civic_variant_to_clinvar

VHL Variants with ClinVar ID.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from civicpy import civic\n",
    "import csv"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "vhl = civic.get_gene_by_id(58)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('civic_to_clinvar_id.csv', 'w', newline='') as f:\n",
    "    writer = csv.writer(f)\n",
    "    writer.writerow(['CIViC ID', 'CIViC Name', 'ClinVar ID'])\n",
    "    for variant in vhl.variants:\n",
    "        try:\n",
    "            int(variant.clinvar_entries[0])\n",
    "        except:\n",
    "            continue\n",
    "        writer.writerow([variant.id, variant.name, variant.clinvar_entries[0]])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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