notebooks/annotations_gpad_file.ipynb

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   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Reading a _Gene Product Association Data_ (GPAD) file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "1. Download a GPAD file\n",
    "2. Load the GPAD file into the GpadReader\n",
    "3. Get Annotations\n",
    "\n",
    "**Bonus: Each line in the GPAD file is stored in a namedtuple**:\n",
    "  * Namedtuple fields\n",
    "  * Print a subset of the namedtuple fields"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1) Download a GPAD file and GO Dag file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "from os.path import exists\n",
    "if not exists('goa_human.gpad'):\n",
    "    !rm -f goa_human.gpad.gz\n",
    "    !wget http://current.geneontology.org/annotations/goa_human.gpad.gz\n",
    "    !gunzip goa_human.gpad.gz"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "if not exists('go-basic.obo'):\n",
    "    !wget http://geneontology.org/ontology/go-basic.obo"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 2) Load the GPAD file into the GpadReader"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "  EXISTS: go-basic.obo\n",
      "go-basic.obo: fmt(1.2) rel(2022-11-03) 46,800 Terms\n",
      "HMS:0:00:16.880690 635,765 annotations READ: goa_human.gpad \n"
     ]
    }
   ],
   "source": [
    "from goatools.base import get_godag\n",
    "from goatools.anno.gpad_reader import GpadReader\n",
    "\n",
    "godag = get_godag(\"go-basic.obo\")\n",
    "anno = GpadReader(\"goa_human.gpad\", godag=godag)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 3) Get Annotations\n",
    "The annotations will be stored in three dicts, one for each GODAG branch, where:\n",
    "  * the key is the protein ID and \n",
    "  * the value is a list of GO IDs associated with the protein."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "ns2assc = anno.get_ns2assc()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MF A0A024RBG1 : GO:0000298 GO:0008486 GO:0034431 GO:0034432 GO:0046872 GO:0050072\n",
      "MF A0A075B6Q5 : GO:0003823 GO:0034987\n",
      "MF A0A075B6R2 : GO:0003823 GO:0034987\n",
      "CC A0A024RBG1 : GO:0005634 GO:0005737 GO:0005829\n",
      "CC A0A075B6H5 : GO:0005886\n",
      "CC A0A075B6H7 : GO:0005615 GO:0005886 GO:0019814\n",
      "BP A0A024RBG1 : GO:0071543 GO:1901907 GO:1901909 GO:1901911\n",
      "BP A0A075B6H5 : GO:0007166\n",
      "BP A0A075B6H7 : GO:0002250 GO:0002377 GO:0006955\n"
     ]
    }
   ],
   "source": [
    "for namespace, associations in ns2assc.items():\n",
    "    for protein_id, go_ids in sorted(associations.items())[:3]:\n",
    "        print(\"{NS} {PROT:7} : {GOs}\".format(\n",
    "            NS=namespace,\n",
    "            PROT=protein_id,\n",
    "            GOs=' '.join(sorted(go_ids))))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Bonus: The GPAD is stored as a list of named tuples\n",
    "The list of namedtuples is stored in the **GpadReader** data member named **_associations_**.\n",
    "\n",
    "Each namedtuple stores data for one line in the GPAD file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ntgpadobj(DB='UniProtKB', DB_ID='A0A024RBG1', Qualifier={'enables'}, GO_ID='GO:0046872', DB_Reference={'GO_REF:0000043'}, ECO='ECO:0000501', Evidence_Code='IEA', With_From={'UniProtKB-KW:KW-0479'}, Taxon=None, Date=datetime.date(2022, 9, 7), Assigned_By='UniProt', Extension=None, Properties={}, NS='MF')\n"
     ]
    }
   ],
   "source": [
    "# Sort the list of GPAD namedtuples by ID\n",
    "nts = sorted(anno.associations, key=lambda nt:nt.DB_ID)\n",
    "\n",
    "# Print one namedtuple\n",
    "print(nts[0])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Namedtuple fields\n",
    "```\n",
    "DB             #  0 required 1              UniProtKB\n",
    "DB_ID          #  1 required 1              P12345\n",
    "DB_Symbol      #  2 required 1              PHO3\n",
    "Qualifier      #  3 optional 0 or greater   NOT\n",
    "GO_ID          #  4 required 1              GO:0003993\n",
    "DB_Reference   #  5 required 1 or greater   PMID:2676709\n",
    "Evidence_Code  #  6 required 1              IMP\n",
    "With_From      #  7 optional 0 or greater   GO:0000346\n",
    "Aspect         #  8 required 1              F\n",
    "DB_Name        #  9 optional 0 or 1         Toll-like receptor 4\n",
    "DB_Synonym     # 10 optional 0 or greater   hToll|Tollbooth\n",
    "DB_Type        # 11 required 1              protein\n",
    "Taxon          # 12 required 1 or 2         taxon:9606\n",
    "Date           # 13 required 1              20090118\n",
    "Assigned_By    # 14 required 1              SGD\n",
    "Annotation_Extension # 15 optional 0 or greater part_of(CL:0000576)\n",
    "Gene_Product_Form_ID # 16 optional 0 or 1       UniProtKB:P12345-2\n",
    "```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Print a subset of the namedtuple fields"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MF A0A024RBG1 GO:0046872 IEA 2022-09-07 UniProt\n",
      "CC A0A024RBG1 GO:0005829 IDA 2016-12-04 HPA\n",
      "BP A0A024RBG1 GO:1901907 IBA 2017-02-28 GO_Central\n",
      "MF A0A024RBG1 GO:0000298 IBA 2017-02-28 GO_Central\n",
      "MF A0A024RBG1 GO:0008486 IBA 2021-05-30 GO_Central\n",
      "CC A0A024RBG1 GO:0005634 IBA 2017-02-28 GO_Central\n",
      "BP A0A024RBG1 GO:1901911 IBA 2017-02-28 GO_Central\n",
      "BP A0A024RBG1 GO:1901909 IBA 2017-02-28 GO_Central\n",
      "MF A0A024RBG1 GO:0034432 IBA 2017-02-28 GO_Central\n",
      "CC A0A024RBG1 GO:0005737 IBA 2017-02-28 GO_Central\n"
     ]
    }
   ],
   "source": [
    "fmtpat = '{NS} {DB_ID} {GO_ID} {Evidence_Code} {Date} {Assigned_By}'\n",
    "for nt_line in nts[:10]:\n",
    "    print(fmtpat.format(**nt_line._asdict()))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Copyright (C) 2010-present, DV Klopfenstein PhD, Haibao Tang. All rights reserved."
   ]
  }
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