All CIViC variants with merged suggested HPO terms

merged_hpo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from civicpy import civic, recipes\n",
    "import csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# get all variant ids\n",
    "variant_ids = civic.get_all_variant_ids()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# get all merged HPO terms for variants\n",
    "evidence_hpo = dict()\n",
    "for evidence, phenotypes in recipes.get_variant_phenotypes_with_suggested_changes_merged(variant_ids):\n",
    "    hpo_records = civic.get_HPO_by_ids(phenotypes)\n",
    "    hpo_ids = [x['hpo_id'] for x in hpo_records]\n",
    "    evidence_hpo[evidence] = hpo_ids"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "# Write variant and HPO info to file\n",
    "\n",
    "with open('variant_hpo_merged.csv', 'w', newline='') as f:\n",
    "    w = csv.writer(f)\n",
    "    w.writerow([\n",
    "        'evidence_id',\n",
    "        'variant_id',\n",
    "        'variant_gene',\n",
    "        'variant_name',\n",
    "        'variant_origin',\n",
    "        'hpo_ids'\n",
    "    ])\n",
    "    for evidence, hpo_ids in evidence_hpo.items():\n",
    "        variant = evidence.variant\n",
    "        origin = evidence.variant_origin\n",
    "        if origin is None or 'Germline' not in origin:\n",
    "            continue\n",
    "        w.writerow((\n",
    "                evidence.id,\n",
    "                variant.id, \n",
    "                variant.entrez_name, \n",
    "                variant.name, \n",
    "                origin,\n",
    "                '|'.join(hpo_ids)))"
   ]
  }
 ],
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