vrs-python-issue-363

vrs-python-issue-363.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "https://github.com/ga4gh/vrs-python/issues/363\n",
    "\n",
    "```md\n",
    "NC_000016.9:g.89306725_89339913del\n",
    "curl -X 'GET' \\\n",
    "  'https://normalize.cancervariants.org/variation/translate_from?variation=NC_000016.9%3Ag.89306725_89339913del&fmt=hgvs' \\\n",
    "  -H 'accept: application/json'\n",
    "```\n",
    "\n",
    "```json\n",
    "{\n",
    "    \"query\": {\n",
    "        \"variation\": \"NC_000016.9:g.89306725_89339913del\",\n",
    "        \"fmt\": \"hgvs\"\n",
    "    },\n",
    "    \"warnings\": [],\n",
    "    \"service_meta_\": {\n",
    "        \"name\": \"variation-normalizer\",\n",
    "        \"version\": \"0.8.1\",\n",
    "        \"response_datetime\": \"2024-03-14T16:06:49.593965Z\",\n",
    "        \"url\": \"https://github.com/cancervariants/variation-normalization\"\n",
    "    },\n",
    "    \"vrs_python_meta_\": {\n",
    "        \"name\": \"vrs-python\",\n",
    "        \"version\": \"2.0.0a2\",\n",
    "        \"url\": \"https://github.com/ga4gh/vrs-python\"\n",
    "    },\n",
    "    \"variation\": {\n",
    "        \"id\": \"ga4gh:VA.jamp0iMJTRCvYcbawsyBODCIAkwldCM7\",\n",
    "        \"type\": \"Allele\",\n",
    "        \"location\": {\n",
    "            \"id\": \"ga4gh:SL.hwDN-Cy3-sBsiuMvCl-X50U4rGeCLWAI\",\n",
    "            \"type\": \"SequenceLocation\",\n",
    "            \"sequenceReference\": {\n",
    "                \"type\": \"SequenceReference\",\n",
    "                \"refgetAccession\": \"SQ.W6wLoIFOn4G7cjopxPxYNk2lcEqhLQFb\"\n",
    "            },\n",
    "            \"start\": 89306723,\n",
    "            \"end\": 89339913\n",
    "        },\n",
    "        \"state\": {\n",
    "            \"type\": \"ReferenceLengthExpression\",\n",
    "            \"length\": 1,\n",
    "            \"sequence\": \"T\",\n",
    "            \"repeatSubunitLength\": 33189\n",
    "        }\n",
    "    }\n",
    "}\n",
    "\n",
    "```\n",
    "\n",
    "```md\n",
    "NC_000016.9:g.89306725_89339913del\n",
    "\n",
    "--- 1-indexed positional coordinates (hgvs)\n",
    "   89306725....89339913\n",
    "       |---------|            \n",
    "   G T T C ... A T C ...\n",
    "--- 0-indexed interbased coordinates (vrs)\n",
    "   G T T C ... A T C ...\n",
    "    |             |\n",
    " 89306723.....89339913\n",
    "\n",
    "RLE.length = 1, sequence = \"T\"\n",
    "```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "  \"id\": \"ga4gh:VA.mROPdv6I2EsC8qwKdiBj4EedteLTRctP\",\n",
      "  \"type\": \"Allele\",\n",
      "  \"digest\": \"mROPdv6I2EsC8qwKdiBj4EedteLTRctP\",\n",
      "  \"location\": {\n",
      "    \"id\": \"ga4gh:SL.BqujMxSzNcw-N3LntN8YSYrFqx8Sx2ig\",\n",
      "    \"type\": \"SequenceLocation\",\n",
      "    \"digest\": \"BqujMxSzNcw-N3LntN8YSYrFqx8Sx2ig\",\n",
      "    \"sequenceReference\": {\n",
      "      \"type\": \"SequenceReference\",\n",
      "      \"refgetAccession\": \"SQ.W6wLoIFOn4G7cjopxPxYNk2lcEqhLQFb\"\n",
      "    },\n",
      "    \"start\": 89306723,\n",
      "    \"end\": 89339913\n",
      "  },\n",
      "  \"state\": {\n",
      "    \"type\": \"ReferenceLengthExpression\",\n",
      "    \"length\": 1,\n",
      "    \"sequence\": \"T\",\n",
      "    \"repeatSubunitLength\": 33189\n",
      "  }\n",
      "}\n",
      "Original sequence length: 33188\n",
      "Normalized sequence length: 33190\n",
      "VRS repeatSubunitLength: 33189\n",
      "original_sequence[:20]='TCGAGACCAGCCTGGCCAAC'\n",
      "normalized_sequence[:20]='TTCGAGACCAGCCTGGCCAA'\n",
      "original_sequence[-20:]='AGGTCAAGAGATCGAGACCA'\n",
      "normalized_sequence[-20:]='GGTCAAGAGATCGAGACCAT'\n"
     ]
    }
   ],
   "source": [
    "import json\n",
    "from ga4gh.vrs.extras.translator import AlleleTranslator\n",
    "from biocommons.seqrepo import SeqRepo\n",
    "from biocommons.seqrepo.dataproxy import SeqRepoDataProxy\n",
    "\n",
    "seqrepo_path = \"/Users/kferrite/dev/biocommons.seqrepo/seqrepo/2021-01-29\"\n",
    "dataproxy = SeqRepoDataProxy(SeqRepo(seqrepo_path))\n",
    "\n",
    "hgvs_expr = \"NC_000016.9:g.89306725_89339913del\"\n",
    "\n",
    "# hgvs coordinates minus 1 to convert to 0-based\n",
    "start_0 = 89306724\n",
    "end_0 = 89339912\n",
    "original_sequence = dataproxy.get_sequence(\"NC_000016.9\", start_0, end_0)\n",
    "\n",
    "translator = AlleleTranslator(dataproxy)\n",
    "\n",
    "allele = translator._from_hgvs(hgvs_expr)\n",
    "print(json.dumps(allele.model_dump(exclude_none=True), indent=2))\n",
    "\n",
    "normalized_start = allele.location.start\n",
    "normalized_end = allele.location.end\n",
    "normalized_sequence = dataproxy.get_sequence(\n",
    "    f\"ga4gh:{allele.location.sequenceReference.refgetAccession}\",\n",
    "    normalized_start,\n",
    "    normalized_end,\n",
    ")\n",
    "print(f\"Original sequence length: {len(original_sequence)}\")\n",
    "print(f\"Normalized sequence length: {len(normalized_sequence)}\")\n",
    "print(f\"VRS repeatSubunitLength: {allele.state.repeatSubunitLength}\")\n",
    "print(f\"{original_sequence[:20]=}\")\n",
    "print(f\"{normalized_sequence[:20]=}\")\n",
    "print(f\"{original_sequence[-20:]=}\")\n",
    "print(f\"{normalized_sequence[-20:]=}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "venv",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.13"
  },
  "orig_nbformat": 4
 },
 "nbformat": 4,
 "nbformat_minor": 2
}