1_Final_MAPS_per_Gene_wrangling_and_exporting.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "94be5fa0",
   "metadata": {},
   "outputs": [],
   "source": [
    "import hail as hl"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "8ad588a7",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "WARNING: An illegal reflective access operation has occurred\n",
      "WARNING: Illegal reflective access by org.apache.spark.unsafe.Platform (file:/Users/adrian/opt/anaconda3/envs/hail/lib/python3.10/site-packages/pyspark/jars/spark-unsafe_2.12-3.1.3.jar) to constructor java.nio.DirectByteBuffer(long,int)\n",
      "WARNING: Please consider reporting this to the maintainers of org.apache.spark.unsafe.Platform\n",
      "WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations\n",
      "WARNING: All illegal access operations will be denied in a future release\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-12-01 12:50:47 WARN  NativeCodeLoader:60 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Setting default log level to \"WARN\".\n",
      "To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-12-01 12:50:48 WARN  Utils:69 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "Running on Apache Spark version 3.1.3\n",
      "SparkUI available at http://192.168.0.181:4041\n",
      "Welcome to\n",
      "     __  __     <>__\n",
      "    / /_/ /__  __/ /\n",
      "   / __  / _ `/ / /\n",
      "  /_/ /_/\\_,_/_/_/   version 0.2.99-57537fea08d4\n",
      "LOGGING: writing to /Users/adrian/BroadIS/hail-20221201-1250-0.2.99-57537fea08d4.log\n"
     ]
    }
   ],
   "source": [
    "hl.init()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "66310ced",
   "metadata": {},
   "outputs": [],
   "source": [
    "maps_table = hl.read_table(\n",
    "'gs://janucik-dataproc-stage/01_maps/v1_30_Nov_2022_MAPS_per_gene_using_arrays/maps_downsampling_multi_model.ht'\n",
    ")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "da5ab46c",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[Stage 6:============================================>              (3 + 1) / 4]\r"
     ]
    },
    {
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       "</tbody></table><p style=\"background: #fdd; padding: 0.4em;\">showing top 4 rows</p>\n"
      ],
      "text/plain": [
       "+-------------------+----------------------+\n",
       "| gene_ids          | lof_csq_collapsed    |\n",
       "+-------------------+----------------------+\n",
       "| str               | str                  |\n",
       "+-------------------+----------------------+\n",
       "| \"ENSG00000000003\" | \"HC\"                 |\n",
       "| \"ENSG00000000003\" | \"missense_variant\"   |\n",
       "| \"ENSG00000000003\" | \"synonymous_variant\" |\n",
       "| \"ENSG00000000005\" | \"HC\"                 |\n",
       "+-------------------+----------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| N_singletons                                                                 |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<int64>                                                                 |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [1,1,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... |\n",
       "| [42,40,19,0,1,2,0,0,15,7,8,4,38,17,16,1,1,0,0,0,14,6,7,6,6,1,0,2,0,1,8,1,... |\n",
       "| [9,8,7,0,1,1,0,0,2,1,1,4,8,7,5,0,0,1,0,0,2,1,0,3,4,0,1,0,0,0,1,0,1,4,0,0,... |\n",
       "| [1,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,... |\n",
       "+------------------------------------------------------------------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| expected_singletons                                                          |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<float64>                                                               |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [5.67e-01,5.59e-01,6.12e-01,0.00e+00,0.00e+00,0.00e+00,0.00e+00,0.00e+00,... |\n",
       "| [3.26e+01,3.21e+01,1.49e+01,1.10e+00,7.23e-01,9.55e-01,8.03e-02,4.24e-01,... |\n",
       "| [1.23e+01,1.21e+01,7.30e+00,3.66e-01,3.63e-01,9.57e-01,0.00e+00,2.32e-01,... |\n",
       "| [1.64e-01,1.58e-01,3.51e-01,0.00e+00,0.00e+00,0.00e+00,0.00e+00,0.00e+00,... |\n",
       "+------------------------------------------------------------------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| N_variants                                                                   |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<int64>                                                                 |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [1,1,1,0,0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,... |\n",
       "| [65,65,27,4,2,3,1,3,26,7,11,9,55,28,23,3,2,1,1,3,23,6,8,8,11,4,1,3,1,3,11... |\n",
       "| [25,25,13,1,1,2,0,1,7,3,1,8,21,15,11,1,0,2,0,1,6,3,0,6,5,1,1,0,0,1,5,0,1,... |\n",
       "| [1,1,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,... |\n",
       "+------------------------------------------------------------------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| ps_agg                                                                       |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<float64>                                                               |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [1.00e+00,1.00e+00,1.00e+00,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,1.00e+00,... |\n",
       "| [6.46e-01,6.15e-01,7.04e-01,0.00e+00,5.00e-01,6.67e-01,0.00e+00,0.00e+00,... |\n",
       "| [3.60e-01,3.20e-01,5.38e-01,0.00e+00,1.00e+00,5.00e-01,NaN,0.00e+00,2.86e... |\n",
       "| [1.00e+00,1.00e+00,1.00e+00,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,1.00e... |\n",
       "+------------------------------------------------------------------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| maps                                                                         |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<float64>                                                               |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [4.33e-01,4.41e-01,3.88e-01,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,4.10e-01,... |\n",
       "| [1.45e-01,1.22e-01,1.51e-01,-2.74e-01,1.38e-01,3.48e-01,-8.03e-02,-1.41e-... |\n",
       "| [-1.31e-01,-1.63e-01,-2.33e-02,-3.66e-01,6.37e-01,2.14e-02,NaN,-2.32e-01,... |\n",
       "| [8.36e-01,8.42e-01,6.49e-01,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,7.31e... |\n",
       "+------------------------------------------------------------------------------+\n",
       "\n",
       "+------------------------------------------------------------------------------+\n",
       "| maps_sem                                                                     |\n",
       "+------------------------------------------------------------------------------+\n",
       "| array<float64>                                                               |\n",
       "+------------------------------------------------------------------------------+\n",
       "| [0.00e+00,0.00e+00,0.00e+00,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,0.00e+00,... |\n",
       "| [5.93e-02,6.03e-02,8.79e-02,0.00e+00,3.54e-01,2.72e-01,0.00e+00,0.00e+00,... |\n",
       "| [9.60e-02,9.33e-02,1.38e-01,0.00e+00,0.00e+00,3.54e-01,NaN,0.00e+00,1.71e... |\n",
       "| [0.00e+00,0.00e+00,0.00e+00,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,NaN,0.00e... |\n",
       "+------------------------------------------------------------------------------+\n",
       "showing top 4 rows"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "maps_table.show(4)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "dfeae616",
   "metadata": {},
   "outputs": [],
   "source": [
    "ht = hl.read_table('gs://gcp-public-data--gnomad/release/3.1.2/ht/genomes/gnomad.genomes.v3.1.2.sites.ht')\n",
    "meta_fields = ht.freq_meta.collect()\n",
    "maps_table = maps_table.annotate_globals(freq_metas = meta_fields)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "996c7306",
   "metadata": {},
   "outputs": [],
   "source": [
    "maps_zipped = maps_table.transmute(\n",
    "data = hl.zip(maps_table.N_singletons, maps_table.expected_singletons, maps_table.N_variants, maps_table.ps_agg, maps_table.maps, maps_table.maps_sem, maps_table.freq_metas[0])\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "bf9d1697",
   "metadata": {},
   "outputs": [],
   "source": [
    "maps_expl = maps_zipped.explode('data')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "89462fe9",
   "metadata": {},
   "outputs": [],
   "source": [
    "maps_clean = maps_expl.annotate(\n",
    "Singletons = maps_expl.data[0],\n",
    "Expected_Singletons = maps_expl.data[1],\n",
    "N_variants = maps_expl.data[2],\n",
    "PS = maps_expl.data[3],\n",
    "MAPS = maps_expl.data[4],\n",
    "MAPS_Sem = maps_expl.data[5],\n",
    "Metadata = maps_expl.data[6].values()\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "621c3d4a",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2022-12-01 12:54:31 Hail: INFO: merging 105 files totalling 781.5M...+ 7) / 104]\n",
      "2022-12-01 12:54:33 Hail: INFO: while writing:                    (8 + 8) / 104]\n",
      "    /Users/adrian/BroadIS/MAPS/01_data/maps_downsampling_multi_model_Per_Gene.csv\n",
      "  merge time: 2.032s\n",
      "2022-12-01 12:55:15 Hail: INFO: merging 105 files totalling 4.9M...2 + 2) / 104]\n",
      "2022-12-01 12:55:15 Hail: INFO: while writing:\n",
      "    /Users/adrian/BroadIS/MAPS/01_data/maps_clean_global_Per_gene.csv\n",
      "  merge time: 48.507ms\n",
      "[Stage 13:>                                                         (0 + 1) / 1]\r"
     ]
    },
    {
     "data": {
      "text/html": [
       "<table><thead><tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;\"></div></td></tr><tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">gene_ids</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">lof_csq_collapsed</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">Singletons</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">Expected_Singletons</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">N_variants</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">PS</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">MAPS</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">MAPS_Sem</div></td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \" colspan=\"1\"><div style=\"text-align: left;border-bottom: solid 2px #000; padding-bottom: 5px\">population</div></td></tr><tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">str</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">str</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">int64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">float64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">int64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">float64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">float64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">float64</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; text-align: left;\">str</td></tr>\n",
       "</thead><tbody><tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000003&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;HC&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">5.67e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.00e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.33e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">0.00e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000003&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;missense_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">42</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">3.26e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">65</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6.46e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.45e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">5.93e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000003&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;synonymous_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">9</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.23e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">25</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">3.60e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">-1.31e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">9.60e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000005&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;HC&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.64e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.00e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">8.36e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">0.00e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000005&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;missense_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">30</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">2.77e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">57</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">5.26e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.05e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6.61e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000005&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;synonymous_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">14</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.46e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">30</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.67e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">-2.02e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">9.11e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000419&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;HC&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.31e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">9</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6.67e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.88e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.57e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000419&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;missense_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">62</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">5.10e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">102</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6.08e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.08e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.83e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000419&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;synonymous_variant&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">22</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">2.62e+01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">49</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">4.49e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">-8.59e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">7.11e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "<tr><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;ENSG00000000457&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;HC&quot;</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">5.26e+00</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">10</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">6.00e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">7.44e-02</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">1.55e-01</td><td style=\"white-space: nowrap; max-width: 500px; overflow: hidden; text-overflow: ellipsis; \">&quot;adj&quot;</td></tr>\n",
       "</tbody></table><p style=\"background: #fdd; padding: 0.4em;\">showing top 10 rows</p>\n"
      ],
      "text/plain": [
       "+-------------------+----------------------+------------+---------------------+\n",
       "| gene_ids          | lof_csq_collapsed    | Singletons | Expected_Singletons |\n",
       "+-------------------+----------------------+------------+---------------------+\n",
       "| str               | str                  |      int64 |             float64 |\n",
       "+-------------------+----------------------+------------+---------------------+\n",
       "| \"ENSG00000000003\" | \"HC\"                 |          1 |            5.67e-01 |\n",
       "| \"ENSG00000000003\" | \"missense_variant\"   |         42 |            3.26e+01 |\n",
       "| \"ENSG00000000003\" | \"synonymous_variant\" |          9 |            1.23e+01 |\n",
       "| \"ENSG00000000005\" | \"HC\"                 |          1 |            1.64e-01 |\n",
       "| \"ENSG00000000005\" | \"missense_variant\"   |         30 |            2.77e+01 |\n",
       "| \"ENSG00000000005\" | \"synonymous_variant\" |         14 |            1.46e+01 |\n",
       "| \"ENSG00000000419\" | \"HC\"                 |          6 |            4.31e+00 |\n",
       "| \"ENSG00000000419\" | \"missense_variant\"   |         62 |            5.10e+01 |\n",
       "| \"ENSG00000000419\" | \"synonymous_variant\" |         22 |            2.62e+01 |\n",
       "| \"ENSG00000000457\" | \"HC\"                 |          6 |            5.26e+00 |\n",
       "+-------------------+----------------------+------------+---------------------+\n",
       "\n",
       "+------------+----------+-----------+----------+------------+\n",
       "| N_variants |       PS |      MAPS | MAPS_Sem | population |\n",
       "+------------+----------+-----------+----------+------------+\n",
       "|      int64 |  float64 |   float64 |  float64 | str        |\n",
       "+------------+----------+-----------+----------+------------+\n",
       "|          1 | 1.00e+00 |  4.33e-01 | 0.00e+00 | \"adj\"      |\n",
       "|         65 | 6.46e-01 |  1.45e-01 | 5.93e-02 | \"adj\"      |\n",
       "|         25 | 3.60e-01 | -1.31e-01 | 9.60e-02 | \"adj\"      |\n",
       "|          1 | 1.00e+00 |  8.36e-01 | 0.00e+00 | \"adj\"      |\n",
       "|         57 | 5.26e-01 |  4.05e-02 | 6.61e-02 | \"adj\"      |\n",
       "|         30 | 4.67e-01 | -2.02e-02 | 9.11e-02 | \"adj\"      |\n",
       "|          9 | 6.67e-01 |  1.88e-01 | 1.57e-01 | \"adj\"      |\n",
       "|        102 | 6.08e-01 |  1.08e-01 | 4.83e-02 | \"adj\"      |\n",
       "|         49 | 4.49e-01 | -8.59e-02 | 7.11e-02 | \"adj\"      |\n",
       "|         10 | 6.00e-01 |  7.44e-02 | 1.55e-01 | \"adj\"      |\n",
       "+------------+----------+-----------+----------+------------+\n",
       "showing top 10 rows"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "maps_clean_global =  maps_clean.filter(\n",
    "    (maps_clean.Metadata[0] == 'adj') & (maps_clean.Metadata.length() == 1))\n",
    "\n",
    "maps_clean_global = maps_clean_global.annotate(\n",
    "    population = maps_clean_global.Metadata[0])\n",
    "\n",
    "maps_clean_global = maps_clean_global.select('Singletons', 'Expected_Singletons', 'N_variants', 'PS', 'MAPS', 'MAPS_Sem', 'population')\n",
    "\n",
    "maps_clean_global.export('/Users/adrian/BroadIS/MAPS/01_data/maps_clean_global_Per_gene.csv', delimiter = \",\")\n",
    "\n",
    "maps_clean_global.show()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "bd62bfb1",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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