COVID19-Quick-Start.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### COVID-19 Quick Start Notebook  \n",
    "- If this is your first time using the IBM Functional Genomics Platform SDK, please see our [installation documentation](https://ibm.github.io/omxware-pypi-docs/build/html/installation.html) and [Getting Started Notebook](https://github.com/IBM/omxware-getting-started/blob/master/GettingStarted.ipynb) or [Getting Started Documentation](https://ibm.github.io/omxware-pypi-docs/build/html/usage.html). \n",
    "- If you have any questions, please feel free to reach out to us via our forums http://ibm.biz/functional-genomics-forum."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Verify Python 3**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Alrite! We are using Python 3\n"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "\n",
    "if sys.version_info[0] < 3:\n",
    "    raise \"Must be using Python 3\"\n",
    "else:\n",
    "    print(\"Alrite! We are using Python \"+str(sys.version_info[0]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Install or Update the OMXWare Package (if needed)**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found existing installation: omxware 0.1.45\n",
      "Uninstalling omxware-0.1.45:\n",
      "  Would remove:\n",
      "    /home/vader/Projects/python3_env/lib/python3.7/site-packages/omxware-0.1.45.dist-info/*\n",
      "    /home/vader/Projects/python3_env/lib/python3.7/site-packages/omxware/*\n",
      "Proceed (y/n)?   Successfully uninstalled omxware-0.1.45\n",
      "Collecting omxware\n",
      "  Downloading omxware-0.1.45-py2.py3-none-any.whl (34 kB)\n",
      "Requirement already satisfied: pycryptodome in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (3.9.8)\n",
      "Requirement already satisfied: simplejson>=3.16.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (3.17.0)\n",
      "Requirement already satisfied: urllib3<=1.24.2 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (1.24.2)\n",
      "Requirement already satisfied: requests in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (2.23.0)\n",
      "Requirement already satisfied: matplotlib in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (3.2.0)\n",
      "Requirement already satisfied: python-keycloak>=0.16.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (0.20.0)\n",
      "Requirement already satisfied: configparser in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (5.0.0)\n",
      "Requirement already satisfied: pandas in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (1.0.1)\n",
      "Requirement already satisfied: IPython in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from omxware) (7.15.0)\n",
      "Requirement already satisfied: chardet<4,>=3.0.2 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from requests->omxware) (3.0.4)\n",
      "Requirement already satisfied: idna<3,>=2.5 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from requests->omxware) (2.9)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from requests->omxware) (2020.4.5.2)\n",
      "Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from matplotlib->omxware) (2.4.6)\n",
      "Requirement already satisfied: kiwisolver>=1.0.1 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from matplotlib->omxware) (1.1.0)\n",
      "Requirement already satisfied: cycler>=0.10 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from matplotlib->omxware) (0.10.0)\n",
      "Requirement already satisfied: numpy>=1.11 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from matplotlib->omxware) (1.18.1)\n",
      "Requirement already satisfied: python-dateutil>=2.1 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from matplotlib->omxware) (2.8.1)\n",
      "Requirement already satisfied: python-jose>=1.4.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from python-keycloak>=0.16.0->omxware) (3.1.0)\n",
      "Requirement already satisfied: pytz>=2017.2 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from pandas->omxware) (2019.3)\n",
      "Requirement already satisfied: backcall in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (0.1.0)\n",
      "Requirement already satisfied: pexpect; sys_platform != \"win32\" in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (4.8.0)\n",
      "Requirement already satisfied: jedi>=0.10 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (0.17.0)\n",
      "Requirement already satisfied: decorator in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (4.4.2)\n",
      "Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (3.0.5)\n",
      "Requirement already satisfied: pygments in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (2.6.1)\n",
      "Requirement already satisfied: traitlets>=4.2 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (4.3.3)\n",
      "Requirement already satisfied: setuptools>=18.5 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (45.2.0)\n",
      "Requirement already satisfied: pickleshare in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from IPython->omxware) (0.7.5)\n",
      "Requirement already satisfied: six in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from cycler>=0.10->matplotlib->omxware) (1.14.0)\n",
      "Requirement already satisfied: pyasn1 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from python-jose>=1.4.0->python-keycloak>=0.16.0->omxware) (0.4.8)\n",
      "Requirement already satisfied: ecdsa<1.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from python-jose>=1.4.0->python-keycloak>=0.16.0->omxware) (0.15)\n",
      "Requirement already satisfied: rsa in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from python-jose>=1.4.0->python-keycloak>=0.16.0->omxware) (4.0)\n",
      "Requirement already satisfied: ptyprocess>=0.5 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from pexpect; sys_platform != \"win32\"->IPython->omxware) (0.6.0)\n",
      "Requirement already satisfied: parso>=0.7.0 in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from jedi>=0.10->IPython->omxware) (0.7.0)\n",
      "Requirement already satisfied: wcwidth in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->IPython->omxware) (0.2.4)\n",
      "Requirement already satisfied: ipython-genutils in /home/vader/Projects/python3_env/lib/python3.7/site-packages (from traitlets>=4.2->IPython->omxware) (0.2.0)\n",
      "Installing collected packages: omxware\n",
      "Successfully installed omxware-0.1.45\n",
      "\u001b[33mWARNING: You are using pip version 20.0.2; however, version 20.2.3 is available.\n",
      "You should consider upgrading via the '/home/vader/Projects/python3_env/bin/python -m pip install --upgrade pip' command.\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!echo 'y' | pip uninstall omxware\n",
    "\n",
    "#Install OMXWare client\n",
    "!pip install --no-cache-dir omxware\n",
    "\n",
    "# #Install PrettyPrint\n",
    "# !pip install --no-cache-dir pprint\n",
    "\n",
    "# #Install py4j to use Dynamic forms\n",
    "# !pip install --no-cache-dir py4j\n",
    "\n",
    "# #Install panda\n",
    "# !pip install --no-cache-dir pandas"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Name: omxware\r\n",
      "Version: 0.1.45\r\n",
      "Summary: IBM Functional Genomics Platform SDK to explore data.\r\n",
      "Home-page: https://github.ibm.com/GrandChallenge-Almaden/omxware-pypi\r\n",
      "Author: Harsha Krishnareddy\r\n",
      "Author-email: hvkrishn@us.ibm.com\r\n",
      "License: IBM\r\n",
      "Location: /home/vader/Projects/python3_env/lib/python3.7/site-packages\r\n",
      "Requires: urllib3, python-keycloak, configparser, pycryptodome, pandas, matplotlib, simplejson, requests, IPython\r\n",
      "Required-by: \r\n"
     ]
    }
   ],
   "source": [
    "!pip show omxware"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Import OMXWare and initialize**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "%matplotlib inline\n",
    "\n",
    "import json\n",
    "import pprint\n",
    "import math\n",
    "pp = pprint.PrettyPrinter(indent=4)\n",
    "\n",
    "from IPython.display import display\n",
    "\n",
    "import omxware\n",
    "\n",
    "# --- Authentication options --- #\n",
    "# generate token with OMXWare user name and password (likely done once and then stored in file, see usage below)\n",
    "token = omxware.get_token('username', 'password') # fill in password to initiate token\n",
    "\n",
    "# or\n",
    "\n",
    "# use previously generated token loaded from file\n",
    "# token_path = \"./omxware_collaborative_work/super_awesome_token\"  # update for your path to the token file you create\n",
    "# f = open(token_path)\n",
    "# token = f.readline()\n",
    "\n",
    "\n",
    "# provide your token to authenticate\n",
    "omx = omxware.omxware(token)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Access OMXWare Help**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Help on omxware in module omxware.omxware object:\n",
      "\n",
      "class omxware(builtins.object)\n",
      " |  omxware(omxware_token, env='public')\n",
      " |  \n",
      " |  Methods defined here:\n",
      " |  \n",
      " |  __init__(self, omxware_token, env='public')\n",
      " |      Initialize a session.\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param omxware_token: OMXWare Token. use\n",
      " |          :type omxware_token: str\n",
      " |      \n",
      " |          :param env: OMXWare `env` type. Must be one of ['master', 'dev', 'dev_search', 'local']\n",
      " |          :type env: str\n",
      " |  \n",
      " |  domains(self, ids=None, sequence=None, genus_names=None, protein_ids=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)\n",
      " |      Get OMXWare Domains.\n",
      " |      \n",
      " |      Parameters:\n",
      " |      \n",
      " |          :param ids: List of domain ids\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param sequence: Domain sequence\n",
      " |          :type sequence: str\n",
      " |      \n",
      " |          :param genus_names: List of Genus names\n",
      " |          :type genus_names: [str]\n",
      " |      \n",
      " |          :param protein_ids: List of Protein ids\n",
      " |          :type protein_ids: [str]\n",
      " |      \n",
      " |          :param go_terms:\n",
      " |          :type go_terms: [str]\n",
      " |      \n",
      " |          :param ipr_ids:\n",
      " |          :type ipr_ids: [str]\n",
      " |      \n",
      " |          :param sequence_length:\n",
      " |          :type sequence_length: str\n",
      " |      \n",
      " |          :param classification: Must only be one of {'bacteria', 'virus', 'all'}\n",
      " |          :type classification: str\n",
      " |      \n",
      " |          :param collection: List of Collection names. e.g: 'covid19' (collections is a pre-defined set of data tagged by the platform team)\n",
      " |          :type collection: [str]\n",
      " |      \n",
      " |          :param page_number: (int): Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: (int): Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Domain\n",
      " |  \n",
      " |  genes(self, ids=None, sequence=None, gene_name=None, genome_ids=None, genus_names=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)\n",
      " |      Get Genes.\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param ids: List of gene ids\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param sequence: Gene sequence\n",
      " |          :type sequence: str\n",
      " |      \n",
      " |          :param gene_name:\n",
      " |          :type gene_name: str\n",
      " |      \n",
      " |          :param genome_ids: List of Genome IDs\n",
      " |          :type genome_ids: [str]\n",
      " |      \n",
      " |          :param genus_names: List of Genus names\n",
      " |          :type genus_names: [str]\n",
      " |      \n",
      " |          :param go_terms:\n",
      " |          :type go_terms: [str]\n",
      " |      \n",
      " |          :param ipr_ids:\n",
      " |          :type ipr_ids: [str]\n",
      " |      \n",
      " |          :param sequence_length:\n",
      " |          :type sequence_length: str\n",
      " |      \n",
      " |          :param classification: Must only be one of {'bacteria', 'virus', 'all'}\n",
      " |          :type classification: str\n",
      " |      \n",
      " |          :param collection: List of Collection names. e.g: 'covid19' (collections is a pre-defined set of data tagged by the platform team)\n",
      " |          :type collection: [str]\n",
      " |      \n",
      " |          :param page_number: (int): Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: (int): Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Gene\n",
      " |  \n",
      " |  genomes(self, ids=None, genus_names=None, genome_type=None, genome_taxid=None, classification=None, collection=None, created_before=None, created_after=None, modified_before=None, modified_after=None, page_size=25, page_number=1)\n",
      " |      Get Genomes by List of Genome ID(s) and/or Genus name(s) .\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param ids: List of Genome IDs\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param genus_names: List of Genus names\n",
      " |          :type genus_names: [str]\n",
      " |      \n",
      " |          :param genome_type: List of Genome Types. Must be one of { 'REFSEQ’, 'SRA’, ‘GENBANK’ }\n",
      " |          :type genome_type: [str]\n",
      " |      \n",
      " |          :param genome_taxid: List of Genome Tax ids\n",
      " |          :type genome_taxid: [str]\n",
      " |      \n",
      " |          :param classification: Must only be one of {'bacteria', 'virus', 'all'}\n",
      " |          :type classification: str\n",
      " |      \n",
      " |          :param collection: List of Collection names. e.g: 'covid19' (collections is a pre-defined set of data tagged by the platform team)\n",
      " |          :type collection: [str]\n",
      " |      \n",
      " |          :param created_before: Date - Created / Imported before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY\n",
      " |          :type created_before: [str]\n",
      " |      \n",
      " |          :param created_after: Date - Created / Imported after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY\n",
      " |          :type created_after: [str]\n",
      " |      \n",
      " |          :param modified_before: Date - Modified before. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY\n",
      " |          :type modified_before: [str]\n",
      " |      \n",
      " |          :param modified_after: Date - Modified after. Must be in YYYY-MM-DD format. Can also be YYYY-MM or Just YYYY\n",
      " |          :type modified_after: [str]\n",
      " |      \n",
      " |          :param page_number: Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Genome\n",
      " |  \n",
      " |  genus(self, genus_names=None, page_size=25, page_number=1)\n",
      " |      Get Genera by names .\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param genus_names: List of Genus names\n",
      " |          :type genus_names: [str]\n",
      " |      \n",
      " |          :param page_number: Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Genus\n",
      " |  \n",
      " |  go(self, ids=None, categories=None, classification=None, collection=None, page_size=25, page_number=1)\n",
      " |      Get OMXWare GO Terms by List of GO ID(s) and/or Category name(s) .\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param ids: List of GO Term IDs\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param categories: List of GO Term Categories. Must be one of { 'MOLECULAR_FUNCTION', 'BIOLOGICAL_PROCESS', 'CELLULAR_COMPONENT' }\n",
      " |          :type categories: [str]\n",
      " |      \n",
      " |          :param classification: Must only be one of {'bacteria', 'virus', 'all'}\n",
      " |          :type classification: str\n",
      " |      \n",
      " |          :param collection: List of Collection names. e.g: 'covid19' (collections is a pre-defined set of data tagged by the platform team)\n",
      " |          :type collection: [str]\n",
      " |      \n",
      " |          :param page_number: Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Go\n",
      " |  \n",
      " |  ipr(self, ids=None, categories=None, classification=None, collection=None, page_size=25, page_number=1)\n",
      " |      Get OMXWare IPRs by List of IPR Code(s) and/or Category name(s) .\n",
      " |      \n",
      " |      Parameters:\n",
      " |          :param ids: List of IPR IDs\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param categories: List of IPR Categories.\n",
      " |          :type categories: [str]\n",
      " |      \n",
      " |          :param classification: Must only be one of {'bacteria', 'virus', 'all'}\n",
      " |          :type classification: str\n",
      " |      \n",
      " |          :param collection: List of Collection names. e.g: 'covid19' (collections is a pre-defined set of data tagged by the platform team)\n",
      " |          :type collection: [str]\n",
      " |      \n",
      " |          :param page_number: Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Ipr\n",
      " |  \n",
      " |  jobs(self)\n",
      " |      Get a list of all the jobs a user has provisioned so far\n",
      " |      Returns:\n",
      " |          :return:    OmxResponse :   User\n",
      " |  \n",
      " |  proteins(self, ids=None, sequence=None, protein_name=None, genome_ids=None, genus_names=None, domain_ids=None, go_terms=None, ipr_ids=None, sequence_length=None, classification=None, collection=None, page_size=25, page_number=1)\n",
      " |      Get Proteins.\n",
      " |      \n",
      " |      Parameters:\n",
      " |      \n",
      " |          :param ids: List of Protein ids\n",
      " |          :type ids: [str]\n",
      " |      \n",
      " |          :param sequence: Protein sequence\n",
      " |          :type sequence: str\n",
      " |      \n",
      " |          :param protein_name:\n",
      " |          :type protein_name: str\n",
      " |      \n",
      " |          :param genome_ids: List of Genome IDs\n",
      " |          :type genome_ids: [str]\n",
      " |      \n",
      " |          :param genus_names: List of Genus names\n",
      " |          :type genus_names: [str]\n",
      " |      \n",
      " |          :param domain_ids:\n",
      " |          :type domain_ids: [str]\n",
      " |      \n",
      " |          :param go_terms:\n",
      " |          :type go_terms: [str]\n",
      " |      \n",
      " |          :param ipr_ids:\n",
      " |          :type ipr_ids: [str]\n",
      " |      \n",
      " |          :param sequence_length:\n",
      " |          :type sequence_length: str\n",
      " |      \n",
      " |          :param page_number: (int): Page Number\n",
      " |          :type page_number: int\n",
      " |      \n",
      " |          :param page_size: (int): Results page size\n",
      " |          :type page_size: int\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse: Protein\n",
      " |  \n",
      " |  whoami(self)\n",
      " |      Get OMXWare User info .\n",
      " |      \n",
      " |      Returns:\n",
      " |          :return:    OmxResponse :   User\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data descriptors defined here:\n",
      " |  \n",
      " |  __dict__\n",
      " |      dictionary for instance variables (if defined)\n",
      " |  \n",
      " |  __weakref__\n",
      " |      list of weak references to the object (if defined)\n",
      " |  \n",
      " |  ----------------------------------------------------------------------\n",
      " |  Data and other attributes defined here:\n",
      " |  \n",
      " |  PAGE_INDEX_DEFAULT = 1\n",
      " |  \n",
      " |  PAGE_SIZE_DEFAULT = 25\n",
      "\n"
     ]
    }
   ],
   "source": [
    "help(omx)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Search for Details About a Specific Gene Sequence**  \n",
    "- Since the IBM Functional Genomics Platform has pre-computed millions of genes, proteins, etc. and stored all of the unique sequences, we can access the data with a simple retrieval to see if a sequence already exists. If that sequence exists, you can then just connect out to other related biological entities e.g. query a gene then find the relevant domains for its protein sequences.  \n",
    "- If you're interested in a fuzzy search, this can be accomplished by retrieving sequences of interest and using your aligner/classifier of choice. Those sequences of interest can be retrieved as a dataframe, JSON, or FASTA format.\n",
    "- Alternatively, you can complete a fuzzy search using our [BLAST application](http://ibm.biz/functional-genomics-blast)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total Number of Results: 1\n",
      "Gene Name(s): ['Oligopeptide transport ATP-binding protein OppF']\n",
      "Gene UID: 000002b370e57ecc5b92dec8cae249cf\n",
      "Number of Genomes this sequence is found in: 5\n"
     ]
    }
   ],
   "source": [
    "search_term = \"ATGATCGAGATACAACACCTTAACCTGACGTTTGGCGAGGGCGAGAAGCGTAATCAGGTGCTGGACGATGTGAATATCAGCGTGAGGGAGGGGGAGATTTACGGCCTGGTGGGGGAGTCCGGTTCGGGCAAAACCACGGTGCTGAAATGCCTTGCCGGGCTGTTTACCCACTGGGAGGGCGAGCTGGCGATTAACGGCAAGCGGCTGGAAAAACGTATCAGCCAGGAACGCTGCCGCCGGGTGCAGATGGTATTTCAGGATCCGTACGGCTCTTTGCATCCGCGTCACACCATCGGCGATATTCTGGAAGAGCCGCTGCACATTCACCGCATAAAAGATCGGGAGCGGCGCGTTCACGCCCTGCTGGATAAAGTTGGGCTTAATCGGGCGTTTCGCGATCGCTATCCGCACCAGCTTTCCGGCGGGCAGCGCCAGCGCGTGGCGATTGCCAGGGCGCTGATTCTGGAGCCGCAGGTGCTGCTGCTGGATGAACCTACCTCGGCGCTGGACGTCTCGGTGCAGGCGGAAATCCTCAACCTGCTGGCGGAACTTCAGCGTGAGTCGAACCTGACCTACCTGATGGTCACCCACGATCTGGGCGTGATTGCCCATCTGTGTCAGAAGGTGGCGGTAATGCAGTATGGCAAAATCCTTGAAAGCCTGACGGTGGACGAACTGGTCGCCGGGCAGGCCAAAACCGACTATACGCGGATGCTGGTCAATGCCTCACAGCAGTATTCCCGCGAGATGGCGCGGGAGGTGGCGGTGTATTAG\"\n",
    "\n",
    "genes = omx.genes(sequence = search_term,page_size=25)\n",
    "#search for sequence is an exact string search and is case insensitive\n",
    "\n",
    "total_results = genes.total_results()\n",
    "#search will only return one result since we are looking for a specific sequence\n",
    "\n",
    "print('Total Number of Results: %d' % total_results)\n",
    "\n",
    "for each_gene in genes.results():\n",
    "    print('Gene Name(s): {}'.format(each_gene.name()))\n",
    "    print('Gene UID:',each_gene.id())\n",
    "    genomes = each_gene.genomes()\n",
    "    print('Number of Genomes this sequence is found in:',genomes.total_results())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Search for Details About a Specific Gene By Name**\n",
    "- Here we provide an example of how to search a gene name to a specific classification of data e.g. bacteria, virus, or all as well as layering on a limitation to data only associated with SARS-CoV-2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total Unique Sequences for (Bacteria) Spike Glycoprotein: 3712\n",
      "Total Unique Sequences for (Virus) Spike Glycoprotein: 12654\n",
      "Total Unique Sequences for (All) Spike Glycoprotein: 16366\n",
      "Total Unique Sequences for (SARS-COV-2) Spike Glycoprotein: 6898\n"
     ]
    }
   ],
   "source": [
    "search_term = 'Spike Glycoprotein'\n",
    "\n",
    "genes_bacteria = omx.genes(gene_name=search_term, page_size=25,classification='bacteria')\n",
    "#default classification is 'bacteria'\n",
    "\n",
    "genes_virus = omx.genes(gene_name=search_term, page_size=25,classification='virus')\n",
    "genes_all = omx.genes(gene_name=search_term, page_size=25,classification='all')\n",
    "genes_sars_cov2 = omx.genes(gene_name=search_term,page_size=25,collection=['covid19'],classification='virus')\n",
    "# search is case insensitive and will match partial strings\n",
    "\n",
    "print('Total Unique Sequences for (Bacteria) %s: %d' % (search_term, genes_bacteria.total_results()))\n",
    "print('Total Unique Sequences for (Virus) %s: %d' % (search_term, genes_virus.total_results()))\n",
    "print('Total Unique Sequences for (All) %s: %d' % (search_term, genes_all.total_results()))\n",
    "print('Total Unique Sequences for (SARS-COV-2) %s: %d' % (search_term, genes_sars_cov2.total_results()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Getting all Results for a query**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total Number of Results should be: 6898\n",
      "Total Number of Pages to be queried: 69\n",
      "Total Final Results: 6698\n",
      "Total Final Unique Results: 6698\n",
      "Total Gene UID returned: 6698\n",
      "Total Unique Gene UID returned: 6698\n"
     ]
    }
   ],
   "source": [
    "search_term = 'Spike Glycoprotein'\n",
    "genes_sars_cov2 = omx.genes(gene_name=search_term,page_size=100,collection=['covid19'],classification='virus')\n",
    "total = genes_sars_cov2.total_results()\n",
    "print('Total Number of Results should be:',total)\n",
    "pages = math.ceil(total/100)\n",
    "print('Total Number of Pages to be queried:',pages)\n",
    "final_results = []\n",
    "list_uid = []\n",
    "for counter in range(1,pages+1):\n",
    "    results = omx.genes(gene_name=search_term,page_size=100,collection=['covid19'],classification='virus',page_number=counter)\n",
    "    results = results.results(type='list')\n",
    "    for item in results:\n",
    "        final_results.append(item)\n",
    "        list_uid.append(item.id())\n",
    "print('Total Final Results:',len(final_results))\n",
    "print('Total Final Unique Results:',len(set(final_results)))\n",
    "print('Total Gene UID returned:',len(list_uid))\n",
    "print('Total Unique Gene UID returned:',len(set(list_uid)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Get results in a dataframe** *to get results in other formats, see: https://github.com/IBM/omxware-getting-started/blob/master/RetrieveDataFormats.ipynb*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>genera</th>\n",
       "      <th>genomes</th>\n",
       "      <th>sequence_length</th>\n",
       "      <th>status</th>\n",
       "      <th>go_codes</th>\n",
       "      <th>interproscan_ids</th>\n",
       "      <th>omx_creation_ts</th>\n",
       "      <th>omx_modified_ts</th>\n",
       "      <th>classification</th>\n",
       "      <th>collection</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6efa65acd677199d20be1e98835ff23b</td>\n",
       "      <td>[Spike glycoprotein]</td>\n",
       "      <td>gene</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_419876]</td>\n",
       "      <td>3822</td>\n",
       "      <td>active</td>\n",
       "      <td>[GO:0016021, GO:0019031, GO:0019064, GO:003965...</td>\n",
       "      <td>[IPR002552, IPR018548, IPR027400, IPR036326]</td>\n",
       "      <td>2020-04-06T14:54:16.000Z</td>\n",
       "      <td>2020-07-30T21:34:53.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>72af05fd86a0f8a1773968711c38cb2e</td>\n",
       "      <td>[Spike glycoprotein]</td>\n",
       "      <td>gene</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_475945]</td>\n",
       "      <td>3822</td>\n",
       "      <td>active</td>\n",
       "      <td>[GO:0016021, GO:0019031, GO:0019064, GO:003965...</td>\n",
       "      <td>[IPR002552, IPR018548, IPR027400, IPR036326, I...</td>\n",
       "      <td>2020-07-28T19:11:17.000Z</td>\n",
       "      <td>2020-07-28T19:11:17.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>8efa2cc66568eae7d6e1e3a4824970e4</td>\n",
       "      <td>[Spike glycoprotein]</td>\n",
       "      <td>gene</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_486511]</td>\n",
       "      <td>3822</td>\n",
       "      <td>active</td>\n",
       "      <td>[GO:0016021, GO:0019031, GO:0019064, GO:003965...</td>\n",
       "      <td>[IPR002552, IPR018548, IPR027400, IPR036326, I...</td>\n",
       "      <td>2020-07-28T16:18:04.000Z</td>\n",
       "      <td>2020-07-28T16:18:04.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2703e2ed0dd3c122fbe80a36ab4948af</td>\n",
       "      <td>[Spike glycoprotein]</td>\n",
       "      <td>gene</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_512988]</td>\n",
       "      <td>3822</td>\n",
       "      <td>active</td>\n",
       "      <td>[GO:0016021, GO:0019031, GO:0019064, GO:003965...</td>\n",
       "      <td>[IPR002552, IPR018548, IPR027400, IPR032500, I...</td>\n",
       "      <td>2020-08-18T14:12:33.000Z</td>\n",
       "      <td>2020-08-18T14:12:33.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>b33e2c68c42bf0f8be8b508550b939db</td>\n",
       "      <td>[Spike glycoprotein]</td>\n",
       "      <td>gene</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[MT451074.1]</td>\n",
       "      <td>3822</td>\n",
       "      <td>active</td>\n",
       "      <td>[GO:0016021, GO:0019031, GO:0019064, GO:003965...</td>\n",
       "      <td>[IPR002552, IPR018548, IPR027400, IPR036326, I...</td>\n",
       "      <td>2020-06-02T16:49:13.000Z</td>\n",
       "      <td>2020-06-02T21:07:46.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 id                  name  type  \\\n",
       "0  6efa65acd677199d20be1e98835ff23b  [Spike glycoprotein]  gene   \n",
       "1  72af05fd86a0f8a1773968711c38cb2e  [Spike glycoprotein]  gene   \n",
       "2  8efa2cc66568eae7d6e1e3a4824970e4  [Spike glycoprotein]  gene   \n",
       "3  2703e2ed0dd3c122fbe80a36ab4948af  [Spike glycoprotein]  gene   \n",
       "4  b33e2c68c42bf0f8be8b508550b939db  [Spike glycoprotein]  gene   \n",
       "\n",
       "              genera           genomes  sequence_length  status  \\\n",
       "0  [betacoronavirus]  [EPI_ISL_419876]             3822  active   \n",
       "1  [betacoronavirus]  [EPI_ISL_475945]             3822  active   \n",
       "2  [betacoronavirus]  [EPI_ISL_486511]             3822  active   \n",
       "3  [betacoronavirus]  [EPI_ISL_512988]             3822  active   \n",
       "4  [betacoronavirus]      [MT451074.1]             3822  active   \n",
       "\n",
       "                                            go_codes  \\\n",
       "0  [GO:0016021, GO:0019031, GO:0019064, GO:003965...   \n",
       "1  [GO:0016021, GO:0019031, GO:0019064, GO:003965...   \n",
       "2  [GO:0016021, GO:0019031, GO:0019064, GO:003965...   \n",
       "3  [GO:0016021, GO:0019031, GO:0019064, GO:003965...   \n",
       "4  [GO:0016021, GO:0019031, GO:0019064, GO:003965...   \n",
       "\n",
       "                                    interproscan_ids  \\\n",
       "0       [IPR002552, IPR018548, IPR027400, IPR036326]   \n",
       "1  [IPR002552, IPR018548, IPR027400, IPR036326, I...   \n",
       "2  [IPR002552, IPR018548, IPR027400, IPR036326, I...   \n",
       "3  [IPR002552, IPR018548, IPR027400, IPR032500, I...   \n",
       "4  [IPR002552, IPR018548, IPR027400, IPR036326, I...   \n",
       "\n",
       "            omx_creation_ts           omx_modified_ts classification  \\\n",
       "0  2020-04-06T14:54:16.000Z  2020-07-30T21:34:53.000Z        [virus]   \n",
       "1  2020-07-28T19:11:17.000Z  2020-07-28T19:11:17.000Z        [virus]   \n",
       "2  2020-07-28T16:18:04.000Z  2020-07-28T16:18:04.000Z        [virus]   \n",
       "3  2020-08-18T14:12:33.000Z  2020-08-18T14:12:33.000Z        [virus]   \n",
       "4  2020-06-02T16:49:13.000Z  2020-06-02T21:07:46.000Z        [virus]   \n",
       "\n",
       "                                          collection  \n",
       "0  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "1  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "2  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "3  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "4  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "genes_virus_df = genes_virus.results(type='df')\n",
    "genes_virus_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Get distribution of genes across genera**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "genes_all.show_facets(name = 'genera',topN=3)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Retrieve Additional Gene Data (e.g. Sequence) from OMXWare as Object**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Returns: List of gene objects \n",
      "Results: 1\n",
      "\n",
      "Id  \t\t=> 6efa65acd677199d20be1e98835ff23b\n",
      "Name   \t\t=> ['Spike glycoprotein']\n",
      "Sequence   \t=> ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACAC...\n",
      "Sequence length => 3822\n",
      "\n",
      "\n",
      " JSON:\n",
      "{'id': '6efa65acd677199d20be1e98835ff23b', 'name': ['Spike glycoprotein'], 'type': 'gene', 'genera': ['betacoronavirus'], 'genomes': ['EPI_ISL_419876'], 'sequence_length': 3822, 'status': 'active', 'go_codes': ['GO:0016021', 'GO:0019031', 'GO:0019064', 'GO:0039654', 'GO:0046813', 'GO:0055036', 'GO:0061025', 'GO:0075509'], 'interproscan_ids': ['IPR002552', 'IPR018548', 'IPR027400', 'IPR036326'], 'omx_creation_ts': '2020-04-06T14:54:16.000Z', 'omx_modified_ts': '2020-07-30T21:34:53.000Z', 'classification': ['virus'], 'collection': ['sars cov 2', 'sars-cov-2', 'sars cov2', 'covid-19', 'covid19', 'covid 19', 'coronavirus', 'corona virus']}\n"
     ]
    }
   ],
   "source": [
    "gene_list = genes_virus.results(type='list')\n",
    "\n",
    "# By default, the API returns a `list`\n",
    "print(\"Returns: List of {} objects \\nResults: {}\\n\".format(genes.type(), genes.total_results()) )\n",
    "    \n",
    "gene = gene_list[0]\n",
    "print(\"Id  \\t\\t=> \" + gene.id())\n",
    "print(\"Name   \\t\\t=> {}\".format(gene.name()))\n",
    "print(\"Sequence   \\t=> \" + gene.sequence()[:100] + \"...\")\n",
    "print(\"Sequence length => \" + str(gene.sequence_length()))\n",
    "\n",
    "print(\"\\n\\n JSON:\")\n",
    "print(gene.json())\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Search for Details About a Specific Protein from SARS-COV-2 genomes**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Total Results for Replicase polyprotein 1a: 19005\n"
     ]
    }
   ],
   "source": [
    "search_term = 'Replicase polyprotein 1a'\n",
    "proteins = omx.proteins(protein_name=search_term,page_size=25,classification='virus',collection = ['sars-cov-2'])\n",
    "#default classification is bacteria, so when searching for sars-cov-2 results, classification must be specified as 'virus' and specify collection as covid19\n",
    "\n",
    "print('Total Results for %s: %d' % (search_term, proteins.total_results()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Get results in a dataframe** to get results in other formats, see: https://github.com/IBM/omxware-getting-started/blob/master/RetrieveDataFormats.ipynb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>id</th>\n",
       "      <th>name</th>\n",
       "      <th>type</th>\n",
       "      <th>genera</th>\n",
       "      <th>genomes</th>\n",
       "      <th>sequence_length</th>\n",
       "      <th>status</th>\n",
       "      <th>domains</th>\n",
       "      <th>go_codes</th>\n",
       "      <th>interproscan_ids</th>\n",
       "      <th>omx_creation_ts</th>\n",
       "      <th>omx_modified_ts</th>\n",
       "      <th>classification</th>\n",
       "      <th>collection</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1c81adb857270aca06cc8343aa18c3dc</td>\n",
       "      <td>[Replicase polyprotein 1a]</td>\n",
       "      <td>protein</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[MT811486.1, EPI_ISL_483479, EPI_ISL_483479, E...</td>\n",
       "      <td>4405</td>\n",
       "      <td>active</td>\n",
       "      <td>[028ab10bc2de9122272f202f21002779, 1190692a318...</td>\n",
       "      <td>[GO:0003676, GO:0003723, GO:0003727, GO:000396...</td>\n",
       "      <td>[IPR002589, IPR008740, IPR009003, IPR013016, I...</td>\n",
       "      <td>2020-07-30T20:37:28.000Z</td>\n",
       "      <td>2020-08-11T19:00:08.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>5e1dd4ef46dd995c8da2fbc70c7a4bd2</td>\n",
       "      <td>[Replicase polyprotein 1a]</td>\n",
       "      <td>protein</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[MT350239.1, MT350248.1, MT350249.1, MT791963....</td>\n",
       "      <td>4405</td>\n",
       "      <td>active</td>\n",
       "      <td>[1190692a318ed72059f48624fa681f1c, 13e8f292b89...</td>\n",
       "      <td>[GO:0003676, GO:0003723, GO:0003727, GO:000396...</td>\n",
       "      <td>[IPR002589, IPR008740, IPR009003, IPR013016, I...</td>\n",
       "      <td>2020-05-11T23:22:06.000Z</td>\n",
       "      <td>2020-08-11T18:10:05.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>a050789016c04aba1138a9693b8d52d5</td>\n",
       "      <td>[Replicase polyprotein 1a]</td>\n",
       "      <td>protein</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_437662]</td>\n",
       "      <td>3607</td>\n",
       "      <td>active</td>\n",
       "      <td>[1190692a318ed72059f48624fa681f1c, 13e8f292b89...</td>\n",
       "      <td>[GO:0003676, GO:0003727, GO:0003968, GO:000419...</td>\n",
       "      <td>[IPR002589, IPR008740, IPR009003, IPR013016, I...</td>\n",
       "      <td>2020-05-12T02:23:15.000Z</td>\n",
       "      <td>2020-05-12T02:23:15.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2d8b1a4c0bedf770464c826f431077bc</td>\n",
       "      <td>[Replicase polyprotein 1a]</td>\n",
       "      <td>protein</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_490580]</td>\n",
       "      <td>4405</td>\n",
       "      <td>active</td>\n",
       "      <td>[1190692a318ed72059f48624fa681f1c, 13e8f292b89...</td>\n",
       "      <td>[GO:0003676, GO:0003723, GO:0003727, GO:000396...</td>\n",
       "      <td>[IPR002589, IPR008740, IPR009003, IPR013016, I...</td>\n",
       "      <td>2020-07-30T22:20:29.000Z</td>\n",
       "      <td>2020-07-30T22:20:29.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4f2ae9a607cb2cdc5548faca065706e2</td>\n",
       "      <td>[Replicase polyprotein 1a]</td>\n",
       "      <td>protein</td>\n",
       "      <td>[betacoronavirus]</td>\n",
       "      <td>[EPI_ISL_485165, EPI_ISL_485287]</td>\n",
       "      <td>4405</td>\n",
       "      <td>active</td>\n",
       "      <td>[1190692a318ed72059f48624fa681f1c, 13e8f292b89...</td>\n",
       "      <td>[GO:0003676, GO:0003723, GO:0003727, GO:000396...</td>\n",
       "      <td>[IPR002589, IPR008740, IPR009003, IPR013016, I...</td>\n",
       "      <td>2020-07-30T22:14:21.000Z</td>\n",
       "      <td>2020-08-03T17:33:45.000Z</td>\n",
       "      <td>[virus]</td>\n",
       "      <td>[sars cov 2, sars-cov-2, sars cov2, covid-19, ...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                 id                        name     type  \\\n",
       "0  1c81adb857270aca06cc8343aa18c3dc  [Replicase polyprotein 1a]  protein   \n",
       "1  5e1dd4ef46dd995c8da2fbc70c7a4bd2  [Replicase polyprotein 1a]  protein   \n",
       "2  a050789016c04aba1138a9693b8d52d5  [Replicase polyprotein 1a]  protein   \n",
       "3  2d8b1a4c0bedf770464c826f431077bc  [Replicase polyprotein 1a]  protein   \n",
       "4  4f2ae9a607cb2cdc5548faca065706e2  [Replicase polyprotein 1a]  protein   \n",
       "\n",
       "              genera                                            genomes  \\\n",
       "0  [betacoronavirus]  [MT811486.1, EPI_ISL_483479, EPI_ISL_483479, E...   \n",
       "1  [betacoronavirus]  [MT350239.1, MT350248.1, MT350249.1, MT791963....   \n",
       "2  [betacoronavirus]                                   [EPI_ISL_437662]   \n",
       "3  [betacoronavirus]                                   [EPI_ISL_490580]   \n",
       "4  [betacoronavirus]                   [EPI_ISL_485165, EPI_ISL_485287]   \n",
       "\n",
       "   sequence_length  status                                            domains  \\\n",
       "0             4405  active  [028ab10bc2de9122272f202f21002779, 1190692a318...   \n",
       "1             4405  active  [1190692a318ed72059f48624fa681f1c, 13e8f292b89...   \n",
       "2             3607  active  [1190692a318ed72059f48624fa681f1c, 13e8f292b89...   \n",
       "3             4405  active  [1190692a318ed72059f48624fa681f1c, 13e8f292b89...   \n",
       "4             4405  active  [1190692a318ed72059f48624fa681f1c, 13e8f292b89...   \n",
       "\n",
       "                                            go_codes  \\\n",
       "0  [GO:0003676, GO:0003723, GO:0003727, GO:000396...   \n",
       "1  [GO:0003676, GO:0003723, GO:0003727, GO:000396...   \n",
       "2  [GO:0003676, GO:0003727, GO:0003968, GO:000419...   \n",
       "3  [GO:0003676, GO:0003723, GO:0003727, GO:000396...   \n",
       "4  [GO:0003676, GO:0003723, GO:0003727, GO:000396...   \n",
       "\n",
       "                                    interproscan_ids  \\\n",
       "0  [IPR002589, IPR008740, IPR009003, IPR013016, I...   \n",
       "1  [IPR002589, IPR008740, IPR009003, IPR013016, I...   \n",
       "2  [IPR002589, IPR008740, IPR009003, IPR013016, I...   \n",
       "3  [IPR002589, IPR008740, IPR009003, IPR013016, I...   \n",
       "4  [IPR002589, IPR008740, IPR009003, IPR013016, I...   \n",
       "\n",
       "            omx_creation_ts           omx_modified_ts classification  \\\n",
       "0  2020-07-30T20:37:28.000Z  2020-08-11T19:00:08.000Z        [virus]   \n",
       "1  2020-05-11T23:22:06.000Z  2020-08-11T18:10:05.000Z        [virus]   \n",
       "2  2020-05-12T02:23:15.000Z  2020-05-12T02:23:15.000Z        [virus]   \n",
       "3  2020-07-30T22:20:29.000Z  2020-07-30T22:20:29.000Z        [virus]   \n",
       "4  2020-07-30T22:14:21.000Z  2020-08-03T17:33:45.000Z        [virus]   \n",
       "\n",
       "                                          collection  \n",
       "0  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "1  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "2  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "3  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  \n",
       "4  [sars cov 2, sars-cov-2, sars cov2, covid-19, ...  "
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proteins_df = proteins.results(type='df')\n",
    "proteins_df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Retrieve Protein Data from OMXWare as Object**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Returns: List of protein objects \n",
      "Results: 19005\n",
      "\n",
      "Id  \t\t=> 1c81adb857270aca06cc8343aa18c3dc\n",
      "Name   \t\t=> ['Replicase polyprotein 1a']\n",
      "Sequence   \t=> MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRS...\n",
      "Sequence length => 4405\n",
      "\n",
      "\n",
      " JSON:\n",
      "{'id': '1c81adb857270aca06cc8343aa18c3dc', 'name': ['Replicase polyprotein 1a'], 'type': 'protein', 'genera': ['betacoronavirus'], 'genomes': ['MT811486.1', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479', 'EPI_ISL_483479'], 'sequence_length': 4405, 'status': 'active', 'domains': ['028ab10bc2de9122272f202f21002779', '1190692a318ed72059f48624fa681f1c', '13e8f292b899ebc27bf4162c72194b91', '1694db56a69408c55e33f2a29f7f3030', '173be79f5a6fd85a7edb5c75cdc41fa3', '203d3dfb51d7d9ea9bbb9e67af2a0abb', '2aa71827a62e16b53fef7d62d67ca42c', '2dab89f0d20a6a1df5ae39d903cdf193', '2fb6257792c06810ae0bf9657e63569f', '301be4c5d8e4f33f3ea86dca60107c82', '307ed469bf72158795d153fbbdd4fe89', '31649590255eb25618a989941edecd7f', '462543a0f72f9e5ff6affc00e1b38e54', '49447f95439ec40070baaa4b209c71a8', '4b769cf3511ec6d2757ef13a32386510', '4e388f266a5b8ec97bc6749a73cc74e7', '5103fd6aebf6100026ad68bfdfb1f1ed', '55a42297245680283d709b3b50b347cb', '58b950fd36ce3d9751f1b9bb249bff7c', '59c1c1c6ba8a031ebb30ec9417a2217b', '5b5749ab5d2158a34e560fa23988cfd2', '5e1d35bf2d5b151728c19a5ee64aa7de', '63eaad285de785e7ae13166e035cdd3f', '79704391ad59c9b4c2bb96cbc5822521', '813fa1a4f8aaec81cc7835f53617f8ac', '85a0cef6fdb25d0fcf3245b7e51ea39e', '89689ff07b3ed97338e9f0cc8c079aef', '8c32758bc2f4b49ed8c6dfe7caa7ea49', '974b92ee8bc358969844e53b995384a8', '99abc04e476cccb7863aaec17e52120b', '9e38d1ad5849850f9f3c2799b7ad1a5a', 'a024f39db96b45d43e3e4f0ae8d5223d', 'a32587e00f1592c02c2f1f43e7095dcd', 'b10b0390b91a5460e55fafc97dfae749', 'c74fca287480e44f9b80c5a165f16646', 'cdca0c01f0bd47e7173b3c96bb02d125', 'cf7f060c46f02321159a99f22ce4de58', 'cfd5e1f3bff88a36cc1dc226f44b9704', 'd3deb8b8a1384044cc67542092b77f5d', 'd4556125ba41c9d85dfa05f2861c55d1', 'd64fba844d7962080c5ee110d9fecada', 'd927f1784cbe71c25d9396f623d011ad', 'dc25381610e21ff38e6433078516a6d6', 'dc6436f559bc873ac013085f6e56d467', 'e4b8e3836d595eff739a13a9b5197afe', 'f593162a13a13af1173db2a05a50dbfa', 'fd19fe9dfb2070b67783458d16d1a30b', 'fdae11c8e0de45d7b902ef4d281da05c', 'fec9ff0d891018f08b526b8c9a9180d1', 'feee837a7db7d1a2805a4e39b43c2c34'], 'go_codes': ['GO:0003676', 'GO:0003723', 'GO:0003727', 'GO:0003968', 'GO:0004197', 'GO:0006508', 'GO:0008233', 'GO:0008234', 'GO:0008242', 'GO:0008270', 'GO:0016740', 'GO:0019079', 'GO:0019082'], 'interproscan_ids': ['IPR002589', 'IPR008740', 'IPR009003', 'IPR013016', 'IPR014822', 'IPR014828', 'IPR014829', 'IPR018995', 'IPR021590', 'IPR022733', 'IPR024358', 'IPR024375', 'IPR032505', 'IPR032592', 'IPR036333', 'IPR036499', 'IPR037204', 'IPR037230', 'IPR038030', 'IPR038083', 'IPR038123', 'IPR038166', 'IPR038400', 'IPR042570', 'IPR043177', 'IPR043178', 'IPR043472', 'IPR043476', 'IPR043477', 'IPR043478', 'IPR043503', 'IPR043504', 'IPR043610', 'IPR043611', 'IPR043612', 'IPR043613', 'IPR043615'], 'omx_creation_ts': '2020-07-30T20:37:28.000Z', 'omx_modified_ts': '2020-08-11T19:00:08.000Z', 'classification': ['virus'], 'collection': ['sars cov 2', 'sars-cov-2', 'sars cov2', 'covid-19', 'covid19', 'covid 19', 'coronavirus', 'corona virus']}\n"
     ]
    }
   ],
   "source": [
    "protein_list = proteins.results(type='list')\n",
    "\n",
    "# By default, the API returns a `list`\n",
    "print(\"Returns: List of {} objects \\nResults: {}\\n\".format(proteins.type(), proteins.total_results()) )\n",
    "    \n",
    "protein = protein_list[0]\n",
    "print(\"Id  \\t\\t=> \" + protein.id())\n",
    "print(\"Name   \\t\\t=> {}\".format(protein.name()))\n",
    "print(\"Sequence   \\t=> \" + protein.sequence()[:100] + \"...\")\n",
    "print(\"Sequence length => \" + str(protein.sequence_length()))\n",
    "\n",
    "print(\"\\n\\n JSON:\")\n",
    "print(protein.json())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Get IPR codes for Protein**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Note: not all proteins may have ipr codes attached to them\n",
    "print(\"UID of protein sequence: \", protein.id())\n",
    "protein_ipr = protein.ipr()\n",
    "print(\"Total IPR codes on protein %s are: %d\" % (protein.id(),protein_ipr.total_results()))\n",
    "protein_ipr_list = protein_ipr.results(type='list')\n",
    "list_ipr_codes = []\n",
    "for each_ipr in protein_ipr_list:\n",
    "    list_ipr_codes.append(each_ipr.id())\n",
    "print(\"IPR Codes on Protein:\",list_ipr_codes)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**Get Domains for Protein**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "protein_domains = protein.domains()\n",
    "print(\"Total Domains on protein %s are: %d\" % (protein.id(),protein_domains.total_results()))\n",
    "protein_domains_list = protein_domains.results(type='list')\n",
    "list_domains_uid = []\n",
    "for each_domain in protein_domains_list:\n",
    "    list_domains_uid.append(each_domain.id())\n",
    "print(\"Domains on Protein:\",list_domains_uid)"
   ]
  }
 ],
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