Add VR index to VICC records

vr-spec-index.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from ga4gh.core import ga4gh_digest\n",
    "from ga4gh.vr import __version__, ga4gh_identify, ga4gh_serialize, models, normalize\n",
    "from ga4gh.vr.extras.dataproxy import SeqRepoRESTDataProxy\n",
    "from ga4gh.vr.extras.translator import Translator\n",
    "\n",
    "seqrepo_rest_service_url = \"http://localhost:5000/seqrepo\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "dp = SeqRepoRESTDataProxy(base_url=seqrepo_rest_service_url)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "tlr = Translator(data_proxy=dp)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from bioutils.exceptions import BioutilsError"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def vr_file_encode(sourcename):\n",
    "    with open('{}.json'.format(sourcename), 'r') as infile, open('{}.vr.json'.format(sourcename), 'w') as outfile:\n",
    "        for record in infile:\n",
    "            json_record = json.loads(record)\n",
    "            vr_record_encode(json_record)\n",
    "            json.dump(json_record, outfile)\n",
    "            outfile.write('\\n')\n",
    "    return '{} complete.'.format(sourcename)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def vr_record_encode(record):\n",
    "    vr_set = set()\n",
    "    for feature in record['features']:\n",
    "        feature_vr_set = set()\n",
    "        feature_ga4gh = list()\n",
    "        if 'hgvs' not in feature:\n",
    "            continue\n",
    "        for hgvs_string in feature['hgvs']:\n",
    "            try:\n",
    "                vr_obj = tlr.from_hgvs(hgvs_string)\n",
    "            except (KeyError, ValueError, BioutilsError, AttributeError):\n",
    "                continue\n",
    "            vr_obj_dict = vr_obj.as_dict()\n",
    "            va_id = vr_obj_dict['id'].split(':')[-1]\n",
    "            vl_id = vr_obj_dict['location']['id'].split(':')[-1]\n",
    "            sq_id = vr_obj_dict['location']['sequence_id'].split(':')[-1]\n",
    "            if va_id not in feature_vr_set:\n",
    "                feature_vr_set.add(va_id)\n",
    "                feature_ga4gh.append(vr_obj_dict)\n",
    "            vr_set.update([va_id, vl_id, sq_id])\n",
    "        feature['ga4gh'] = feature_ga4gh\n",
    "    text_obj = models.Text(definition=record['feature_names'])\n",
    "    t_id = ga4gh_identify(text_obj)\n",
    "    record['text_object'] = text_obj.as_dict()\n",
    "    vr_set.add(t_id.split(':')[-1])\n",
    "    record['ga4gh'] = list(vr_set)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pmkb_records = list()\n",
    "with open('pmkb.json','r') as infile:\n",
    "    for record in infile:\n",
    "        pmkb_records.append(json.loads(record))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from collections import Counter\n",
    "\n",
    "c = Counter()\n",
    "for record in pmkb_records:\n",
    "    # vr_record_encode(record)\n",
    "    if not isinstance(record['feature_names'], list):\n",
    "        c['strings'] += 1\n",
    "    elif len(record['feature_names']) > 0:\n",
    "        c['terms'] += 1\n",
    "    else:\n",
    "        c[None] += 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "vr_record_encode(pmkb_records[1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'definition': 'MPL W515K, MPL W515L, MPL codon(s) 515 missense',\n",
       " 'id': 'ga4gh:VT.Bbyyg0vqd2ExVierd2pH1UvC6XwHSzTe',\n",
       " 'type': 'Text'}"
      ]
     },
     "execution_count": 88,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pmkb_records[1]['text_object']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import multiprocessing as mp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "pool = mp.Pool()\n",
    "sources = ['brca','cgi','civic','jax','molecularmatch','oncokb','pmkb']\n",
    "result = pool.map(vr_file_encode, sources)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['brca complete.',\n",
       " 'cgi complete.',\n",
       " 'civic complete.',\n",
       " 'jax complete.',\n",
       " 'molecularmatch complete.',\n",
       " 'oncokb complete.',\n",
       " 'pmkb complete.']"
      ]
     },
     "execution_count": 97,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "result"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# TODO: convert jax_trials to string for feature_names field"
   ]
  }
 ],
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