notebooks/parents_and_ancestors.ipynb

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    "# How to traverse to GO parents and ancestors\n",
    "Traverse immediate parents or all ancestors with or without user-specified optional relationships\n",
    "\n",
    "  * **Parents and Ancestors described**\n",
    "  * **Code to get Parents and Ancestors**\n",
    "    * **Get parents through *is_a* relationship**\n",
    "    * **Get parents through *is_a* relationship and optional relationship, *regulates*.**\n",
    "    * **Get ancestors through *is_a* relationship**\n",
    "    * **Get ancestors through *is_a* relationship and optional relationship, *regulates*.**"
   ]
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    "## Parents and Ancestors\n",
    "\n",
    "### Parents\n",
    "Parents are terms directly above a GO term\n",
    "\n",
    "#### The yellow term, *regulation of metabolic process*, has one or two parents.\n",
    "\n",
    "* 1) If using only the default ***is_a*** relationship, the only parent is circled in green:\n",
    "  * *regulation of biological process*\n",
    "\n",
    "* 2) If adding the optional relationship, ***regulates***, the two parents are circled in purple:\n",
    "  * *regulation of biological process*    \n",
    "  * *metabolic process*    \n",
    "  \n",
    "### Ancestors\n",
    "Ancestors are all terms above a GO term, traversing up all of the GO hierarchy.\n",
    "\n",
    "* 3) If adding the optional relationship, ***regulates***, there are four ancestors are circled in blue:\n",
    "  * *biological_process*\n",
    "  * *biological regulation*\n",
    "  * *regulation of biological process*    \n",
    "  * *metabolic process*\n",
    "\n",
    "* If using only the default ***is_a*** relationship, there are three ancestors (not circled)\n",
    "  * *biological_process*\n",
    "  * *biological regulation*\n",
    "  * *regulation of biological process*    \n",
    "  \n",
    "<img src=\"images/parents_and_ancestors.png\" alt=\"parents_and_ancestors\" width=\"550\">\n",
    "\n",
    "## Code to get Parents and Ancestors"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "../tests/data/i126/viral_gene_silence.obo: fmt(1.2) rel(2019-04-17) 79 GO Terms; optional_attrs(relationship)\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "from goatools.obo_parser import GODag\n",
    "\n",
    "# Load a small test GO DAG and all the optional relationships,\n",
    "# like 'regulates' and 'part_of'\n",
    "godag = GODag('../tests/data/i126/viral_gene_silence.obo',\n",
    "              optional_attrs={'relationship'})"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Get parents through *is_a* relationship\n",
    "Parent is circled in green"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "GO_ID = 'GO:0019222'  # regulation of metabolic process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0019222 parent: {'GO:0050789'}\n"
     ]
    }
   ],
   "source": [
    "from goatools.godag.go_tasks import get_go2parents\n",
    "\n",
    "optional_relationships = set()\n",
    "go2parents_isa = get_go2parents(godag, optional_relationships)\n",
    "print('{GO} parent: {P}'.format(\n",
    "    GO=GO_ID,\n",
    "    P=go2parents_isa[GO_ID]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Get parents through *is_a* relationship and optional relationship, *regulates*\n",
    "Parents are circled in purple"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0019222 parents: {'GO:0050789', 'GO:0008152'}\n"
     ]
    }
   ],
   "source": [
    "optional_relationships = {'regulates', 'negatively_regulates', 'positively_regulates'}\n",
    "go2parents_reg = get_go2parents(godag, optional_relationships)\n",
    "print('{GO} parents: {P}'.format(\n",
    "    GO=GO_ID,\n",
    "    P=go2parents_reg[GO_ID]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Get ancestors through *is_a* relationship\n",
    "Not circled, but can be seen in figure"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0019222 ancestors: {'GO:0050789', 'GO:0008150', 'GO:0065007'}\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "\n",
    "gosubdag_r0 = GoSubDag([GO_ID], godag, prt=None)\n",
    "print('{GO} ancestors: {P}'.format(\n",
    "    GO=GO_ID,\n",
    "    P=gosubdag_r0.rcntobj.go2ancestors[GO_ID]))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Get ancestors through *is_a* relationship and optional relationship, *regulates*\n",
    "Circles in blue"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0019222 ancestors: {'GO:0008150', 'GO:0065007', 'GO:0050789', 'GO:0008152'}\n"
     ]
    }
   ],
   "source": [
    "gosubdag_r1 = GoSubDag([GO_ID], godag, relationships=optional_relationships, prt=None)\n",
    "print('{GO} ancestors: {P}'.format(\n",
    "    GO=GO_ID,\n",
    "    P=gosubdag_r1.rcntobj.go2ancestors[GO_ID]))"
   ]
  }
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