benign',\n 'NC_000019.10:g.10793829G>A': 'Pathogenic',\n 'NC_000011.10:g.47347030C>T': 'Pathogenic',\n 'NC_000011.10:g.61779416G>A': 'Benign',\n 'NC_000021.9:g.45204677G>A': 'Pathogenic',\n 'NC_000005.10:g.42694991T>C': 'Pathogenic',\n 'NC_000023.11:g.85278646C>A': 'Benign',\n 'NC_000002.12:g.47804958G>T': 'Pathogenic',\n 'NC_000006.12:g.107210572T>C': 'Pathogenic',\n 'NC_000011.10:g.2166536C>A': 'Pathogenic',\n 'NC_000016.10:g.13952260G>C': 'Benign',\n 'NC_000005.10:g.177297644A>G': 'Benign',\n 'NC_000011.10:g.22623948A>C': 'Benign',\n 'NC_000002.12:g.47476522G>T': 'Pathogenic',\n 'NC_000005.10:g.78777216A>C': 'Benign',\n 'NC_000010.11:g.66379281G>A': 'Benign',\n 'NC_000001.11:g.5867887G>A': 'Pathogenic',\n 'NC_000023.11:g.38403741G>A': 'Pathogenic',\n 'NC_000003.12:g.179401278C>T': 'Benign',\n 'NC_000005.10:g.126595022C>T': 'Pathogenic',\n 'NC_000004.12:g.78543278C>T': 'Benign',\n 'NC_000002.12:g.84670377A>G': 'Benign',\n 'NC_000009.12:g.132912382A>C': 'Pathogenic',\n 'NC_000019.10:g.38572182C>T': 'Pathogenic',\n 'NC_000011.10:g.103223087G>A': 'Pathogenic',\n 'NC_000005.10:g.122450978A>G': 'Benign',\n 'NC_000002.12:g.227022135G>A': 'Pathogenic',\n 'NC_000006.12:g.144188373T>C': 'Benign',\n 'NC_000003.12:g.129440351G>C': 'Pathogenic',\n 'NC_000004.12:g.186191943C>G': 'Pathogenic',\n 'NC_000015.10:g.92941868G>T': 'Pathogenic',\n 'NC_000011.10:g.44262610C>T': 'Benign',\n 'NC_000018.10:g.6958610T>G': 'Benign',\n 'NC_000012.12:g.110645031G>T': 'Benign',\n 'NC_000002.12:g.169510430G>A': 'Benign',\n 'NC_000002.12:g.47800965C>G': 'Pathogenic',\n 'NC_000017.11:g.28398985G>A': 'Benign',\n 'NC_000023.11:g.70352640C>T': 'Benign',\n 'NC_000001.11:g.173833470A>G': 'Benign',\n 'NC_000001.11:g.149927993A>G': 'Benign',\n 'NC_000023.11:g.139561941T>A': 'Pathogenic',\n 'NC_000018.10:g.31390712T>C': 'Pathogenic',\n 'NC_000001.11:g.12012726C>A': 'Benign',\n 'NC_000002.12:g.27313074G>A': 'Pathogenic',\n 'NC_000005.10:g.137625765G>A': 'Pathogenic',\n 'NC_000007.14:g.50458565A>G': 'Benign',\n 'NC_000002.12:g.135126596A>G': 'Benign',\n 'NC_000013.11:g.32342530T>A': 'Benign',\n 'NC_000001.11:g.156130658G>T': 'Pathogenic',\n 'NC_000015.10:g.101065640A>G': 'Benign',\n 'NC_000011.10:g.17396980C>T': 'Pathogenic',\n 'NC_000002.12:g.47800369G>T': 'Pathogenic',\n 'NC_000002.12:g.172475080G>A': 'Benign',\n 'NC_000017.11:g.50195099C>A': 'Pathogenic',\n 'NC_000002.12:g.26195184C>G': 'Pathogenic',\n 'NC_000008.11:g.15766208A>C': 'Benign',\n 'NC_000019.10:g.49960413T>G': 'Benign',\n 'NC_000001.11:g.100206504T>C': 'Benign',\n 'NC_000017.11:g.63405208C>T': 'Pathogenic',\n 'NC_000007.14:g.117540311T>C': 'Pathogenic',\n 'NC_000009.12:g.130470873T>C': 'Pathogenic',\n 'NC_000022.11:g.42631376A>G': 'Pathogenic',\n 'NC_000017.11:g.74795600C>G': 'Benign',\n 'NC_000009.12:g.92719041G>A': 'Pathogenic',\n 'NC_000007.14:g.43787943C>T': 'Pathogenic',\n 'NC_000007.14:g.117611743T>G': 'Pathogenic',\n 'NC_000002.12:g.208128258C>T': 'Pathogenic',\n 'NC_000017.11:g.42796196A>G': 'Pathogenic',\n 'NC_000023.11:g.134413910C>T': 'Pathogenic',\n 'NC_000009.12:g.120409126C>G': 'Pathogenic',\n 'NC_000023.11:g.41346351A>G': 'Pathogenic',\n 'NC_000001.11:g.67328273A>G': 'Benign',\n 'NC_000015.10:g.48526247C>A': 'Pathogenic',\n 'NC_000008.11:g.125436432G>T': 'Benign',\n 'NC_000001.11:g.75137116C>T': 'Benign',\n 'NC_000002.12:g.25239153C>T': 'Pathogenic',\n 'NC_000011.10:g.65868522G>A': 'Pathogenic',\n 'NC_000020.11:g.51475656T>C': 'Benign',\n 'NC_000007.14:g.16089546T>G': 'Benign',\n 'NC_000013.11:g.32349851A>G': 'Benign',\n 'NC_000002.12:g.165992053C>T': 'Pathogenic',\n 'NC_000014.9:g.20477412G>A': 'Benign',\n 'NC_000001.11:g.42830459C>T': 'Benign',\n 'NC_000001.11:g.150559429C>A': 'Benign',\n 'NC_000023.11:g.150658011G>A': 'Pathogenic',\n 'NC_000023.11:g.50086338A>G': 'Pathogenic',\n 'NC_000006.12:g.33446710C>T': 'Pathogenic',\n 'NC_000017.11:g.75843133G>C': 'Benign',\n 'NC_000001.11:g.11796205C>A': 'Pathogenic',\n 'NC_000003.12:g.45968585C>T': 'Benign',\n 'NC_000013.11:g.110492105G>A': 'Pathogenic',\n 'NC_000019.10:g.50790783C>T': 'Pathogenic',\n 'NC_000006.12:g.3129046C>T': 'Benign',\n 'NC_000004.12:g.523774G>A': 'Benign',\n 'NC_000006.12:g.5216622C>A': 'Pathogenic',\n 'NC_000019.10:g.17200417G>A': 'Benign',\n 'NC_000019.10:g.1221977G>T': 'Pathogenic',\n 'NC_000009.12:g.2622134C>T': 'Benign',\n 'NC_000007.14:g.42026345G>A': 'Pathogenic',\n 'NC_000023.11:g.25010274C>A': 'Pathogenic',\n 'NC_000016.10:g.70921012G>T': 'Benign',\n 'NC_000003.12:g.10142104C>G': 'Pathogenic',\n 'NC_000013.11:g.32338752T>G': 'Pathogenic',\n 'NC_000003.12:g.126492435C>T': 'Benign',\n 'NC_000023.11:g.108668399G>T': 'Pathogenic',\n 'NC_000009.12:g.133448718T>G': 'Pathogenic',\n 'NC_000001.11:g.220182355C>T': 'Pathogenic',\n 'NC_000015.10:g.48465820G>A': 'Pathogenic',\n 'NC_000015.10:g.42387752G>A': 'Pathogenic',\n 'NC_000022.11:g.33273571C>T': 'Benign',\n 'NC_000017.11:g.50191463C>T': 'Pathogenic',\n 'NC_000022.11:g.20993977G>A': 'Pathogenic',\n 'NC_000002.12:g.43794627T>C': 'Benign',\n 'NC_000015.10:g.72355591A>C': 'Pathogenic',\n 'NC_000016.10:g.9760532C>G': 'Benign',\n 'NC_000001.11:g.11802880C>T': 'Pathogenic',\n 'NC_000011.10:g.36577025G>A': 'Benign',\n 'NC_000001.11:g.197328841C>T': 'Pathogenic',\n 'NC_000022.11:g.17108904C>A': 'Benign',\n 'NC_000023.11:g.150658044A>G': 'Benign',\n 'NC_000011.10:g.117397296C>A': 'Benign',\n 'NC_000010.11:g.133368964G>T': 'Pathogenic',\n 'NC_000011.10:g.6615199A>C': 'Pathogenic',\n 'NC_000019.10:g.1227605A>G': 'Benign',\n 'NC_000014.9:g.50752531C>T': 'Benign',\n 'NC_000009.12:g.37436700G>A': 'Pathogenic',\n 'NC_000009.12:g.21864293T>G': 'Benign',\n 'NC_000011.10:g.61962524C>G': 'Pathogenic',\n 'NC_000018.10:g.23907863A>T': 'Pathogenic',\n 'NC_000017.11:g.65536549G>A': 'Pathogenic',\n 'NC_000020.11:g.18542380C>T': 'Pathogenic',\n 'NC_000017.11:g.17221630T>C': 'Pathogenic',\n 'NC_000006.12:g.158111350T>C': 'Benign',\n 'NC_000009.12:g.74762494C>T': 'Benign',\n 'NC_000007.14:g.156762153T>G': 'Benign',\n 'NC_000009.12:g.35792936T>A': 'Pathogenic',\n 'NC_000017.11:g.31182604T>A': 'Pathogenic',\n 'NC_000023.11:g.49689423T>C': 'Benign',\n 'NC_000011.10:g.644568C>G': 'Benign',\n 'NC_000008.11:g.67112031G>T': 'Pathogenic',\n 'NC_000011.10:g.124922771T>C': 'Benign',\n 'NC_000023.11:g.134498655G>A': 'Pathogenic',\n 'NC_000008.11:g.143561751G>A': 'Benign',\n 'NC_000015.10:g.89318986G>A': 'Pathogenic',\n 'NC_000013.11:g.51937495G>A': 'Pathogenic',\n 'NC_000009.12:g.94639223C>A': 'Pathogenic',\n 'NC_000003.12:g.196065442C>A': 'Pathogenic',\n 'NC_000006.12:g.43615612A>T': 'Benign',\n 'NC_000019.10:g.13303877G>A': 'Pathogenic',\n 'NC_000008.11:g.37765736C>G': 'Pathogenic',\n 'NC_000002.12:g.26502301G>A': 'Pathogenic',\n 'NC_000016.10:g.89286064G>T': 'Pathogenic',\n 'NC_000005.10:g.78002523T>C': 'Benign',\n 'NC_000021.9:g.34859477G>A': 'Pathogenic',\n 'NC_000017.11:g.80108396C>A': 'Pathogenic',\n 'NC_000019.10:g.39488079C>T': 'Pathogenic',\n 'NC_000017.11:g.48530622G>T': 'Benign',\n 'NC_000015.10:g.48428438C>T': 'Pathogenic',\n 'NC_000007.14:g.117480096T>A': 'Pathogenic',\n 'NC_000001.11:g.225419442C>T': 'Benign',\n 'NC_000016.10:g.23629779G>C': 'Pathogenic',\n 'NC_000005.10:g.226041T>A': 'Pathogenic',\n 'NC_000011.10:g.108307914C>T': 'Pathogenic',\n 'NC_000018.10:g.58329105C>T': 'Benign',\n 'NC_000012.12:g.118139489A>G': 'Benign',\n 'NC_000004.12:g.54297211T>C': 'Benign',\n 'NC_000001.11:g.171108133G>T': 'Benign',\n 'NC_000003.12:g.48572712C>T': 'Pathogenic',\n 'NC_000014.9:g.65102437C>A': 'Benign',\n 'NC_000003.12:g.124745795T>G': 'Benign',\n 'NC_000006.12:g.70303288G>C': 'Benign',\n 'NC_000008.11:g.117804894C>G': 'Pathogenic',\n 'NC_000006.12:g.24875663T>A': 'Benign',\n 'NC_000014.9:g.21324872C>T': 'Pathogenic',\n 'NC_000001.11:g.155040566C>T': 'Benign',\n 'NC_000012.12:g.49029118G>A': 'Pathogenic',\n 'NC_000005.10:g.78141268G>A': 'Pathogenic',\n 'NC_000019.10:g.29702133G>A': 'Benign',\n 'NC_000017.11:g.44075831C>T': 'Pathogenic',\n 'NC_000017.11:g.49990191A>T': 'Benign',\n 'NC_000005.10:g.53092663C>T': 'Benign',\n 'NC_000007.14:g.116797134G>T': 'Benign',\n 'NC_000015.10:g.71851302A>T': 'Benign',\n 'NC_000019.10:g.48303998C>T': 'Benign',\n 'NC_000016.10:g.1791460G>A': 'Benign',\n 'NC_000005.10:g.90625152C>A': 'Benign',\n 'NC_000008.11:g.99134644C>T': 'Pathogenic',\n 'NC_000017.11:g.74310164G>C': 'Pathogenic',\n 'NC_000002.12:g.227256385G>T': 'Benign',\n 'NC_000023.11:g.53534101C>G': 'Pathogenic',\n 'NC_000003.12:g.52452217C>A': 'Pathogenic',\n 'NC_000021.9:g.45981811C>T': 'Benign',\n 'NC_000001.11:g.12007217C>G': 'Pathogenic',\n 'NC_000005.10:g.37051871T>G': 'Pathogenic',\n 'NC_000017.11:g.75946274C>T': 'Benign',\n 'NC_000015.10:g.23644619G>A': 'Pathogenic',\n 'NC_000017.11:g.80183975G>A': 'Pathogenic',\n 'NC_000017.11:g.8077117G>A': 'Pathogenic',\n 'NC_000011.10:g.64804507G>A': 'Pathogenic',\n 'NC_000002.12:g.68158384G>C': 'Benign',\n 'NC_000017.11:g.44250125G>T': 'Benign',\n 'NC_000023.11:g.153954282C>T': 'Benign',\n 'NC_000006.12:g.43519737T>C': 'Pathogenic',\n 'NC_000023.11:g.108626257C>T': 'Pathogenic',\n 'NC_000004.12:g.95155876A>G': 'Benign',\n 'NC_000022.11:g.38132881C>T': 'Benign',\n 'NC_000002.12:g.206146919G>A': 'Pathogenic',\n 'NC_000017.11:g.15230744G>A': 'Benign',\n 'NC_000023.11:g.46880727A>C': 'Benign',\n 'NC_000001.11:g.42752551G>A': 'Pathogenic',\n 'NC_000001.11:g.226982996C>T': 'Pathogenic',\n 'NC_000007.14:g.150951493T>C': 'Pathogenic',\n 'NC_000017.11:g.10455267G>T': 'Benign',\n 'NC_000023.11:g.32644175T>A': 'Pathogenic',\n 'NC_000004.12:g.47406706C>T': 'Pathogenic',\n 'NC_000002.12:g.26464893G>A': 'Benign',\n 'NC_000014.9:g.91968613G>A': 'Benign',\n 'NC_000003.12:g.50345533A>C': 'Pathogenic',\n 'NC_000011.10:g.44126956G>T': 'Pathogenic',\n 'NC_000016.10:g.55506314C>T': 'Benign',\n 'NC_000012.12:g.49050035G>A': 'Pathogenic',\n 'NC_000011.10:g.125958678G>A': 'Benign',\n 'NC_000007.14:g.45713998G>T': 'Benign',\n 'NC_000005.10:g.53072695A>G': 'Benign',\n 'NC_000016.10:g.1200389A>G': 'Benign',\n 'NC_000023.11:g.154957120T>C': 'Pathogenic',\n 'NC_000001.11:g.162790832G>C': 'Benign',\n 'NC_000002.12:g.178591977C>T': 'Pathogenic',\n 'NC_000010.11:g.72009749C>T': 'Benign',\n 'NC_000021.9:g.44886223G>T': 'Benign',\n 'NC_000001.11:g.216198476G>C': 'Pathogenic',\n 'NC_000001.11:g.11790858A>G': 'Pathogenic',\n 'NC_000009.12:g.132897293G>A': 'Pathogenic',\n 'NC_000004.12:g.78515936G>A': 'Benign',\n 'NC_000011.10:g.6393961A>C': 'Pathogenic',\n 'NC_000004.12:g.87846039G>A': 'Benign',\n 'NC_000005.10:g.37048502G>A': 'Pathogenic',\n 'NC_000013.11:g.31331184A>G': 'Benign',\n 'NC_000023.11:g.658804G>A': 'Benign',\n 'NC_000023.11:g.100406586G>C': 'Pathogenic',\n 'NC_000015.10:g.100472931C>T': 'Pathogenic',\n 'NC_000018.10:g.49826100A>G': 'Benign',\n 'NC_000017.11:g.73200670A>G': 'Benign',\n 'NC_000023.11:g.154362417C>T': 'Pathogenic',\n 'NC_000001.11:g.218443793C>G': 'Benign',\n 'NC_000001.11:g.176771044G>T': 'Benign',\n 'NC_000001.11:g.42929736G>A': 'Pathogenic',\n 'NC_000011.10:g.13492506G>A': 'Pathogenic',\n 'NC_000001.11:g.119422277C>T': 'Pathogenic',\n 'NC_000008.11:g.144095991G>T': 'Pathogenic',\n 'NC_000018.10:g.57695188C>A': 'Pathogenic',\n 'NC_000002.12:g.71528403T>C': 'Pathogenic',\n 'NC_000009.12:g.104598728C>G': 'Benign',\n 'NC_000003.12:g.10150259G>A': 'Benign',\n 'NC_000003.12:g.12599717C>G': 'Pathogenic',\n 'NC_000011.10:g.2776029G>A': 'Pathogenic',\n 'NC_000017.11:g.31227607G>T': 'Pathogenic',\n 'NC_000007.14:g.117611652C>T': 'Pathogenic',\n 'NC_000007.14:g.136869276G>A': 'Benign',\n 'NC_000019.10:g.7647478A>G': 'Benign',\n 'NC_000002.12:g.206308165C>T': 'Benign',\n 'NC_000013.11:g.32338416C>T': 'Benign',\n 'NC_000016.10:g.2111872C>G': 'Pathogenic',\n 'NC_000010.11:g.43128364C>T': 'Benign',\n 'NC_000006.12:g.52048491C>T': 'Pathogenic',\n 'NC_000005.10:g.37206339C>A': 'Pathogenic',\n 'NC_000021.9:g.32631194G>A': 'Benign',\n 'NC_000017.11:g.50185863A>G': 'Pathogenic',\n 'NC_000005.10:g.143300556A>T': 'Pathogenic',\n 'NC_000018.10:g.55225482G>A': 'Benign',\n 'NC_000014.9:g.103563042C>G': 'Benign',\n 'NC_000001.11:g.11970750G>C': 'Pathogenic',\n 'NC_000001.11:g.193135441C>T': 'Pathogenic',\n 'NC_000007.14:g.117590355C>A': 'Pathogenic',\n 'NC_000009.12:g.134699923G>T': 'Pathogenic',\n 'NC_000001.11:g.220102258T>C': 'Pathogenic',\n 'NC_000005.10:g.149895228C>T': 'Pathogenic',\n 'NC_000002.12:g.84697699T>C': 'Benign',\n 'NC_000017.11:g.42911449T>C': 'Benign',\n 'NC_000004.12:g.80202243T>C': 'Pathogenic',\n 'NC_000003.12:g.36993660A>C': 'Pathogenic',\n 'NC_000002.12:g.55923729C>T': 'Benign',\n 'NC_000023.11:g.32485072G>A': 'Pathogenic',\n 'NC_000015.10:g.45116589C>G': 'Pathogenic',\n 'NC_000002.12:g.151617397C>G': 'Benign',\n 'NC_000022.11:g.50624290C>T': 'Benign',\n 'NC_000006.12:g.133528828C>T': 'Benign',\n 'NC_000007.14:g.156683987G>A': 'Benign',\n 'NC_000009.12:g.6532544G>A': 'Benign',\n 'NC_000016.10:g.8783005A>G': 'Benign',\n 'NC_000017.11:g.61952972G>A': 'Benign',\n 'NC_000020.11:g.46725461G>T': 'Pathogenic',\n 'NC_000014.9:g.77508758T>A': 'Benign',\n 'NC_000001.11:g.154571759C>G': 'Pathogenic',\n 'NC_000013.11:g.32380037C>T': 'Pathogenic',\n 'NC_000009.12:g.132906004C>G': 'Benign',\n 'NC_000023.11:g.22212959G>A': 'Pathogenic',\n 'NC_000004.12:g.148259978C>T': 'Pathogenic',\n 'NC_000023.11:g.38367344C>T': 'Pathogenic',\n 'NC_000020.11:g.9479280A>G': 'Benign',\n 'NC_000010.11:g.44984913G>C': 'Benign',\n 'NC_000011.10:g.119091497C>T': 'Pathogenic',\n 'NC_000015.10:g.84817040A>G': 'Benign',\n 'NC_000023.11:g.85911292G>A': 'Pathogenic',\n 'NC_000015.10:g.100569891T>C': 'Benign',\n 'NC_000023.11:g.77620442C>T': 'Pathogenic',\n 'NC_000019.10:g.41985090A>T': 'Pathogenic',\n 'NC_000017.11:g.14102230C>A': 'Pathogenic',\n 'NC_000005.10:g.150053838G>C': 'Benign',\n 'NC_000021.9:g.31659782G>A': 'Pathogenic',\n 'NC_000006.12:g.36291501C>A': 'Pathogenic',\n 'NC_000002.12:g.165344627G>A': 'Pathogenic',\n 'NC_000018.10:g.46560274G>T': 'Pathogenic',\n 'NC_000014.9:g.45154011C>A': 'Pathogenic',\n 'NC_000006.12:g.64902211G>T': 'Pathogenic',\n 'NC_000023.11:g.32816541G>A': 'Pathogenic',\n 'NC_000019.10:g.51965074G>A': 'Benign',\n 'NC_000002.12:g.188997736G>C': 'Pathogenic',\n 'NC_000011.10:g.93699288T>G': 'Benign',\n 'NC_000006.12:g.146159536C>T': 'Pathogenic',\n 'NC_000007.14:g.33367863G>A': 'Pathogenic',\n 'NC_000002.12:g.178574569C>A': 'Pathogenic',\n 'NC_000003.12:g.10142188G>A': 'Pathogenic',\n 'NC_000004.12:g.6302710G>C': 'Benign',\n 'NC_000001.11:g.52692726C>A': 'Pathogenic',\n 'NC_000001.11:g.21873980C>T': 'Benign',\n 'NC_000002.12:g.144396585A>T': 'Pathogenic',\n 'NC_000001.11:g.156876496G>C': 'Pathogenic',\n 'NC_000005.10:g.33453311G>A': 'Benign',\n 'NC_000023.11:g.45200617C>G': 'Benign',\n 'NC_000004.12:g.52029884A>G': 'Benign',\n 'NC_000006.12:g.33432769C>T': 'Pathogenic',\n 'NC_000013.11:g.32340645C>T': 'Benign',\n 'NC_000012.12:g.32642736T>C': 'Benign',\n 'NC_000016.10:g.4797316C>T': 'Benign',\n 'NC_000016.10:g.2060754C>T': 'Pathogenic',\n 'NC_000019.10:g.7267833A>G': 'Pathogenic',\n 'NC_000002.12:g.165991529C>A': 'Pathogenic',\n 'NC_000019.10:g.15160965G>C': 'Pathogenic',\n 'NC_000005.10:g.55220382C>T': 'Pathogenic',\n 'NC_000002.12:g.47412413G>C': 'Pathogenic',\n 'NC_000015.10:g.99973659C>T': 'Benign',\n 'NC_000023.11:g.108694874T>C': 'Pathogenic',\n 'NC_000002.12:g.48963187A>G': 'Pathogenic',\n 'NC_000016.10:g.67942731T>C': 'Pathogenic',\n 'NC_000007.14:g.117540230C>T': 'Pathogenic',\n 'NC_000012.12:g.76345181A>G': 'Benign',\n 'NC_000009.12:g.92031456C>A': 'Benign',\n 'NC_000007.14:g.117509132T>G': 'Pathogenic',\n 'NC_000015.10:g.63042489G>C': 'Benign',\n 'NC_000005.10:g.7897078C>T': 'Benign',\n 'NC_000017.11:g.3661809A>G': 'Benign',\n 'NC_000002.12:g.74363045T>G': 'Benign',\n 'NC_000012.12:g.64495483C>A': 'Benign',\n 'NC_000008.11:g.19951791G>A': 'Pathogenic',\n 'NC_000013.11:g.114324518A>T': 'Pathogenic',\n 'NC_000020.11:g.63692937G>A': 'Benign',\n 'NC_000002.12:g.47369587G>T': 'Benign',\n 'NC_000003.12:g.139350318T>C': 'Pathogenic',\n 'NC_000009.12:g.121326518G>T': 'Benign',\n 'NC_000007.14:g.76434087C>G': 'Pathogenic',\n 'NC_000009.12:g.109141360C>T': 'Pathogenic',\n 'NC_000011.10:g.64805078A>T': 'Pathogenic',\n 'NC_000017.11:g.7848173C>T': 'Benign',\n 'NC_000008.11:g.125091668A>G': 'Benign',\n 'NC_000006.12:g.51632705C>A': 'Benign',\n 'NC_000020.11:g.32808730A>G': 'Benign',\n 'NC_000004.12:g.145639497C>T': 'Pathogenic',\n 'NC_000007.14:g.22942613C>A': 'Benign',\n 'NC_000019.10:g.36006456C>G': 'Benign',\n 'NC_000013.11:g.32367646T>G': 'Benign',\n 'NC_000022.11:g.23791780C>T': 'Pathogenic',\n 'NC_000009.12:g.114094364A>G': 'Benign',\n 'NC_000016.10:g.75473355T>A': 'Benign',\n 'NC_000002.12:g.178579850T>G': 'Pathogenic',\n 'NC_000001.11:g.110198158C>G': 'Pathogenic',\n 'NC_000004.12:g.93829734G>C': 'Benign',\n 'NC_000023.11:g.101353935C>G': 'Pathogenic',\n 'NC_000010.11:g.125815094T>C': 'Pathogenic',\n 'NC_000016.10:g.8783997C>G': 'Benign',\n 'NC_000016.10:g.1362609A>G': 'Pathogenic',\n 'NC_000007.14:g.117665547G>T': 'Pathogenic',\n 'NC_000016.10:g.89645972G>A': 'Benign',\n 'NC_000004.12:g.1002377G>A': 'Benign',\n 'NC_000001.11:g.9262261C>G': 'Pathogenic',\n 'NC_000018.10:g.51067041C>T': 'Pathogenic',\n 'NC_000016.10:g.89268645G>A': 'Pathogenic',\n 'NC_000017.11:g.58216664A>T': 'Pathogenic',\n 'NC_000006.12:g.45547304G>C': 'Pathogenic',\n 'NC_000002.12:g.188993434G>A': 'Pathogenic',\n 'NC_000007.14:g.117559643C>A': 'Pathogenic',\n 'NC_000002.12:g.190969701A>G': 'Benign',\n 'NC_000002.12:g.39023134A>G': 'Pathogenic',\n 'NC_000001.11:g.34761477C>T': 'Benign',\n 'NC_000001.11:g.215628906G>A': 'Benign',\n 'NC_000012.12:g.52646920C>T': 'Benign',\n 'NC_000012.12:g.95972920G>A': 'Benign',\n 'NC_000002.12:g.46903938G>C': 'Benign',\n 'NC_000003.12:g.129533704G>A': 'Pathogenic',\n 'NC_000003.12:g.196708668A>G': 'Benign',\n 'NC_000018.10:g.49837607T>C': 'Benign',\n 'NC_000019.10:g.17783027C>T': 'Pathogenic',\n 'NC_000020.11:g.10673963C>T': 'Benign',\n 'NC_000019.10:g.48993294A>C': 'Benign',\n 'NC_000001.11:g.147908094G>A': 'Pathogenic',\n 'NC_000009.12:g.35685529G>A': 'Pathogenic',\n 'NC_000003.12:g.38560210G>C': 'Pathogenic',\n 'NC_000013.11:g.102736971A>G': 'Benign',\n 'NC_000011.10:g.77183146C>A': 'Pathogenic',\n 'NC_000017.11:g.43063882C>T': 'Pathogenic',\n 'NC_000009.12:g.137101647G>A': 'Benign',\n 'NC_000017.11:g.31375026A>T': 'Benign',\n 'NC_000005.10:g.90519160T>A': 'Benign',\n 'NC_000010.11:g.89225111A>C': 'Pathogenic',\n 'NC_000009.12:g.2654048G>A': 'Benign',\n 'NC_000002.12:g.201723437C>T': 'Benign',\n 'NC_000013.11:g.32316450C>T': 'Benign',\n 'NC_000012.12:g.101770097A>G': 'Pathogenic',\n 'NC_000010.11:g.26067063A>G': 'Benign',\n 'NC_000002.12:g.189003410G>A': 'Pathogenic',\n 'NC_000016.10:g.3596275G>A': 'Benign',\n 'NC_000002.12:g.218809755G>A': 'Pathogenic',\n 'NC_000008.11:g.24952575T>A': 'Benign',\n 'NC_000010.11:g.103077491G>A': 'Benign',\n 'NC_000020.11:g.9409080G>T': 'Pathogenic',\n 'NC_000005.10:g.38481049T>G': 'Benign',\n 'NC_000004.12:g.56011500G>A': 'Pathogenic',\n 'NC_000003.12:g.128909411G>A': 'Pathogenic',\n 'NC_000012.12:g.122263594T>G': 'Benign',\n 'NC_000001.11:g.160143102G>A': 'Benign',\n 'NC_000018.10:g.59273075G>T': 'Benign',\n 'NC_000012.12:g.132618878G>A': 'Benign',\n 'NC_000014.9:g.75015205A>G': 'Benign',\n 'NC_000001.11:g.152311468G>A': 'Pathogenic',\n 'NC_000009.12:g.123382480G>A': 'Benign',\n 'NC_000023.11:g.137567448T>A': 'Pathogenic',\n 'NC_000001.11:g.22647250C>T': 'Pathogenic',\n 'NC_000017.11:g.17221628C>T': 'Pathogenic',\n 'NC_000010.11:g.104041526A>C': 'Pathogenic',\n 'NC_000013.11:g.23324837G>A': 'Benign',\n 'NC_000023.11:g.136648280G>A': 'Benign',\n 'NC_000011.10:g.61398269G>C': 'Benign',\n 'NC_000002.12:g.227297683G>A': 'Pathogenic',\n 'NC_000018.10:g.55224766A>T': 'Benign',\n 'NC_000012.12:g.2696466C>A': 'Benign',\n 'NC_000018.10:g.27985701T>G': 'Pathogenic',\n 'NC_000006.12:g.157196221C>T': 'Pathogenic',\n 'NC_000001.11:g.218442109A>C': 'Benign',\n 'NC_000003.12:g.121781760A>G': 'Benign',\n 'NC_000019.10:g.1221244G>T': 'Pathogenic',\n 'NC_000010.11:g.125816436C>T': 'Pathogenic',\n 'NC_000023.11:g.22248011C>T': 'Benign',\n 'NC_000001.11:g.207468716G>A': 'Pathogenic',\n 'NC_000022.11:g.25207069G>C': 'Pathogenic',\n 'NC_000002.12:g.219484029C>T': 'Benign',\n 'NC_000005.10:g.177282463A>G': 'Pathogenic',\n 'NC_000016.10:g.56914609T>C': 'Benign',\n 'NC_000014.9:g.24163394G>C': 'Benign',\n 'NC_000002.12:g.178549786T>C': 'Benign',\n 'NC_000018.10:g.22181504A>G': 'Pathogenic',\n 'NC_000020.11:g.58446008G>A': 'Benign',\n 'NC_000019.10:g.38585055C>A': 'Pathogenic',\n 'NC_000013.11:g.113118772T>G': 'Pathogenic',\n 'NC_000016.10:g.89918723C>T': 'Benign',\n 'NC_000001.11:g.103006314C>T': 'Pathogenic',\n 'NC_000023.11:g.108597507G>A': 'Pathogenic',\n 'NC_000017.11:g.75943977T>G': 'Benign',\n 'NC_000001.11:g.236899132T>C': 'Benign',\n 'NC_000022.11:g.50583170C>T': 'Benign',\n 'NC_000017.11:g.41817156G>A': 'Pathogenic',\n 'NC_000002.12:g.222232086G>A': 'Pathogenic',\n 'NC_000007.14:g.117592610G>T': 'Pathogenic',\n 'NC_000005.10:g.137619172A>G': 'Benign',\n 'NC_000001.11:g.215817108G>T': 'Pathogenic',\n 'NC_000011.10:g.47358974G>C': 'Pathogenic',\n 'NC_000004.12:g.168179310T>C': 'Benign',\n 'NC_000005.10:g.157211279G>A': 'Benign',\n 'NC_000017.11:g.31232071A>G': 'Pathogenic',\n 'NC_000007.14:g.94409403G>C': 'Pathogenic',\n 'NC_000007.14:g.117548732C>A': 'Pathogenic',\n 'NC_000005.10:g.90685794C>T': 'Benign',\n 'NC_000001.11:g.204159399C>T': 'Pathogenic',\n 'NC_000001.11:g.99875251G>T': 'Pathogenic',\n 'NC_000023.11:g.53248814G>A': 'Pathogenic',\n 'NC_000014.9:g.35402026C>T': 'Benign',\n 'NC_000017.11:g.37733624G>A': 'Pathogenic',\n 'NC_000012.12:g.65247960G>A': 'Benign',\n 'NC_000002.12:g.165342470G>T': 'Pathogenic',\n 'NC_000023.11:g.100850151C>T': 'Benign',\n 'NC_000011.10:g.121309363C>G': 'Benign',\n 'NC_000002.12:g.70965201C>T': 'Benign',\n 'NC_000014.9:g.74262221G>A': 'Benign',\n 'NC_000023.11:g.154904518C>A': 'Pathogenic',\n 'NC_000006.12:g.151585974G>A': 'Benign',\n 'NC_000017.11:g.49990501C>G': 'Benign',\n 'NC_000023.11:g.24715204G>A': 'Pathogenic',\n 'NC_000009.12:g.3827824C>T': 'Benign',\n 'NC_000004.12:g.106247274G>C': 'Benign',\n 'NC_000020.11:g.32435423A>G': 'Benign',\n 'NC_000017.11:g.57105642G>A': 'Benign',\n 'NC_000002.12:g.11826462C>T': 'Benign',\n 'NC_000011.10:g.128840064G>C': 'Pathogenic',\n 'NC_000019.10:g.38466204G>A': 'Pathogenic',\n 'NC_000009.12:g.70225775T>C': 'Benign',\n 'NC_000010.11:g.80275178G>A': 'Pathogenic',\n 'NC_000010.11:g.62655641G>C': 'Benign',\n 'NC_000011.10:g.66003949G>A': 'Benign',\n 'NC_000020.11:g.63428365A>C': 'Pathogenic',\n 'NC_000009.12:g.120443703C>T': 'Benign',\n 'NC_000016.10:g.31462770A>G': 'Benign',\n 'NC_000021.9:g.43416986G>A': 'Benign',\n 'NC_000016.10:g.16150710A>G': 'Pathogenic',\n 'NC_000013.11:g.32386560A>G': 'Benign',\n 'NC_000022.11:g.39225723C>G': 'Pathogenic',\n 'NC_000021.9:g.45990467T>C': 'Benign',\n 'NC_000016.10:g.57663680C>T': 'Benign',\n 'NC_000017.11:g.43063953T>C': 'Pathogenic',\n 'NC_000006.12:g.131892793G>A': 'Benign',\n 'NC_000008.11:g.132121756G>A': 'Benign',\n 'NC_000005.10:g.150135834T>A': 'Benign',\n 'NC_000015.10:g.48448812C>G': 'Pathogenic',\n 'NC_000004.12:g.2836305G>T': 'Benign',\n 'NC_000009.12:g.21865843T>C': 'Benign',\n 'NC_000020.11:g.49372990C>T': 'Benign',\n 'NC_000021.9:g.43774287T>G': 'Pathogenic',\n 'NC_000022.11:g.30949809G>A': 'Pathogenic',\n 'NC_000007.14:g.40133169T>C': 'Pathogenic',\n 'NC_000002.12:g.178453567C>G': 'Pathogenic',\n 'NC_000001.11:g.11950412G>T': 'Benign',\n 'NC_000008.11:g.125032239A>T': 'Pathogenic',\n 'NC_000015.10:g.88838815T>C': 'Pathogenic',\n 'NC_000016.10:g.78425054C>T': 'Pathogenic',\n 'NC_000002.12:g.47412453A>T': 'Pathogenic',\n 'NC_000003.12:g.4665285A>G': 'Pathogenic',\n 'NC_000010.11:g.71322806A>G': 'Benign',\n 'NC_000003.12:g.124745172T>G': 'Benign',\n 'NC_000003.12:g.50377538G>A': 'Pathogenic',\n 'NC_000016.10:g.16177554C>G': 'Pathogenic',\n 'NC_000001.11:g.222628319A>T': 'Benign',\n 'NC_000003.12:g.93905799T>C': 'Pathogenic',\n 'NC_000009.12:g.128218678C>G': 'Benign',\n 'NC_000019.10:g.47842526G>C': 'Benign',\n 'NC_000009.12:g.133540980C>T': 'Pathogenic',\n 'NC_000012.12:g.26065230G>A': 'Benign',\n 'NC_000001.11:g.100230732C>A': 'Pathogenic',\n 'NC_000001.11:g.218443370G>A': 'Benign',\n 'NC_000023.11:g.111401157T>C': 'Pathogenic',\n 'NC_000014.9:g.73958229G>A': 'Pathogenic',\n 'NC_000002.12:g.188999349G>A': 'Pathogenic',\n 'NC_000023.11:g.150596504C>T': 'Pathogenic',\n 'NC_000006.12:g.49457791T>C': 'Pathogenic',\n 'NC_000004.12:g.157076258C>T': 'Benign',\n 'NC_000023.11:g.20187971C>G': 'Pathogenic',\n 'NC_000002.12:g.26727958A>G': 'Pathogenic',\n 'NC_000001.11:g.12011869A>G': 'Benign',\n 'NC_000003.12:g.33014263C>A': 'Pathogenic',\n 'NC_000023.11:g.108655403G>T': 'Pathogenic',\n 'NC_000007.14:g.117602824A>G': 'Pathogenic',\n 'NC_000004.12:g.54267639G>A': 'Benign',\n 'NC_000007.14:g.92086295A>G': 'Benign',\n 'NC_000002.12:g.73452829C>T': 'Benign',\n 'NC_000005.10:g.914504C>T': 'Pathogenic',\n 'NC_000017.11:g.43063372C>T': 'Pathogenic',\n 'NC_000004.12:g.2835513C>T': 'Benign',\n 'NC_000010.11:g.80272689G>C': 'Benign',\n 'NC_000011.10:g.61783599A>G': 'Pathogenic',\n 'NC_000009.12:g.35657756C>A': 'Pathogenic',\n 'NC_000023.11:g.74742841C>A': 'Benign',\n 'NC_000001.11:g.193130172A>T': 'Pathogenic',\n 'NC_000015.10:g.99972623A>G': 'Benign',\n 'NC_000019.10:g.12767435C>G': 'Benign',\n 'NC_000020.11:g.59301634C>G': 'Pathogenic',\n 'NC_000022.11:g.33304476A>G': 'Pathogenic',\n 'NC_000003.12:g.77580050G>A': 'Benign',\n 'NC_000001.11:g.215998957C>G': 'Benign',\n 'NC_000002.12:g.165761944C>A': 'Benign',\n 'NC_000017.11:g.40398936A>G': 'Benign',\n 'NC_000006.12:g.73594313C>T': 'Benign',\n 'NC_000017.11:g.44913333C>G': 'Pathogenic',\n 'NC_000023.11:g.77589929C>T': 'Pathogenic',\n 'NC_000011.10:g.26598397A>T': 'Pathogenic',\n 'NC_000008.11:g.142872874G>A': 'Benign',\n 'NC_000004.12:g.67755832G>A': 'Benign',\n 'NC_000012.12:g.69350122A>T': 'Benign',\n 'NC_000023.11:g.129561251G>A': 'Benign',\n 'NC_000007.14:g.21698100A>G': 'Benign',\n 'NC_000017.11:g.31232746G>T': 'Pathogenic',\n 'NC_000002.12:g.71570300G>T': 'Pathogenic',\n 'NC_000019.10:g.15551388A>C': 'Benign',\n 'NC_000012.12:g.102851697T>G': 'Pathogenic',\n 'NC_000005.10:g.149858701C>T': 'Benign',\n 'NC_000008.11:g.3369342C>G': 'Benign',\n 'NC_000007.14:g.117587802G>T': 'Pathogenic',\n 'NC_000006.12:g.155182256G>A': 'Benign',\n 'NC_000022.11:g.28734431C>T': 'Pathogenic',\n 'NC_000012.12:g.120979096T>G': 'Pathogenic',\n 'NC_000003.12:g.48432676T>C': 'Benign',\n 'NC_000020.11:g.3912634G>A': 'Pathogenic',\n 'NC_000014.9:g.74781398A>T': 'Benign',\n 'NC_000020.11:g.33288741A>G': 'Benign',\n 'NC_000002.12:g.169259064A>C': 'Pathogenic',\n 'NC_000002.12:g.227685657C>G': 'Benign',\n 'NC_000023.11:g.15456039G>A': 'Benign',\n 'NC_000001.11:g.26797993G>A': 'Benign',\n 'NC_000013.11:g.32336214G>T': 'Benign',\n 'NC_000001.11:g.11796382G>T': 'Pathogenic',\n 'NC_000020.11:g.57562839G>C': 'Benign',\n 'NC_000018.10:g.10759873G>A': 'Pathogenic',\n 'NC_000015.10:g.48644607C>A': 'Pathogenic',\n 'NC_000005.10:g.140675067G>C': 'Benign',\n 'NC_000015.10:g.39988037C>T': 'Pathogenic',\n 'NC_000011.10:g.31788750T>A': 'Benign',\n 'NC_000005.10:g.150129831C>T': 'Benign',\n 'NC_000019.10:g.11176650T>C': 'Benign',\n 'NC_000001.11:g.6466798A>T': 'Benign',\n 'NC_000014.9:g.24240632G>T': 'Pathogenic',\n 'NC_000017.11:g.80112577G>A': 'Pathogenic',\n 'NC_000003.12:g.38485223G>C': 'Benign',\n 'NC_000004.12:g.48010800G>A': 'Benign',\n 'NC_000004.12:g.2831582C>A': 'Pathogenic',\n 'NC_000017.11:g.44349166T>C': 'Pathogenic',\n 'NC_000016.10:g.173266C>G': 'Benign',\n 'NC_000014.9:g.23415669A>G': 'Pathogenic',\n ...}"
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "parse_benchmark(bench)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "outputs": [
    {
     "data": {
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     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "parse_predictor(pred_baseline)\n"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "outputs": [],
   "source": [
    "def calculate_coordinates(predictor_score_dict, benchmark_dict, out_filepath):\n",
    "    \"\"\"\n",
    "        Calculates coordinates of x and y based on the predictor scores.\n",
    "        :param predictor_score_dict: a dictionary with scores produced by parse_predictor()\n",
    "        :param benchmark_dict: a dictionary with benchmark classifications produced by parse_benchmark()\n",
    "        :param out_filepath: a str with the output .png file path\n",
    "        :return: lists of coordinates for the ROC plot (TPR and FPR), and a list of sorted predictor scores\n",
    "    \"\"\"\n",
    "\n",
    "    # Get a list of tuples from predictor_score_dict: (predictor score, HGVS ID)\n",
    "    score_hgvs_pairs = [(v, k) for k, v in predictor_score_dict.items()]\n",
    "\n",
    "    sorted_score_hgvs_pairs = score_hgvs_pairs\n",
    "    #########################\n",
    "    ### START CODING HERE ###\n",
    "    #########################\n",
    "\n",
    "    if type_predictor == 'polyphen':\n",
    "        sorted_score_hgvs_pairs = sorted(score_hgvs_pairs)\n",
    "    else:\n",
    "        sorted_score_hgvs_pairs = sorted(score_hgvs_pairs, reverse=True)\n",
    "\n",
    "    #########################\n",
    "    ###  END CODING HERE  ###\n",
    "    #########################\n",
    "\n",
    "    # Later, each coordinate in the ROC plot will be associated with a predictor score (a threshold score). Thus, we\n",
    "    # need a separate list for predictor scores\n",
    "    coordinate_score = [sorted_score_hgvs_pairs[0][0]]\n",
    "\n",
    "    # Create lists to store coordinates. Starts in (0,0)\n",
    "    tpr = [0.0]\n",
    "    fpr = [0.0]\n",
    "\n",
    "    # Create variables to keep track of the number of true positives (TPs) and false positives (FPs)\n",
    "    num_benign = 0\n",
    "    num_pathogenic = 0\n",
    "\n",
    "    # Get the total number of positives (P) and negatives (N) (benign and pathogenic)\n",
    "    total_benign, total_pathogenic = count_total_results(predictor_score_dict, benchmark_dict)\n",
    "\n",
    "    # Get a list of indices of scores before breakpoints\n",
    "    index_prebreakpoint_score = []\n",
    "    previous_score = sorted_score_hgvs_pairs[0][0]\n",
    "    for i in range(len(sorted_score_hgvs_pairs)):\n",
    "        score = sorted_score_hgvs_pairs[i][0]\n",
    "        if previous_score != score:\n",
    "            # Add index of the score before the breakpoint\n",
    "            index_prebreakpoint_score.append(i - 1)\n",
    "        previous_score = score\n",
    "\n",
    "    # Add index of the last score (for the last coordinate)\n",
    "    index_prebreakpoint_score.append(len(sorted_score_hgvs_pairs) - 1)\n",
    "\n",
    "    # Iterate over HGVS IDs of SNPs and corresponding sorted predictor scores\n",
    "    for i in range(len(sorted_score_hgvs_pairs)):\n",
    "        score = sorted_score_hgvs_pairs[i][0]\n",
    "        hgvs = sorted_score_hgvs_pairs[i][1]\n",
    "\n",
    "        #########################\n",
    "        ### START CODING HERE ###\n",
    "        #########################\n",
    "        # Determine whether the SNP is classified by the benchmark as:\n",
    "        #    Pathogenic -> actual negative, thus a false positive (x-coordinate)\n",
    "        #    Benign  -> actual positive, thus a true positive (y-coordinate)\n",
    "\n",
    "        # Increase the respective value of num_benign or num_pathogenic\n",
    "        if benchmark_dict[hgvs] == 'Benign':\n",
    "            num_benign+=1\n",
    "        else:\n",
    "            num_pathogenic+=1\n",
    "\n",
    "        # Now, you need to calculate TPR and FPR for unique scores as TP/P and FP/N, respectively,\n",
    "        # using num_benign, num_pathogenic, total_benign, and total_pathogenic correctly. Append the values\n",
    "        # to the corresponding lists: tpr is a list of y-coordinates and fpr is a list of x-coordinates.\n",
    "        # Calculate the rates if HGVS score index i is the index of the score before a breakpoint\n",
    "        # (use index_prebreakpoint_score). Also, append the score to coordinate_score.\n",
    "\n",
    "        if i in index_prebreakpoint_score:\n",
    "            tpr.append(num_benign/total_benign)\n",
    "            fpr.append(num_pathogenic/total_pathogenic)\n",
    "            coordinate_score.append(score)\n",
    "\n",
    "        #########################\n",
    "        ###  END CODING HERE  ###\n",
    "        #########################\n",
    "    if out_filepath:\n",
    "        out_dir, out_filename = os.path.split(out_filepath)\n",
    "        # Write coordinates to a .tsv file\n",
    "        with open(os.path.join(out_dir, out_filename.split('.')[0] + '_xy.tsv'), 'w') as f:\n",
    "            for a, b in zip(fpr, tpr):\n",
    "                f.write(str(a) + '\\t' + str(b) + '\\n')\n",
    "\n",
    "    return tpr, fpr, coordinate_score"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "outputs": [
    {
     "data": {
      "text/plain": "([0.0,\n  0.058333333333333334,\n  0.135,\n  0.39,\n  0.6166666666666667,\n  0.79,\n  0.8966666666666666,\n  1.0],\n [0.0,\n  0.0033333333333333335,\n  0.03833333333333333,\n  0.19333333333333333,\n  0.3283333333333333,\n  0.5166666666666667,\n  0.77,\n  1.0],\n [3.0, 3.0, 2.0, 1.0, 0.0, -1.0, -2.0, -3.0])"
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "calculate_coordinates(parse_predictor(pred_baseline),parse_benchmark(bench),None)"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "outputs": [],
   "source": [
    "def integrate(fpr, tpr):\n",
    "    \"\"\"\n",
    "        Calculates the Area Under the Curve (AUC) for a given list of coordinates.\n",
    "        :param fpr: a list of FPRs\n",
    "        :param tpr: a list of TPRs\n",
    "        :return: a float with AUC\n",
    "    \"\"\"\n",
    "\n",
    "    auc = 0.\n",
    "    last_fpr = fpr[0]\n",
    "    last_tpr = tpr[0]\n",
    "\n",
    "    for cur_fpr, cur_tpr in list(zip(fpr, tpr))[1:]:\n",
    "        #########################\n",
    "        ### START CODING HERE ###\n",
    "        #########################\n",
    "        # Trapezoid rule\n",
    "        auc += (cur_fpr - last_fpr) * (cur_tpr+last_tpr)/2\n",
    "\n",
    "        #########################\n",
    "        ###  END CODING HERE  ###\n",
    "        #########################\n",
    "        last_fpr = cur_fpr\n",
    "        last_tpr = cur_tpr\n",
    "\n",
    "    return auc"
   ],
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    "pycharm": {
     "name": "#%%\n"
    }
   }
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "outputs": [
    {
     "data": {
      "text/plain": "0.8858000000000001"
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tpr, fpr, score=calculate_coordinates(parse_predictor(pred_polyphen),\n",
    "                                      parse_benchmark(bench),None)\n",
    "integrate(fpr, tpr)\n",
    "\n"
   ],
   "metadata": {
    "collapsed": false,
    "pycharm": {
     "name": "#%%\n"
    }
   }
  }
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