notebook/Examples.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pyhml\n",
    "hmlparser = pyhml.HmlParser()\n",
    "hml_file = \"hml_1_0_1-example7-ngsFull.xml\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Parse HML file into HML object\n",
    "hml = hmlparser.parse(hml_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ID</th>\n",
       "      <th>Locus</th>\n",
       "      <th>glstring</th>\n",
       "      <th>dbversion</th>\n",
       "      <th>sequence</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>HLA-A*01:01:01+HLA-A*24:02:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>HLA-A*01:01:01+HLA-A*24:02:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>HLA-A*01:01:01+HLA-A*24:02:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-A</td>\n",
       "      <td>HLA-A*01:01:01+HLA-A*24:02:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>HLA-B*08:01:01+HLA-B*57:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>HLA-B*08:01:01+HLA-B*57:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>HLA-B*08:01:01+HLA-B*57:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-B</td>\n",
       "      <td>HLA-B*08:01:01+HLA-B*57:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-C</td>\n",
       "      <td>HLA-C*06:02:01+HLA-C*07:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-C</td>\n",
       "      <td>HLA-C*06:02:01+HLA-C*07:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-C</td>\n",
       "      <td>HLA-C*06:02:01+HLA-C*07:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-C</td>\n",
       "      <td>HLA-C*06:02:01+HLA-C*07:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-DPB1</td>\n",
       "      <td>HLA-DPB1*02:01:02+HLA-DPB1*04:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-DPB1</td>\n",
       "      <td>HLA-DPB1*02:01:02+HLA-DPB1*04:01:01</td>\n",
       "      <td>3.14.0</td>\n",
       "      <td>CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-DRB1</td>\n",
       "      <td>HLA-DRB1*03:01:01+HLA-DRB1*07:01:01</td>\n",
       "      <td>3.15.0</td>\n",
       "      <td>CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>1367-7150-8</td>\n",
       "      <td>HLA-DRB1</td>\n",
       "      <td>HLA-DRB1*03:01:01+HLA-DRB1*07:01:01</td>\n",
       "      <td>3.15.0</td>\n",
       "      <td>CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             ID     Locus                             glstring dbversion  \\\n",
       "0   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0   \n",
       "1   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0   \n",
       "2   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0   \n",
       "3   1367-7150-8     HLA-A        HLA-A*01:01:01+HLA-A*24:02:01    3.14.0   \n",
       "4   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0   \n",
       "5   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0   \n",
       "6   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0   \n",
       "7   1367-7150-8     HLA-B        HLA-B*08:01:01+HLA-B*57:01:01    3.14.0   \n",
       "8   1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0   \n",
       "9   1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0   \n",
       "10  1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0   \n",
       "11  1367-7150-8     HLA-C        HLA-C*06:02:01+HLA-C*07:01:01    3.14.0   \n",
       "12  1367-7150-8  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0   \n",
       "13  1367-7150-8  HLA-DPB1  HLA-DPB1*02:01:02+HLA-DPB1*04:01:01    3.14.0   \n",
       "14  1367-7150-8  HLA-DRB1  HLA-DRB1*03:01:01+HLA-DRB1*07:01:01    3.15.0   \n",
       "15  1367-7150-8  HLA-DRB1  HLA-DRB1*03:01:01+HLA-DRB1*07:01:01    3.15.0   \n",
       "\n",
       "                                             sequence  \n",
       "0   TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...  \n",
       "1   TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCT...  \n",
       "2   TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT...  \n",
       "3   GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCA...  \n",
       "4   CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...  \n",
       "5   GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...  \n",
       "6   CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG...  \n",
       "7   GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG...  \n",
       "8   AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...  \n",
       "9   CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...  \n",
       "10  AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC...  \n",
       "11  CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA...  \n",
       "12  CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...  \n",
       "13  CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...  \n",
       "14  CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...  \n",
       "15  CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Convert HML object to pandas dataframe\n",
    "hml_df = hml.toPandas()\n",
    "hml_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'center_code': '888',\n",
      " 'collection_method': 'buccal swab',\n",
      " 'id': '1367-7150-8',\n",
      " 'seq_records': {'HLA-A': [SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()), id='XHLA-A_0', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_1', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()), id='XHLA-A_2', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_3', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[])],\n",
      "                 'HLA-B': [SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_0', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_1', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_2', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_3', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[])],\n",
      "                 'HLA-C': [SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_0', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_1', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_2', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                           SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_3', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[])],\n",
      "                 'HLA-DPB1': [SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()), id='XHLA-DPB1_0', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                              SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()), id='XHLA-DPB1_1', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[])],\n",
      "                 'HLA-DRB1': [SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_0', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[]),\n",
      "                              SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_1', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[])]},\n",
      " 'typing': [{'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
      "                                    'allele_version': '3.14.0',\n",
      "                                    'date': '2014-10-14',\n",
      "                                    'glstring': ['HLA-A*01:01:01+HLA-A*24:02:01'],\n",
      "                                    'haploid': []}],\n",
      "             'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
      "                                                                   'description': 'HLA-A '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '1',\n",
      "                                                                   'reference_sequence_id': 'ref1',\n",
      "                                                                   'sequence': Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-A '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '2',\n",
      "                                                                   'reference_sequence_id': 'ref1',\n",
      "                                                                   'sequence': Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-A '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '3',\n",
      "                                                                   'reference_sequence_id': 'ref1',\n",
      "                                                                   'sequence': Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-A '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '4',\n",
      "                                                                   'reference_sequence_id': 'ref1',\n",
      "                                                                   'sequence': Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None}],\n",
      "                                     'date': '2014-10-17',\n",
      "                                     'reference_database': [{'availability': 'public',\n",
      "                                                             'curated': True,\n",
      "                                                             'description': 'Genome '\n",
      "                                                                            'Reference '\n",
      "                                                                            'Consortium '\n",
      "                                                                            '(GRC)',\n",
      "                                                             'name': 'GRCh38.p1',\n",
      "                                                             'reference_sequence': [{'accession': 'GL000254.2',\n",
      "                                                                                     'end': 4827813,\n",
      "                                                                                     'id': 'ref1',\n",
      "                                                                                     'name': 'HSCHR6_MHC_MCF_CTG1',\n",
      "                                                                                     'start': 0,\n",
      "                                                                                     'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
      "                                                             'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
      "                                                             'version': 'GRCh38.p1'}]}],\n",
      "             'date': '2014-10-14',\n",
      "             'gene_family': 'HLA',\n",
      "             'seq_records': [SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()), id='XHLA-A_0', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_1', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()), id='XHLA-A_2', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_3', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[])],\n",
      "             'typing_method': None},\n",
      "            {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
      "                                    'allele_version': '3.14.0',\n",
      "                                    'date': '2014-10-14',\n",
      "                                    'glstring': ['HLA-B*08:01:01+HLA-B*57:01:01'],\n",
      "                                    'haploid': []}],\n",
      "             'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
      "                                                                   'description': 'HLA-B '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31272621,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '1',\n",
      "                                                                   'reference_sequence_id': 'ref2',\n",
      "                                                                   'sequence': Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31268182,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-B '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31272621,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '2',\n",
      "                                                                   'reference_sequence_id': 'ref2',\n",
      "                                                                   'sequence': Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31268182,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-B '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31272621,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '3',\n",
      "                                                                   'reference_sequence_id': 'ref2',\n",
      "                                                                   'sequence': Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31268182,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-B '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31272621,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '4',\n",
      "                                                                   'reference_sequence_id': 'ref2',\n",
      "                                                                   'sequence': Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31268182,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None}],\n",
      "                                     'date': '2014-10-17',\n",
      "                                     'reference_database': [{'availability': 'public',\n",
      "                                                             'curated': True,\n",
      "                                                             'description': 'Genome '\n",
      "                                                                            'Reference '\n",
      "                                                                            'Consortium '\n",
      "                                                                            '(GRC)',\n",
      "                                                             'name': 'GRCh38.p1',\n",
      "                                                             'reference_sequence': [{'accession': 'GL000254.2',\n",
      "                                                                                     'end': 4827813,\n",
      "                                                                                     'id': 'ref2',\n",
      "                                                                                     'name': 'HSCHR6_MHC_MCF_CTG1',\n",
      "                                                                                     'start': 0,\n",
      "                                                                                     'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
      "                                                             'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
      "                                                             'version': 'GRCh38.p1'}]}],\n",
      "             'date': '2014-10-14',\n",
      "             'gene_family': 'HLA',\n",
      "             'seq_records': [SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_0', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_1', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_2', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_3', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[])],\n",
      "             'typing_method': None},\n",
      "            {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
      "                                    'allele_version': '3.14.0',\n",
      "                                    'date': '2014-10-14',\n",
      "                                    'glstring': ['HLA-C*06:02:01+HLA-C*07:01:01'],\n",
      "                                    'haploid': []}],\n",
      "             'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
      "                                                                   'description': 'HLA-C '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31357884,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '1',\n",
      "                                                                   'reference_sequence_id': 'ref3',\n",
      "                                                                   'sequence': Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31353589,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-C '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31357884,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '2',\n",
      "                                                                   'reference_sequence_id': 'ref3',\n",
      "                                                                   'sequence': Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31353589,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-C '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31357884,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '3',\n",
      "                                                                   'reference_sequence_id': 'ref3',\n",
      "                                                                   'sequence': Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31353589,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-C '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 31357884,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '3',\n",
      "                                                                   'reference_sequence_id': 'ref3',\n",
      "                                                                   'sequence': Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 31353589,\n",
      "                                                                   'strand': '-1',\n",
      "                                                                   'variant': None}],\n",
      "                                     'date': '2014-10-17',\n",
      "                                     'reference_database': [{'availability': 'public',\n",
      "                                                             'curated': True,\n",
      "                                                             'description': 'Genome '\n",
      "                                                                            'Reference '\n",
      "                                                                            'Consortium '\n",
      "                                                                            '(GRC)',\n",
      "                                                             'name': 'GRCh38.p1',\n",
      "                                                             'reference_sequence': [{'accession': 'GL000254.2',\n",
      "                                                                                     'end': 4827813,\n",
      "                                                                                     'id': 'ref3',\n",
      "                                                                                     'name': 'HSCHR6_MHC_MCF_CTG1',\n",
      "                                                                                     'start': 0,\n",
      "                                                                                     'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
      "                                                             'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
      "                                                             'version': 'GRCh38.p1'}]}],\n",
      "             'date': '2014-10-14',\n",
      "             'gene_family': 'HLA',\n",
      "             'seq_records': [SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_0', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_1', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_2', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_3', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[])],\n",
      "             'typing_method': None},\n",
      "            {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
      "                                    'allele_version': '3.14.0',\n",
      "                                    'date': '2014-10-14',\n",
      "                                    'glstring': ['HLA-DPB1*02:01:02+HLA-DPB1*04:01:01'],\n",
      "                                    'haploid': []}],\n",
      "             'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
      "                                                                   'description': 'HLA-DPB1 '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '1',\n",
      "                                                                   'reference_sequence_id': 'ref4',\n",
      "                                                                   'sequence': Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-DPB1 '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '2',\n",
      "                                                                   'reference_sequence_id': 'ref4',\n",
      "                                                                   'sequence': Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None}],\n",
      "                                     'date': '2014-10-17',\n",
      "                                     'reference_database': [{'availability': 'public',\n",
      "                                                             'curated': True,\n",
      "                                                             'description': 'Genome '\n",
      "                                                                            'Reference '\n",
      "                                                                            'Consortium '\n",
      "                                                                            '(GRC)',\n",
      "                                                             'name': 'GRCh38.p1',\n",
      "                                                             'reference_sequence': [{'accession': 'GL000254.2',\n",
      "                                                                                     'end': 4827813,\n",
      "                                                                                     'id': 'ref4',\n",
      "                                                                                     'name': 'HSCHR6_MHC_MCF_CTG1',\n",
      "                                                                                     'start': 0,\n",
      "                                                                                     'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
      "                                                             'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
      "                                                             'version': 'GRCh38.p1'}]}],\n",
      "             'date': '2014-10-14',\n",
      "             'gene_family': 'HLA',\n",
      "             'seq_records': [SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()), id='XHLA-DPB1_0', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()), id='XHLA-DPB1_1', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[])],\n",
      "             'typing_method': None},\n",
      "            {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
      "                                    'allele_version': '3.15.0',\n",
      "                                    'date': '2014-10-14',\n",
      "                                    'glstring': ['HLA-DRB1*03:01:01+HLA-DRB1*07:01:01'],\n",
      "                                    'haploid': []}],\n",
      "             'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
      "                                                                   'description': 'HLA-DRB1 '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '1',\n",
      "                                                                   'reference_sequence_id': 'ref5',\n",
      "                                                                   'sequence': Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None},\n",
      "                                                                  {'continuity': True,\n",
      "                                                                   'description': 'HLA-DRB1 '\n",
      "                                                                                  'full '\n",
      "                                                                                  'gene',\n",
      "                                                                   'end': 29945809,\n",
      "                                                                   'expected_copy_number': 1,\n",
      "                                                                   'phase_set': '2',\n",
      "                                                                   'reference_sequence_id': 'ref5',\n",
      "                                                                   'sequence': Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()),\n",
      "                                                                   'sequence_quality': None,\n",
      "                                                                   'start': 29942412,\n",
      "                                                                   'strand': '1',\n",
      "                                                                   'variant': None}],\n",
      "                                     'date': '2014-10-17',\n",
      "                                     'reference_database': [{'availability': 'public',\n",
      "                                                             'curated': True,\n",
      "                                                             'description': 'Genome '\n",
      "                                                                            'Reference '\n",
      "                                                                            'Consortium '\n",
      "                                                                            '(GRC)',\n",
      "                                                             'name': 'GRCh38.p1',\n",
      "                                                             'reference_sequence': [{'accession': 'GL000254.2',\n",
      "                                                                                     'end': 29945809,\n",
      "                                                                                     'id': 'ref5',\n",
      "                                                                                     'name': 'ENSE00001731226',\n",
      "                                                                                     'start': 29942412,\n",
      "                                                                                     'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
      "                                                             'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
      "                                                             'version': 'GRCh38.p1'}]}],\n",
      "             'date': '2014-10-14',\n",
      "             'gene_family': 'HLA',\n",
      "             'seq_records': [SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_0', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[]),\n",
      "                             SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_1', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[])],\n",
      "             'typing_method': None}]}\n"
     ]
    }
   ],
   "source": [
    "for subject in hml.sample:\n",
    "    print(subject)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1367-7150-8 ['HLA-A*01:01:01+HLA-A*24:02:01']\n",
      "1367-7150-8 ['HLA-B*08:01:01+HLA-B*57:01:01']\n",
      "1367-7150-8 ['HLA-C*06:02:01+HLA-C*07:01:01']\n",
      "1367-7150-8 ['HLA-DPB1*02:01:02+HLA-DPB1*04:01:01']\n",
      "1367-7150-8 ['HLA-DRB1*03:01:01+HLA-DRB1*07:01:01']\n"
     ]
    }
   ],
   "source": [
    "for subject in hml.sample:\n",
    "    for typing in subject.typing:\n",
    "        for allele_assignment in typing.allele_assignment:\n",
    "            print(subject.id, allele_assignment.glstring)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'project_name': 'LAB',\n",
       " 'reporting_center': {'reporting_center_context': 'NMDP',\n",
       "                      'reporting_center_id': 'NMDP'},\n",
       " 'sample': [{'center_code': '888',\n",
       "             'collection_method': 'buccal swab',\n",
       "             'id': '1367-7150-8',\n",
       "             'seq_records': {'HLA-A': [SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()), id='XHLA-A_0', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_1', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()), id='XHLA-A_2', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_3', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[])],\n",
       "                             'HLA-B': [SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_0', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_1', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_2', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_3', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                             'HLA-C': [SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_0', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_1', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_2', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                       SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_3', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                             'HLA-DPB1': [SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()), id='XHLA-DPB1_0', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                          SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()), id='XHLA-DPB1_1', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                             'HLA-DRB1': [SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_0', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[]),\n",
       "                                          SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_1', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[])]},\n",
       "             'typing': [{'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
       "                                                'allele_version': '3.14.0',\n",
       "                                                'date': '2014-10-14',\n",
       "                                                'glstring': ['HLA-A*01:01:01+HLA-A*24:02:01'],\n",
       "                                                'haploid': []}],\n",
       "                         'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
       "                                                                               'description': 'HLA-A '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '1',\n",
       "                                                                               'reference_sequence_id': 'ref1',\n",
       "                                                                               'sequence': Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-A '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '2',\n",
       "                                                                               'reference_sequence_id': 'ref1',\n",
       "                                                                               'sequence': Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-A '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '3',\n",
       "                                                                               'reference_sequence_id': 'ref1',\n",
       "                                                                               'sequence': Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-A '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '4',\n",
       "                                                                               'reference_sequence_id': 'ref1',\n",
       "                                                                               'sequence': Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None}],\n",
       "                                                 'date': '2014-10-17',\n",
       "                                                 'reference_database': [{'availability': 'public',\n",
       "                                                                         'curated': True,\n",
       "                                                                         'description': 'Genome '\n",
       "                                                                                        'Reference '\n",
       "                                                                                        'Consortium '\n",
       "                                                                                        '(GRC)',\n",
       "                                                                         'name': 'GRCh38.p1',\n",
       "                                                                         'reference_sequence': [{'accession': 'GL000254.2',\n",
       "                                                                                                 'end': 4827813,\n",
       "                                                                                                 'id': 'ref1',\n",
       "                                                                                                 'name': 'HSCHR6_MHC_MCF_CTG1',\n",
       "                                                                                                 'start': 0,\n",
       "                                                                                                 'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
       "                                                                         'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
       "                                                                         'version': 'GRCh38.p1'}]}],\n",
       "                         'date': '2014-10-14',\n",
       "                         'gene_family': 'HLA',\n",
       "                         'seq_records': [SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CTC', IUPACUnambiguousDNA()), id='XHLA-A_0', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCAT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_1', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTT...CAG', IUPACUnambiguousDNA()), id='XHLA-A_2', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGT...ATG', IUPACUnambiguousDNA()), id='XHLA-A_3', name='HLA-A*01:01:01+HLA-A*24:02:01', description='3.14.0', dbxrefs=[])],\n",
       "                         'typing_method': None},\n",
       "                        {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
       "                                                'allele_version': '3.14.0',\n",
       "                                                'date': '2014-10-14',\n",
       "                                                'glstring': ['HLA-B*08:01:01+HLA-B*57:01:01'],\n",
       "                                                'haploid': []}],\n",
       "                         'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
       "                                                                               'description': 'HLA-B '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31272621,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '1',\n",
       "                                                                               'reference_sequence_id': 'ref2',\n",
       "                                                                               'sequence': Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31268182,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-B '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31272621,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '2',\n",
       "                                                                               'reference_sequence_id': 'ref2',\n",
       "                                                                               'sequence': Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31268182,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-B '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31272621,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '3',\n",
       "                                                                               'reference_sequence_id': 'ref2',\n",
       "                                                                               'sequence': Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31268182,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-B '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31272621,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '4',\n",
       "                                                                               'reference_sequence_id': 'ref2',\n",
       "                                                                               'sequence': Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31268182,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None}],\n",
       "                                                 'date': '2014-10-17',\n",
       "                                                 'reference_database': [{'availability': 'public',\n",
       "                                                                         'curated': True,\n",
       "                                                                         'description': 'Genome '\n",
       "                                                                                        'Reference '\n",
       "                                                                                        'Consortium '\n",
       "                                                                                        '(GRC)',\n",
       "                                                                         'name': 'GRCh38.p1',\n",
       "                                                                         'reference_sequence': [{'accession': 'GL000254.2',\n",
       "                                                                                                 'end': 4827813,\n",
       "                                                                                                 'id': 'ref2',\n",
       "                                                                                                 'name': 'HSCHR6_MHC_MCF_CTG1',\n",
       "                                                                                                 'start': 0,\n",
       "                                                                                                 'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
       "                                                                         'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
       "                                                                         'version': 'GRCh38.p1'}]}],\n",
       "                         'date': '2014-10-14',\n",
       "                         'gene_family': 'HLA',\n",
       "                         'seq_records': [SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_0', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_1', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTGTCCTTTAT...TTC', IUPACUnambiguousDNA()), id='XHLA-B_2', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGGACCCGGGG...TTC', IUPACUnambiguousDNA()), id='XHLA-B_3', name='HLA-B*08:01:01+HLA-B*57:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                         'typing_method': None},\n",
       "                        {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
       "                                                'allele_version': '3.14.0',\n",
       "                                                'date': '2014-10-14',\n",
       "                                                'glstring': ['HLA-C*06:02:01+HLA-C*07:01:01'],\n",
       "                                                'haploid': []}],\n",
       "                         'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
       "                                                                               'description': 'HLA-C '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31357884,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '1',\n",
       "                                                                               'reference_sequence_id': 'ref3',\n",
       "                                                                               'sequence': Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31353589,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-C '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31357884,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '2',\n",
       "                                                                               'reference_sequence_id': 'ref3',\n",
       "                                                                               'sequence': Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31353589,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-C '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31357884,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '3',\n",
       "                                                                               'reference_sequence_id': 'ref3',\n",
       "                                                                               'sequence': Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31353589,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-C '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 31357884,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '3',\n",
       "                                                                               'reference_sequence_id': 'ref3',\n",
       "                                                                               'sequence': Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 31353589,\n",
       "                                                                               'strand': '-1',\n",
       "                                                                               'variant': None}],\n",
       "                                                 'date': '2014-10-17',\n",
       "                                                 'reference_database': [{'availability': 'public',\n",
       "                                                                         'curated': True,\n",
       "                                                                         'description': 'Genome '\n",
       "                                                                                        'Reference '\n",
       "                                                                                        'Consortium '\n",
       "                                                                                        '(GRC)',\n",
       "                                                                         'name': 'GRCh38.p1',\n",
       "                                                                         'reference_sequence': [{'accession': 'GL000254.2',\n",
       "                                                                                                 'end': 4827813,\n",
       "                                                                                                 'id': 'ref3',\n",
       "                                                                                                 'name': 'HSCHR6_MHC_MCF_CTG1',\n",
       "                                                                                                 'start': 0,\n",
       "                                                                                                 'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
       "                                                                         'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
       "                                                                         'version': 'GRCh38.p1'}]}],\n",
       "                         'date': '2014-10-14',\n",
       "                         'gene_family': 'HLA',\n",
       "                         'seq_records': [SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_0', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_1', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTCTCAGGCTC...GGG', IUPACUnambiguousDNA()), id='XHLA-C_2', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAAGCCAATCA...GGG', IUPACUnambiguousDNA()), id='XHLA-C_3', name='HLA-C*06:02:01+HLA-C*07:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                         'typing_method': None},\n",
       "                        {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
       "                                                'allele_version': '3.14.0',\n",
       "                                                'date': '2014-10-14',\n",
       "                                                'glstring': ['HLA-DPB1*02:01:02+HLA-DPB1*04:01:01'],\n",
       "                                                'haploid': []}],\n",
       "                         'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
       "                                                                               'description': 'HLA-DPB1 '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '1',\n",
       "                                                                               'reference_sequence_id': 'ref4',\n",
       "                                                                               'sequence': Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-DPB1 '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '2',\n",
       "                                                                               'reference_sequence_id': 'ref4',\n",
       "                                                                               'sequence': Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None}],\n",
       "                                                 'date': '2014-10-17',\n",
       "                                                 'reference_database': [{'availability': 'public',\n",
       "                                                                         'curated': True,\n",
       "                                                                         'description': 'Genome '\n",
       "                                                                                        'Reference '\n",
       "                                                                                        'Consortium '\n",
       "                                                                                        '(GRC)',\n",
       "                                                                         'name': 'GRCh38.p1',\n",
       "                                                                         'reference_sequence': [{'accession': 'GL000254.2',\n",
       "                                                                                                 'end': 4827813,\n",
       "                                                                                                 'id': 'ref4',\n",
       "                                                                                                 'name': 'HSCHR6_MHC_MCF_CTG1',\n",
       "                                                                                                 'start': 0,\n",
       "                                                                                                 'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
       "                                                                         'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
       "                                                                         'version': 'GRCh38.p1'}]}],\n",
       "                         'date': '2014-10-14',\n",
       "                         'gene_family': 'HLA',\n",
       "                         'seq_records': [SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGG', IUPACUnambiguousDNA()), id='XHLA-DPB1_0', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT...TGC', IUPACUnambiguousDNA()), id='XHLA-DPB1_1', name='HLA-DPB1*02:01:02+HLA-DPB1*04:01:01', description='3.14.0', dbxrefs=[])],\n",
       "                         'typing_method': None},\n",
       "                        {'allele_assignment': [{'allele_db': 'IMGT/HLA',\n",
       "                                                'allele_version': '3.15.0',\n",
       "                                                'date': '2014-10-14',\n",
       "                                                'glstring': ['HLA-DRB1*03:01:01+HLA-DRB1*07:01:01'],\n",
       "                                                'haploid': []}],\n",
       "                         'consensus_sequence': [{'consensus_sequence_block': [{'continuity': True,\n",
       "                                                                               'description': 'HLA-DRB1 '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '1',\n",
       "                                                                               'reference_sequence_id': 'ref5',\n",
       "                                                                               'sequence': Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None},\n",
       "                                                                              {'continuity': True,\n",
       "                                                                               'description': 'HLA-DRB1 '\n",
       "                                                                                              'full '\n",
       "                                                                                              'gene',\n",
       "                                                                               'end': 29945809,\n",
       "                                                                               'expected_copy_number': 1,\n",
       "                                                                               'phase_set': '2',\n",
       "                                                                               'reference_sequence_id': 'ref5',\n",
       "                                                                               'sequence': Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()),\n",
       "                                                                               'sequence_quality': None,\n",
       "                                                                               'start': 29942412,\n",
       "                                                                               'strand': '1',\n",
       "                                                                               'variant': None}],\n",
       "                                                 'date': '2014-10-17',\n",
       "                                                 'reference_database': [{'availability': 'public',\n",
       "                                                                         'curated': True,\n",
       "                                                                         'description': 'Genome '\n",
       "                                                                                        'Reference '\n",
       "                                                                                        'Consortium '\n",
       "                                                                                        '(GRC)',\n",
       "                                                                         'name': 'GRCh38.p1',\n",
       "                                                                         'reference_sequence': [{'accession': 'GL000254.2',\n",
       "                                                                                                 'end': 29945809,\n",
       "                                                                                                 'id': 'ref5',\n",
       "                                                                                                 'name': 'ENSE00001731226',\n",
       "                                                                                                 'start': 29942412,\n",
       "                                                                                                 'uri': 'http://www.ncbi.nlm.nih.gov/nuccore/GL000254.2'}],\n",
       "                                                                         'uri': 'http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human',\n",
       "                                                                         'version': 'GRCh38.p1'}]}],\n",
       "                         'date': '2014-10-14',\n",
       "                         'gene_family': 'HLA',\n",
       "                         'seq_records': [SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_0', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[]),\n",
       "                                         SeqRecord(seq=Seq('CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA...ATG', IUPACUnambiguousDNA()), id='XHLA-DRB1_1', name='HLA-DRB1*03:01:01+HLA-DRB1*07:01:01', description='3.15.0', dbxrefs=[])],\n",
       "                         'typing_method': None}]}],\n",
       " 'schema_location': 'http://schemas.nmdp.org/spec/hml/1.0.1  '\n",
       "                    'http://schemas.nmdp.org/spec/hml/1.0.1/hml-1.0.1.xsd',\n",
       " 'version': '1.0.1'}"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "hml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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