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  {
   "cell_type": "markdown",
   "id": "0f6c4513",
   "metadata": {},
   "source": [
    "# OAK rollup command\n",
    "\n",
    "This notebook is intended as a supplement to the [main OAK CLI docs](https://incatools.github.io/ontology-access-kit/cli.html).\n",
    "\n",
    "This notebook provides examples for the `rollup` command which produces a summarization of ontology associations\n",
    "between entities and \"rolled-up\" ancestor terms.\n",
    "\n",
    "## Help Option\n",
    "\n",
    "You can get help on any OAK command using `--help`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "65db4b53",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Usage: runoak rollup [OPTIONS] [TERMS]...\r\n",
      "\r\n",
      "  Produce an association rollup report.\r\n",
      "\r\n",
      "  The report will list associations where the subject is one of the terms\r\n",
      "  provided. The associations will be grouped by any provided --object-group\r\n",
      "  options. This option can be provided multiple times. If the value is a comma\r\n",
      "  separated list of object IDs, the first will be used as a primary grouping\r\n",
      "  dimension and the remainder will be used to create sub-groups.\r\n",
      "\r\n",
      "  Example:\r\n",
      "\r\n",
      "      runoak -i sqlite:go.db -g wb.gaf -G gaf rollup             --object-\r\n",
      "      group GO:0032502,GO:0007568,GO:0048869,GO:0098727             --object-\r\n",
      "      group GO:0008152,GO:0009056,GO:0044238,GO:1901275             --object-\r\n",
      "      group GO:0050896,GO:0051716,GO:0051606,GO:0051606,GO:0014823\r\n",
      "      --object-group=GO:0023052             --output rollup.html\r\n",
      "      WB:WBGene00000417 WB:WBGene00000912 WB:WBGene00000898 WB:WBGene00006752\r\n",
      "\r\n",
      "  By default, is-a relationships between association objects are used to\r\n",
      "  perform the rollup. Use the -p/--predicates option to change this behavior.\r\n",
      "\r\n",
      "Options:\r\n",
      "  -o, --output FILENAME         Output file, e.g. obo file\r\n",
      "  -p, --predicates TEXT         A comma-separated list of predicates\r\n",
      "  --autolabel / --no-autolabel  If set, results will automatically have labels\r\n",
      "                                assigned  [default: autolabel]\r\n",
      "  -O, --output-type TEXT        Desired output type\r\n",
      "  --object-group TEXT           An object ID to group by. If a comma separated\r\n",
      "                                list of IDs is provided, the first one is\r\n",
      "                                interpreted as a top-level grouping and the\r\n",
      "                                remaining IDs are interpreted as sub-groups\r\n",
      "                                within.\r\n",
      "  --help                        Show this message and exit.\r\n"
     ]
    }
   ],
   "source": [
    "!runoak rollup --help"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c8878ac5",
   "metadata": {},
   "source": [
    "## Download example file and setup\n",
    "\n",
    "We will use the HPO Association file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "12a41f0d",
   "metadata": {},
   "outputs": [],
   "source": [
    "!curl -L -s http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt > input/g2p.tsv"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d57ac006",
   "metadata": {},
   "source": [
    "next we will set up an hpo alias"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "dc71c543",
   "metadata": {},
   "outputs": [],
   "source": [
    "alias hp runoak -i sqlite:obo:hp"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6033aa66",
   "metadata": {},
   "source": [
    "Test this out by querying for associations for a particular orpha disease.\n",
    "\n",
    "We need to pass in the association file we downloaded, as well as specify the file type (with `-G`):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "2cfa1be8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "subject\tsubject_label\tpredicate\tobject\tobject_label\tproperty_values\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0000218\tHigh palate\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0001156\tBrachydactyly\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0001830\tPostaxial foot polydactyly\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0001508\tFailure to thrive\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0008678\tRenal hypoplasia/aplasia\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0006101\tFinger syndactyly\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0001643\tPatent ductus arteriosus\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0004383\tHypoplastic left heart\t[]\r",
      "\r\n",
      "NCBIGene:8195\tNone\tNone\tHP:0000807\tGlandular hypospadias\t[]\r",
      "\r\n"
     ]
    }
   ],
   "source": [
    "hp -G hpoa_g2p -g input/g2p.tsv associations -Q subject NCBIGene:8195 -O csv | head"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c9047f55",
   "metadata": {},
   "source": [
    "## Enrichment\n",
    "\n",
    "Next we will enrich based on a gene set"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ab30433e",
   "metadata": {},
   "outputs": [],
   "source": [
    "alias mondo runoak -i sqlite:obo:mondo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f70ff2bc",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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