Part 3.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "biological_process = pd.read_excel('biological process.xlsx')\n",
    "molecular_function = pd.read_excel(\"molecular function.xlsx\")\n",
    "cellular_component = pd.read_excel(\"cellular component.xlsx\")\n",
    "\n",
    "biological_process = biological_process.drop(['Unnamed: 0'], axis=1)\n",
    "molecular_function = molecular_function.drop(['Unnamed: 0'], axis=1)\n",
    "cellular_component = cellular_component.drop(['Unnamed: 0'], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0048675</td>\n",
       "      <td>axon extension</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0007409</td>\n",
       "      <td>axonogenesis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0009987</td>\n",
       "      <td>cellular process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0071363</td>\n",
       "      <td>cellular response to growth factor stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0071375</td>\n",
       "      <td>cellular response to peptide hormone stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44020</th>\n",
       "      <td>GO:0045638</td>\n",
       "      <td>negative regulation of myeloid cell differenti...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44021</th>\n",
       "      <td>GO:0051571</td>\n",
       "      <td>positive regulation of histone H3-K4 methylation</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44022</th>\n",
       "      <td>GO:2001162</td>\n",
       "      <td>positive regulation of histone H3-K79 methylation</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44023</th>\n",
       "      <td>GO:0006368</td>\n",
       "      <td>transcription elongation from RNA polymerase I...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44024</th>\n",
       "      <td>GO:0016055</td>\n",
       "      <td>Wnt signaling pathway</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>44025 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information\n",
       "0      GO:0048675                                     axon extension\n",
       "1      GO:0007409                                       axonogenesis\n",
       "2      GO:0009987                                   cellular process\n",
       "3      GO:0071363        cellular response to growth factor stimulus\n",
       "4      GO:0071375      cellular response to peptide hormone stimulus\n",
       "...           ...                                                ...\n",
       "44020  GO:0045638  negative regulation of myeloid cell differenti...\n",
       "44021  GO:0051571   positive regulation of histone H3-K4 methylation\n",
       "44022  GO:2001162  positive regulation of histone H3-K79 methylation\n",
       "44023  GO:0006368  transcription elongation from RNA polymerase I...\n",
       "44024  GO:0016055                              Wnt signaling pathway\n",
       "\n",
       "[44025 rows x 2 columns]"
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_biological_process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_biological_process = biological_process[['gene_id', 'information']].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0048675</td>\n",
       "      <td>axon extension</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0007409</td>\n",
       "      <td>axonogenesis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0009987</td>\n",
       "      <td>cellular process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0071363</td>\n",
       "      <td>cellular response to growth factor stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0071375</td>\n",
       "      <td>cellular response to peptide hormone stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43995</th>\n",
       "      <td>GO:1904702</td>\n",
       "      <td>regulation of protein localization to adherens...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44006</th>\n",
       "      <td>GO:0042247</td>\n",
       "      <td>establishment of planar polarity of follicular...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44010</th>\n",
       "      <td>GO:1990266</td>\n",
       "      <td>neutrophil migration</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44013</th>\n",
       "      <td>GO:0030834</td>\n",
       "      <td>regulation of actin filament depolymerization</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44022</th>\n",
       "      <td>GO:2001162</td>\n",
       "      <td>positive regulation of histone H3-K79 methylation</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8487 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information\n",
       "0      GO:0048675                                     axon extension\n",
       "1      GO:0007409                                       axonogenesis\n",
       "2      GO:0009987                                   cellular process\n",
       "3      GO:0071363        cellular response to growth factor stimulus\n",
       "4      GO:0071375      cellular response to peptide hormone stimulus\n",
       "...           ...                                                ...\n",
       "43995  GO:1904702  regulation of protein localization to adherens...\n",
       "44006  GO:0042247  establishment of planar polarity of follicular...\n",
       "44010  GO:1990266                               neutrophil migration\n",
       "44013  GO:0030834      regulation of actin filament depolymerization\n",
       "44022  GO:2001162  positive regulation of histone H3-K79 methylation\n",
       "\n",
       "[8487 rows x 2 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_biological_process.drop_duplicates(subset=['gene_id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0048675</td>\n",
       "      <td>axon extension</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0007409</td>\n",
       "      <td>axonogenesis</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0009987</td>\n",
       "      <td>cellular process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0071363</td>\n",
       "      <td>cellular response to growth factor stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0071375</td>\n",
       "      <td>cellular response to peptide hormone stimulus</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>43995</th>\n",
       "      <td>GO:1904702</td>\n",
       "      <td>regulation of protein localization to adherens...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44006</th>\n",
       "      <td>GO:0042247</td>\n",
       "      <td>establishment of planar polarity of follicular...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44010</th>\n",
       "      <td>GO:1990266</td>\n",
       "      <td>neutrophil migration</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44013</th>\n",
       "      <td>GO:0030834</td>\n",
       "      <td>regulation of actin filament depolymerization</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>44022</th>\n",
       "      <td>GO:2001162</td>\n",
       "      <td>positive regulation of histone H3-K79 methylation</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8487 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information\n",
       "0      GO:0048675                                     axon extension\n",
       "1      GO:0007409                                       axonogenesis\n",
       "2      GO:0009987                                   cellular process\n",
       "3      GO:0071363        cellular response to growth factor stimulus\n",
       "4      GO:0071375      cellular response to peptide hormone stimulus\n",
       "...           ...                                                ...\n",
       "43995  GO:1904702  regulation of protein localization to adherens...\n",
       "44006  GO:0042247  establishment of planar polarity of follicular...\n",
       "44010  GO:1990266                               neutrophil migration\n",
       "44013  GO:0030834      regulation of actin filament depolymerization\n",
       "44022  GO:2001162  positive regulation of histone H3-K79 methylation\n",
       "\n",
       "[8487 rows x 2 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_biological_process"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_biological_process = biological_process[['gene_id', 'information']].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_biological_process = ancestors_biological_process.drop_duplicates(subset=['gene_id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "    if gene_id != \"GO:0055114\" and gene_id !=\"GO:0097755\" and gene_id !=\"GO:0021882\" and gene_id !=\"GO:0010870\":"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1 GO IDs NOT FOUND IN GO DAG: GO:0055114\n",
      "I got a KeyError - reason'GO:0055114'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0097755\n",
      "I got a KeyError - reason'GO:0097755'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0021882\n",
      "I got a KeyError - reason'GO:0021882'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0010870\n",
      "I got a KeyError - reason'GO:0010870'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0045715\n",
      "I got a KeyError - reason'GO:0045715'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0045212\n",
      "I got a KeyError - reason'GO:0045212'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0032800\n",
      "I got a KeyError - reason'GO:0032800'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0097756\n",
      "I got a KeyError - reason'GO:0097756'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0018192\n",
      "I got a KeyError - reason'GO:0018192'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0051088\n",
      "I got a KeyError - reason'GO:0051088'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0045716\n",
      "I got a KeyError - reason'GO:0045716'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:2000327\n",
      "I got a KeyError - reason'GO:2000327'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0001324\n",
      "I got a KeyError - reason'GO:0001324'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0021913\n",
      "I got a KeyError - reason'GO:0021913'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0045872\n",
      "I got a KeyError - reason'GO:0045872'\n",
      "1 GO IDs NOT FOUND IN GO DAG: GO:0018323\n",
      "I got a KeyError - reason'GO:0018323'\n",
      "GO:2001162  ------  8487\r"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "# data.apply(lambda row: check_equal(row), axis=1)\n",
    "K=0\n",
    "for index, row in ancestors_biological_process.iterrows() :\n",
    "    K=K+1\n",
    "#     print (K, end=\"\\r\")\n",
    "    \n",
    "    gene_id = row[\"gene_id\"]\n",
    "\n",
    "    #     print(gene_id)\n",
    "    print (gene_id,\" ------ \",K, end=\"\\r\")\n",
    "    ancestor_1,ancestor_2,ancestor_3 = find_ancestors1(gene_id)\n",
    "    ancestors_biological_process.loc[index, 'ancestor_1'] = ancestor_1\n",
    "    ancestors_biological_process.loc[index, 'ancestor_2'] = ancestor_2\n",
    "    ancestors_biological_process.loc[index, 'ancestor_3'] = ancestor_3\n",
    "    if ancestor_1 != \"\" and ancestor_2 !=\"\" and ancestor_3!= \"\":\n",
    "        ancestors_biological_process.loc[index, 'ancestor_1_info'] = godag[ancestor_1].name\n",
    "        ancestors_biological_process.loc[index, 'ancestor_2_info'] = godag[ancestor_2].name\n",
    "        if ancestor_3 != '':\n",
    "            ancestors_biological_process.loc[index, 'ancestor_3_info'] = godag[ancestor_3].name\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_biological_process.to_excel('ancestors biological process.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_biological_process = pd.read_excel(\"ancestors biological process.xlsx\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
       "      <th>ancestor_3</th>\n",
       "      <th>ancestor_1_info</th>\n",
       "      <th>ancestor_2_info</th>\n",
       "      <th>ancestor_3_info</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0048675</td>\n",
       "      <td>axon extension</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0040007</td>\n",
       "      <td>GO:0016049</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>growth</td>\n",
       "      <td>cell growth</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0007409</td>\n",
       "      <td>axonogenesis</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0009987</td>\n",
       "      <td>GO:0048869</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>cellular process</td>\n",
       "      <td>cellular developmental process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0071363</td>\n",
       "      <td>cellular response to growth factor stimulus</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0050896</td>\n",
       "      <td>GO:0042221</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>response to stimulus</td>\n",
       "      <td>response to chemical</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>GO:0021700</td>\n",
       "      <td>developmental maturation</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0032502</td>\n",
       "      <td>GO:0021700</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>developmental process</td>\n",
       "      <td>developmental maturation</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>GO:0051915</td>\n",
       "      <td>induction of synaptic plasticity by chemical s...</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0065007</td>\n",
       "      <td>GO:0050789</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>biological regulation</td>\n",
       "      <td>regulation of biological process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>GO:0047497</td>\n",
       "      <td>mitochondrion transport along microtubule</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0051179</td>\n",
       "      <td>GO:0051234</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>localization</td>\n",
       "      <td>establishment of localization</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47</th>\n",
       "      <td>GO:0007182</td>\n",
       "      <td>common-partner SMAD protein phosphorylation</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0008152</td>\n",
       "      <td>GO:0044237</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>metabolic process</td>\n",
       "      <td>cellular metabolic process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>57</th>\n",
       "      <td>GO:0008344</td>\n",
       "      <td>adult locomotory behavior</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0007610</td>\n",
       "      <td>GO:0030534</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>behavior</td>\n",
       "      <td>adult behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>66</th>\n",
       "      <td>GO:0040011</td>\n",
       "      <td>locomotion</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0040011</td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>179</th>\n",
       "      <td>GO:0060048</td>\n",
       "      <td>cardiac muscle contraction</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0032501</td>\n",
       "      <td>GO:0003008</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>multicellular organismal process</td>\n",
       "      <td>system process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>208</th>\n",
       "      <td>GO:0086091</td>\n",
       "      <td>regulation of heart rate by cardiac conduction</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0023052</td>\n",
       "      <td>GO:0035637</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>signaling</td>\n",
       "      <td>multicellular organismal signaling</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>232</th>\n",
       "      <td>GO:0140374</td>\n",
       "      <td>antiviral innate immune response</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0044419</td>\n",
       "      <td>GO:0051707</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>biological process involved in interspecies in...</td>\n",
       "      <td>response to other organism</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>241</th>\n",
       "      <td>GO:0060744</td>\n",
       "      <td>mammary gland branching involved in thelarche</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0022414</td>\n",
       "      <td>GO:0003006</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>reproductive process</td>\n",
       "      <td>developmental process involved in reproduction</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>282</th>\n",
       "      <td>GO:0045299</td>\n",
       "      <td>otolith mineralization</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0110148</td>\n",
       "      <td>GO:0031214</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>biomineralization</td>\n",
       "      <td>biomineral tissue development</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>302</th>\n",
       "      <td>GO:0007155</td>\n",
       "      <td>cell adhesion</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0022610</td>\n",
       "      <td>GO:0007155</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>biological adhesion</td>\n",
       "      <td>cell adhesion</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>418</th>\n",
       "      <td>GO:0050852</td>\n",
       "      <td>T cell receptor signaling pathway</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0002376</td>\n",
       "      <td>GO:0002253</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>immune system process</td>\n",
       "      <td>activation of immune response</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>455</th>\n",
       "      <td>GO:0048066</td>\n",
       "      <td>developmental pigmentation</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0043473</td>\n",
       "      <td>GO:0048066</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>pigmentation</td>\n",
       "      <td>developmental pigmentation</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>667</th>\n",
       "      <td>GO:0007623</td>\n",
       "      <td>circadian rhythm</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0048511</td>\n",
       "      <td>GO:0007623</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>rhythmic process</td>\n",
       "      <td>circadian rhythm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>965</th>\n",
       "      <td>GO:0035176</td>\n",
       "      <td>social behavior</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0051703</td>\n",
       "      <td>GO:0035176</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>biological process involved in intraspecies in...</td>\n",
       "      <td>social behavior</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1013</th>\n",
       "      <td>GO:0055114</td>\n",
       "      <td>oxidation-reduction process</td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2368</th>\n",
       "      <td>GO:0007565</td>\n",
       "      <td>female pregnancy</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0051704</td>\n",
       "      <td>GO:0044703</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>multi-organism process</td>\n",
       "      <td>multi-organism reproductive process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7709</th>\n",
       "      <td>GO:0046294</td>\n",
       "      <td>formaldehyde catabolic process</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0098754</td>\n",
       "      <td>GO:0044281</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>detoxification</td>\n",
       "      <td>small molecule metabolic process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18633</th>\n",
       "      <td>GO:0019676</td>\n",
       "      <td>ammonia assimilation cycle</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:0019740</td>\n",
       "      <td>GO:0044281</td>\n",
       "      <td>biological_process</td>\n",
       "      <td>nitrogen utilization</td>\n",
       "      <td>small molecule metabolic process</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30389</th>\n",
       "      <td>GO:1905413</td>\n",
       "      <td>regulation of dense core granule exocytosis</td>\n",
       "      <td>GO:0008150</td>\n",
       "      <td>GO:1905413</td>\n",
       "      <td></td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information  \\\n",
       "0      GO:0048675                                     axon extension   \n",
       "1      GO:0007409                                       axonogenesis   \n",
       "3      GO:0071363        cellular response to growth factor stimulus   \n",
       "6      GO:0021700                           developmental maturation   \n",
       "8      GO:0051915  induction of synaptic plasticity by chemical s...   \n",
       "12     GO:0047497          mitochondrion transport along microtubule   \n",
       "47     GO:0007182        common-partner SMAD protein phosphorylation   \n",
       "57     GO:0008344                          adult locomotory behavior   \n",
       "66     GO:0040011                                         locomotion   \n",
       "179    GO:0060048                         cardiac muscle contraction   \n",
       "208    GO:0086091     regulation of heart rate by cardiac conduction   \n",
       "232    GO:0140374                   antiviral innate immune response   \n",
       "241    GO:0060744      mammary gland branching involved in thelarche   \n",
       "282    GO:0045299                             otolith mineralization   \n",
       "302    GO:0007155                                      cell adhesion   \n",
       "418    GO:0050852                  T cell receptor signaling pathway   \n",
       "455    GO:0048066                         developmental pigmentation   \n",
       "667    GO:0007623                                   circadian rhythm   \n",
       "965    GO:0035176                                    social behavior   \n",
       "1013   GO:0055114                        oxidation-reduction process   \n",
       "2368   GO:0007565                                   female pregnancy   \n",
       "7709   GO:0046294                     formaldehyde catabolic process   \n",
       "18633  GO:0019676                         ammonia assimilation cycle   \n",
       "30389  GO:1905413        regulation of dense core granule exocytosis   \n",
       "\n",
       "       ancestor_1  ancestor_2  ancestor_3     ancestor_1_info  \\\n",
       "0      GO:0008150  GO:0040007  GO:0016049  biological_process   \n",
       "1      GO:0008150  GO:0009987  GO:0048869  biological_process   \n",
       "3      GO:0008150  GO:0050896  GO:0042221  biological_process   \n",
       "6      GO:0008150  GO:0032502  GO:0021700  biological_process   \n",
       "8      GO:0008150  GO:0065007  GO:0050789  biological_process   \n",
       "12     GO:0008150  GO:0051179  GO:0051234  biological_process   \n",
       "47     GO:0008150  GO:0008152  GO:0044237  biological_process   \n",
       "57     GO:0008150  GO:0007610  GO:0030534  biological_process   \n",
       "66     GO:0008150  GO:0040011                             NaN   \n",
       "179    GO:0008150  GO:0032501  GO:0003008  biological_process   \n",
       "208    GO:0008150  GO:0023052  GO:0035637  biological_process   \n",
       "232    GO:0008150  GO:0044419  GO:0051707  biological_process   \n",
       "241    GO:0008150  GO:0022414  GO:0003006  biological_process   \n",
       "282    GO:0008150  GO:0110148  GO:0031214  biological_process   \n",
       "302    GO:0008150  GO:0022610  GO:0007155  biological_process   \n",
       "418    GO:0008150  GO:0002376  GO:0002253  biological_process   \n",
       "455    GO:0008150  GO:0043473  GO:0048066  biological_process   \n",
       "667    GO:0008150  GO:0048511  GO:0007623  biological_process   \n",
       "965    GO:0008150  GO:0051703  GO:0035176  biological_process   \n",
       "1013                                                      NaN   \n",
       "2368   GO:0008150  GO:0051704  GO:0044703  biological_process   \n",
       "7709   GO:0008150  GO:0098754  GO:0044281  biological_process   \n",
       "18633  GO:0008150  GO:0019740  GO:0044281  biological_process   \n",
       "30389  GO:0008150  GO:1905413                             NaN   \n",
       "\n",
       "                                         ancestor_2_info  \\\n",
       "0                                                 growth   \n",
       "1                                       cellular process   \n",
       "3                                   response to stimulus   \n",
       "6                                  developmental process   \n",
       "8                                  biological regulation   \n",
       "12                                          localization   \n",
       "47                                     metabolic process   \n",
       "57                                              behavior   \n",
       "66                                                   NaN   \n",
       "179                     multicellular organismal process   \n",
       "208                                            signaling   \n",
       "232    biological process involved in interspecies in...   \n",
       "241                                 reproductive process   \n",
       "282                                    biomineralization   \n",
       "302                                  biological adhesion   \n",
       "418                                immune system process   \n",
       "455                                         pigmentation   \n",
       "667                                     rhythmic process   \n",
       "965    biological process involved in intraspecies in...   \n",
       "1013                                                 NaN   \n",
       "2368                              multi-organism process   \n",
       "7709                                      detoxification   \n",
       "18633                               nitrogen utilization   \n",
       "30389                                                NaN   \n",
       "\n",
       "                                      ancestor_3_info  \n",
       "0                                         cell growth  \n",
       "1                      cellular developmental process  \n",
       "3                                response to chemical  \n",
       "6                            developmental maturation  \n",
       "8                    regulation of biological process  \n",
       "12                      establishment of localization  \n",
       "47                         cellular metabolic process  \n",
       "57                                     adult behavior  \n",
       "66                                                NaN  \n",
       "179                                    system process  \n",
       "208                multicellular organismal signaling  \n",
       "232                        response to other organism  \n",
       "241    developmental process involved in reproduction  \n",
       "282                     biomineral tissue development  \n",
       "302                                     cell adhesion  \n",
       "418                     activation of immune response  \n",
       "455                        developmental pigmentation  \n",
       "667                                  circadian rhythm  \n",
       "965                                   social behavior  \n",
       "1013                                              NaN  \n",
       "2368              multi-organism reproductive process  \n",
       "7709                 small molecule metabolic process  \n",
       "18633                small molecule metabolic process  \n",
       "30389                                             NaN  "
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_biological_process.drop_duplicates(subset=['ancestor_2'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 268,
   "metadata": {
    "scrolled": true
   },
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0005519</td>\n",
       "      <td>cytoskeletal regulatory protein binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0008017</td>\n",
       "      <td>microtubule binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0005543</td>\n",
       "      <td>phospholipid binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0044877</td>\n",
       "      <td>protein-containing complex binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20079</th>\n",
       "      <td>GO:0008929</td>\n",
       "      <td>methylglyoxal synthase activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20081</th>\n",
       "      <td>GO:0004807</td>\n",
       "      <td>triose-phosphate isomerase activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20099</th>\n",
       "      <td>GO:0034986</td>\n",
       "      <td>iron chaperone activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20123</th>\n",
       "      <td>GO:0004511</td>\n",
       "      <td>tyrosine 3-monooxygenase activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20168</th>\n",
       "      <td>GO:0042625</td>\n",
       "      <td>ATPase-coupled ion transmembrane transporter a...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2742 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information\n",
       "0      GO:0003779                                      actin binding\n",
       "1      GO:0005519            cytoskeletal regulatory protein binding\n",
       "2      GO:0008017                                microtubule binding\n",
       "3      GO:0005543                               phospholipid binding\n",
       "4      GO:0044877                 protein-containing complex binding\n",
       "...           ...                                                ...\n",
       "20079  GO:0008929                    methylglyoxal synthase activity\n",
       "20081  GO:0004807                triose-phosphate isomerase activity\n",
       "20099  GO:0034986                            iron chaperone activity\n",
       "20123  GO:0004511                  tyrosine 3-monooxygenase activity\n",
       "20168  GO:0042625  ATPase-coupled ion transmembrane transporter a...\n",
       "\n",
       "[2742 rows x 2 columns]"
      ]
     },
     "execution_count": 268,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_molecular_function"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function = molecular_function[['gene_id', 'information']].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function = ancestors_molecular_function.drop_duplicates(subset=['gene_id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0042625  ------  2742\r"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "# data.apply(lambda row: check_equal(row), axis=1)\n",
    "K=0\n",
    "for index, row in ancestors_molecular_function.iterrows() :\n",
    "    K=K+1\n",
    "#     print (K, end=\"\\r\")\n",
    "    gene_id = row[\"gene_id\"]\n",
    "#     print(gene_id)\n",
    "    print (gene_id,\" ------ \",K, end=\"\\r\")\n",
    "    if gene_id != \"GO:0030375\" and gene_id !=\"GO:0003712\" and gene_id !=\"GO:0045155\" and gene_id != \"GO:0003714\" and gene_id != \"GO:0030374\" and gene_id != \"GO:0003713\":\n",
    "        ancestor_1,ancestor_2,ancestor_3 = find_ancestors(gene_id)\n",
    "        ancestors_molecular_function.loc[index, 'ancestor_1'] = ancestor_1\n",
    "        ancestors_molecular_function.loc[index, 'ancestor_2'] = ancestor_2\n",
    "        ancestors_molecular_function.loc[index, 'ancestor_3'] = ancestor_3\n",
    "        ancestors_molecular_function.loc[index, 'ancestor_1_info'] = godag[ancestor_1].name\n",
    "        ancestors_molecular_function.loc[index, 'ancestor_2_info'] = godag[ancestor_2].name\n",
    "        if ancestor_3 != '':\n",
    "            ancestors_molecular_function.loc[index, 'ancestor_3_info'] = godag[ancestor_3].name\n",
    "    #     print(\"ssssss\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "GO:0003714  ------  170\n",
    "GO:0030374  ------  446\n",
    "GO:0003713  ------  55\n",
    "GO:0003712  ------  214"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function.to_excel('ancestors molecular function1.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function1 = molecular_function[['gene_id', 'information']].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function1 = ancestors_molecular_function1.drop_duplicates(subset=['gene_id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0042625  ------  2742\r"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "# data.apply(lambda row: check_equal(row), axis=1)\n",
    "K=0\n",
    "for index, row in ancestors_molecular_function1.iterrows() :\n",
    "    K=K+1\n",
    "#     print (K, end=\"\\r\")\n",
    "    \n",
    "    gene_id = row[\"gene_id\"]\n",
    "    if gene_id != \"GO:0030375\" and gene_id !=\"GO:0045155\":\n",
    "    #     print(gene_id)\n",
    "        print (gene_id,\" ------ \",K, end=\"\\r\")\n",
    "        ancestor_1,ancestor_2,ancestor_3 = find_ancestors1(gene_id)\n",
    "        ancestors_molecular_function1.loc[index, 'ancestor_1'] = ancestor_1\n",
    "        ancestors_molecular_function1.loc[index, 'ancestor_2'] = ancestor_2\n",
    "        ancestors_molecular_function1.loc[index, 'ancestor_3'] = ancestor_3\n",
    "        ancestors_molecular_function1.loc[index, 'ancestor_1_info'] = godag[ancestor_1].name\n",
    "        ancestors_molecular_function1.loc[index, 'ancestor_2_info'] = godag[ancestor_2].name\n",
    "        if ancestor_3 != '':\n",
    "            ancestors_molecular_function1.loc[index, 'ancestor_3_info'] = godag[ancestor_3].name\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_molecular_function1.to_excel('ancestors molecular function.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
       "      <th>ancestor_3</th>\n",
       "      <th>ancestor_1_info</th>\n",
       "      <th>ancestor_2_info</th>\n",
       "      <th>ancestor_3_info</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>protein binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1011</th>\n",
       "      <td>GO:0030375</td>\n",
       "      <td>thyroid hormone receptor coactivator activity</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         gene_id                                    information  ancestor_1  \\\n",
       "0     GO:0003779                                  actin binding  GO:0003674   \n",
       "1011  GO:0030375  thyroid hormone receptor coactivator activity         NaN   \n",
       "\n",
       "      ancestor_2  ancestor_3     ancestor_1_info ancestor_2_info  \\\n",
       "0     GO:0005488  GO:0005515  molecular_function         binding   \n",
       "1011         NaN         NaN                 NaN             NaN   \n",
       "\n",
       "      ancestor_3_info  \n",
       "0     protein binding  \n",
       "1011              NaN  "
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_molecular_function1.drop_duplicates(subset=['ancestor_1'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
       "      <th>ancestor_3</th>\n",
       "      <th>ancestor_1_info</th>\n",
       "      <th>ancestor_2_info</th>\n",
       "      <th>ancestor_3_info</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>protein binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>GO:0005200</td>\n",
       "      <td>structural constituent of cytoskeleton</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005198</td>\n",
       "      <td>GO:0005200</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>structural molecule activity</td>\n",
       "      <td>structural constituent of cytoskeleton</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>GO:0016887</td>\n",
       "      <td>ATPase activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0003824</td>\n",
       "      <td>GO:0016787</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>catalytic activity</td>\n",
       "      <td>hydrolase activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>GO:0019829</td>\n",
       "      <td>ATPase-coupled cation transmembrane transporte...</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005215</td>\n",
       "      <td>GO:0022857</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>transporter activity</td>\n",
       "      <td>transmembrane transporter activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>52</th>\n",
       "      <td>GO:0106006</td>\n",
       "      <td>cytoskeletal protein-membrane anchor activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0060090</td>\n",
       "      <td>GO:0030674</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular adaptor activity</td>\n",
       "      <td>protein-macromolecule adaptor activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>61</th>\n",
       "      <td>GO:0015459</td>\n",
       "      <td>potassium channel regulator activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0098772</td>\n",
       "      <td>GO:0016247</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular function regulator</td>\n",
       "      <td>channel regulator activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>337</th>\n",
       "      <td>GO:0003700</td>\n",
       "      <td>DNA-binding transcription factor activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140110</td>\n",
       "      <td>GO:0003700</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>transcription regulator activity</td>\n",
       "      <td>DNA-binding transcription factor activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>375</th>\n",
       "      <td>GO:0016209</td>\n",
       "      <td>antioxidant activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0016209</td>\n",
       "      <td></td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>antioxidant activity</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>618</th>\n",
       "      <td>GO:0004888</td>\n",
       "      <td>transmembrane signaling receptor activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0060089</td>\n",
       "      <td>GO:0038023</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular transducer activity</td>\n",
       "      <td>signaling receptor activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>968</th>\n",
       "      <td>GO:0045182</td>\n",
       "      <td>translation regulator activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0045182</td>\n",
       "      <td></td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>translation regulator activity</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1011</th>\n",
       "      <td>GO:0030375</td>\n",
       "      <td>thyroid hormone receptor coactivator activity</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1292</th>\n",
       "      <td>GO:0061608</td>\n",
       "      <td>nuclear import signal receptor activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140104</td>\n",
       "      <td>GO:0140142</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular carrier activity</td>\n",
       "      <td>nucleocytoplasmic carrier activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1303</th>\n",
       "      <td>GO:0016964</td>\n",
       "      <td>alpha-2 macroglobulin receptor activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0038024</td>\n",
       "      <td>GO:0016964</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>cargo receptor activity</td>\n",
       "      <td>alpha-2 macroglobulin receptor activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1475</th>\n",
       "      <td>GO:0044183</td>\n",
       "      <td>protein folding chaperone</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0044183</td>\n",
       "      <td></td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>protein folding chaperone</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2147</th>\n",
       "      <td>GO:0031386</td>\n",
       "      <td>protein tag</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0031386</td>\n",
       "      <td></td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>protein tag</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5739</th>\n",
       "      <td>GO:0016251</td>\n",
       "      <td>RNA polymerase II general transcription initia...</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140223</td>\n",
       "      <td>GO:0016251</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>general transcription initiation factor activity</td>\n",
       "      <td>RNA polymerase II general transcription initia...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8380</th>\n",
       "      <td>GO:0090729</td>\n",
       "      <td>toxin activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0090729</td>\n",
       "      <td></td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>toxin activity</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16480</th>\n",
       "      <td>GO:0140311</td>\n",
       "      <td>protein sequestering activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140313</td>\n",
       "      <td>GO:0140311</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular sequestering activity</td>\n",
       "      <td>protein sequestering activity</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information  \\\n",
       "0      GO:0003779                                      actin binding   \n",
       "18     GO:0005200             structural constituent of cytoskeleton   \n",
       "20     GO:0016887                                    ATPase activity   \n",
       "21     GO:0019829  ATPase-coupled cation transmembrane transporte...   \n",
       "52     GO:0106006      cytoskeletal protein-membrane anchor activity   \n",
       "61     GO:0015459               potassium channel regulator activity   \n",
       "337    GO:0003700          DNA-binding transcription factor activity   \n",
       "375    GO:0016209                               antioxidant activity   \n",
       "618    GO:0004888          transmembrane signaling receptor activity   \n",
       "968    GO:0045182                     translation regulator activity   \n",
       "1011   GO:0030375      thyroid hormone receptor coactivator activity   \n",
       "1292   GO:0061608            nuclear import signal receptor activity   \n",
       "1303   GO:0016964            alpha-2 macroglobulin receptor activity   \n",
       "1475   GO:0044183                          protein folding chaperone   \n",
       "2147   GO:0031386                                        protein tag   \n",
       "5739   GO:0016251  RNA polymerase II general transcription initia...   \n",
       "8380   GO:0090729                                     toxin activity   \n",
       "16480  GO:0140311                      protein sequestering activity   \n",
       "\n",
       "       ancestor_1  ancestor_2  ancestor_3     ancestor_1_info  \\\n",
       "0      GO:0003674  GO:0005488  GO:0005515  molecular_function   \n",
       "18     GO:0003674  GO:0005198  GO:0005200  molecular_function   \n",
       "20     GO:0003674  GO:0003824  GO:0016787  molecular_function   \n",
       "21     GO:0003674  GO:0005215  GO:0022857  molecular_function   \n",
       "52     GO:0003674  GO:0060090  GO:0030674  molecular_function   \n",
       "61     GO:0003674  GO:0098772  GO:0016247  molecular_function   \n",
       "337    GO:0003674  GO:0140110  GO:0003700  molecular_function   \n",
       "375    GO:0003674  GO:0016209              molecular_function   \n",
       "618    GO:0003674  GO:0060089  GO:0038023  molecular_function   \n",
       "968    GO:0003674  GO:0045182              molecular_function   \n",
       "1011          NaN         NaN         NaN                 NaN   \n",
       "1292   GO:0003674  GO:0140104  GO:0140142  molecular_function   \n",
       "1303   GO:0003674  GO:0038024  GO:0016964  molecular_function   \n",
       "1475   GO:0003674  GO:0044183              molecular_function   \n",
       "2147   GO:0003674  GO:0031386              molecular_function   \n",
       "5739   GO:0003674  GO:0140223  GO:0016251  molecular_function   \n",
       "8380   GO:0003674  GO:0090729              molecular_function   \n",
       "16480  GO:0003674  GO:0140313  GO:0140311  molecular_function   \n",
       "\n",
       "                                        ancestor_2_info  \\\n",
       "0                                               binding   \n",
       "18                         structural molecule activity   \n",
       "20                                   catalytic activity   \n",
       "21                                 transporter activity   \n",
       "52                           molecular adaptor activity   \n",
       "61                         molecular function regulator   \n",
       "337                    transcription regulator activity   \n",
       "375                                antioxidant activity   \n",
       "618                       molecular transducer activity   \n",
       "968                      translation regulator activity   \n",
       "1011                                                NaN   \n",
       "1292                         molecular carrier activity   \n",
       "1303                            cargo receptor activity   \n",
       "1475                          protein folding chaperone   \n",
       "2147                                        protein tag   \n",
       "5739   general transcription initiation factor activity   \n",
       "8380                                     toxin activity   \n",
       "16480                   molecular sequestering activity   \n",
       "\n",
       "                                         ancestor_3_info  \n",
       "0                                        protein binding  \n",
       "18                structural constituent of cytoskeleton  \n",
       "20                                    hydrolase activity  \n",
       "21                    transmembrane transporter activity  \n",
       "52                protein-macromolecule adaptor activity  \n",
       "61                            channel regulator activity  \n",
       "337            DNA-binding transcription factor activity  \n",
       "375                                                  NaN  \n",
       "618                          signaling receptor activity  \n",
       "968                                                  NaN  \n",
       "1011                                                 NaN  \n",
       "1292                  nucleocytoplasmic carrier activity  \n",
       "1303             alpha-2 macroglobulin receptor activity  \n",
       "1475                                                 NaN  \n",
       "2147                                                 NaN  \n",
       "5739   RNA polymerase II general transcription initia...  \n",
       "8380                                                 NaN  \n",
       "16480                      protein sequestering activity  "
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_molecular_function1.drop_duplicates(subset=['ancestor_2'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
       "      <th>ancestor_3</th>\n",
       "      <th>ancestor_1_info</th>\n",
       "      <th>ancestor_2_info</th>\n",
       "      <th>ancestor_3_info</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0005515</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>protein binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0005543</td>\n",
       "      <td>phospholipid binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0008289</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>lipid binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0044877</td>\n",
       "      <td>protein-containing complex binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0044877</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>protein-containing complex binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>GO:0005200</td>\n",
       "      <td>structural constituent of cytoskeleton</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005198</td>\n",
       "      <td>GO:0005200</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>structural molecule activity</td>\n",
       "      <td>structural constituent of cytoskeleton</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>GO:0005524</td>\n",
       "      <td>ATP binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:0097159</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>organic cyclic compound binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15603</th>\n",
       "      <td>GO:0140416</td>\n",
       "      <td>DNA-binding transcription factor inhibitor act...</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0098772</td>\n",
       "      <td>GO:0140416</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular function regulator</td>\n",
       "      <td>transcription regulator inhibitor activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16007</th>\n",
       "      <td>GO:0005344</td>\n",
       "      <td>oxygen carrier activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140104</td>\n",
       "      <td>GO:0005344</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular carrier activity</td>\n",
       "      <td>oxygen carrier activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16297</th>\n",
       "      <td>GO:0004134</td>\n",
       "      <td>4-alpha-glucanotransferase activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0003824</td>\n",
       "      <td>GO:0004133</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>catalytic activity</td>\n",
       "      <td>glycogen debranching enzyme activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16480</th>\n",
       "      <td>GO:0140311</td>\n",
       "      <td>protein sequestering activity</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0140313</td>\n",
       "      <td>GO:0140311</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>molecular sequestering activity</td>\n",
       "      <td>protein sequestering activity</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18954</th>\n",
       "      <td>GO:1904593</td>\n",
       "      <td>prostaglandin binding</td>\n",
       "      <td>GO:0003674</td>\n",
       "      <td>GO:0005488</td>\n",
       "      <td>GO:1901567</td>\n",
       "      <td>molecular_function</td>\n",
       "      <td>binding</td>\n",
       "      <td>fatty acid derivative binding</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>87 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information  \\\n",
       "0      GO:0003779                                      actin binding   \n",
       "3      GO:0005543                               phospholipid binding   \n",
       "4      GO:0044877                 protein-containing complex binding   \n",
       "18     GO:0005200             structural constituent of cytoskeleton   \n",
       "19     GO:0005524                                        ATP binding   \n",
       "...           ...                                                ...   \n",
       "15603  GO:0140416  DNA-binding transcription factor inhibitor act...   \n",
       "16007  GO:0005344                            oxygen carrier activity   \n",
       "16297  GO:0004134                4-alpha-glucanotransferase activity   \n",
       "16480  GO:0140311                      protein sequestering activity   \n",
       "18954  GO:1904593                              prostaglandin binding   \n",
       "\n",
       "       ancestor_1  ancestor_2  ancestor_3     ancestor_1_info  \\\n",
       "0      GO:0003674  GO:0005488  GO:0005515  molecular_function   \n",
       "3      GO:0003674  GO:0005488  GO:0008289  molecular_function   \n",
       "4      GO:0003674  GO:0005488  GO:0044877  molecular_function   \n",
       "18     GO:0003674  GO:0005198  GO:0005200  molecular_function   \n",
       "19     GO:0003674  GO:0005488  GO:0097159  molecular_function   \n",
       "...           ...         ...         ...                 ...   \n",
       "15603  GO:0003674  GO:0098772  GO:0140416  molecular_function   \n",
       "16007  GO:0003674  GO:0140104  GO:0005344  molecular_function   \n",
       "16297  GO:0003674  GO:0003824  GO:0004133  molecular_function   \n",
       "16480  GO:0003674  GO:0140313  GO:0140311  molecular_function   \n",
       "18954  GO:0003674  GO:0005488  GO:1901567  molecular_function   \n",
       "\n",
       "                       ancestor_2_info  \\\n",
       "0                              binding   \n",
       "3                              binding   \n",
       "4                              binding   \n",
       "18        structural molecule activity   \n",
       "19                             binding   \n",
       "...                                ...   \n",
       "15603     molecular function regulator   \n",
       "16007       molecular carrier activity   \n",
       "16297               catalytic activity   \n",
       "16480  molecular sequestering activity   \n",
       "18954                          binding   \n",
       "\n",
       "                                  ancestor_3_info  \n",
       "0                                 protein binding  \n",
       "3                                   lipid binding  \n",
       "4              protein-containing complex binding  \n",
       "18         structural constituent of cytoskeleton  \n",
       "19                organic cyclic compound binding  \n",
       "...                                           ...  \n",
       "15603  transcription regulator inhibitor activity  \n",
       "16007                     oxygen carrier activity  \n",
       "16297        glycogen debranching enzyme activity  \n",
       "16480               protein sequestering activity  \n",
       "18954               fatty acid derivative binding  \n",
       "\n",
       "[87 rows x 8 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_molecular_function1.drop_duplicates(subset=['ancestor_3'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "data1 = pd.read_excel('ancestors molecular functionnn.xlsx')\n",
    "data2 = pd.read_excel('ancestors molecular function1.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "0\n",
      "7496652\n"
     ]
    }
   ],
   "source": [
    "# belong to data1 and doesn't belong to data_HRMS\n",
    "data1_u = data1[~data1['ancestor_1'].isin(data2 ['ancestor_1'])]\n",
    "print(len(data1_u))\n",
    "# belong to data_HRMS and doesn't belong to data1\n",
    "data2_u = data2[~data2['ancestor_1'].isin(data1 ['ancestor_1'])]\n",
    "print(len(data2_u))\n",
    "common = pd.merge(data1, data2, on=[\"ancestor_1\"])\n",
    "print(len(common))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 126,
   "metadata": {
    "scrolled": true
   },
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0097440</td>\n",
       "      <td>apical dendrite</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0030424</td>\n",
       "      <td>axon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0097441</td>\n",
       "      <td>basal dendrite</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cell projection</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0005856</td>\n",
       "      <td>cytoskeleton</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30253</th>\n",
       "      <td>GO:0005862</td>\n",
       "      <td>muscle thin filament tropomyosin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30417</th>\n",
       "      <td>GO:0033178</td>\n",
       "      <td>proton-transporting two-sector ATPase complex ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30468</th>\n",
       "      <td>GO:0090637</td>\n",
       "      <td>inner dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30471</th>\n",
       "      <td>GO:0090636</td>\n",
       "      <td>outer dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30499</th>\n",
       "      <td>GO:0055087</td>\n",
       "      <td>Ski complex</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1378 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information\n",
       "0      GO:0097440                                    apical dendrite\n",
       "1      GO:0030424                                               axon\n",
       "2      GO:0097441                                     basal dendrite\n",
       "3      GO:0042995                                    cell projection\n",
       "4      GO:0005856                                       cytoskeleton\n",
       "...           ...                                                ...\n",
       "30253  GO:0005862                   muscle thin filament tropomyosin\n",
       "30417  GO:0033178  proton-transporting two-sector ATPase complex ...\n",
       "30468  GO:0090637                    inner dense plaque of desmosome\n",
       "30471  GO:0090636                    outer dense plaque of desmosome\n",
       "30499  GO:0055087                                        Ski complex\n",
       "\n",
       "[1378 rows x 2 columns]"
      ]
     },
     "execution_count": 126,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_cellular_component"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 176,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_cellular_component = cellular_component[['gene_id', 'information']].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 177,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_cellular_component = ancestors_cellular_component.drop_duplicates(subset=['gene_id'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 179,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0055087  ------  1378265 ------  869\r"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "# data.apply(lambda row: check_equal(row), axis=1)\n",
    "K=0\n",
    "for index, row in ancestors_cellular_component.iterrows() :\n",
    "    K=K+1\n",
    "#     print (K, end=\"\\r\")\n",
    "    gene_id = row[\"gene_id\"]\n",
    "#     print(gene_id)\n",
    "    print (gene_id,\" ------ \",K, end=\"\\r\")\n",
    "    ancestor_1,ancestor_2,ancestor_3 = find_ancestors(gene_id)\n",
    "    ancestors_cellular_component.loc[index, 'ancestor_1'] = ancestor_1\n",
    "    ancestors_cellular_component.loc[index, 'ancestor_2'] = ancestor_2\n",
    "    ancestors_cellular_component.loc[index, 'ancestor_3'] = ancestor_3\n",
    "    ancestors_cellular_component.loc[index, 'ancestor_1_info'] = godag[ancestor_1].name\n",
    "    ancestors_cellular_component.loc[index, 'ancestor_2_info'] = godag[ancestor_2].name\n",
    "    if ancestor_3 != '':\n",
    "        ancestors_cellular_component.loc[index, 'ancestor_3_info'] = godag[ancestor_3].name\n",
    "#     print(\"ssssss\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 180,
   "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>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
       "      <th>ancestor_3</th>\n",
       "      <th>ancestor_1_info</th>\n",
       "      <th>ancestor_2_info</th>\n",
       "      <th>ancestor_3_info</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>GO:0097440</td>\n",
       "      <td>apical dendrite</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>cell projection</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GO:0030424</td>\n",
       "      <td>axon</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>cell projection</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>GO:0097441</td>\n",
       "      <td>basal dendrite</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>cell projection</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cell projection</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>cell projection</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GO:0005856</td>\n",
       "      <td>cytoskeleton</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0005622</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>intracellular anatomical structure</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30253</th>\n",
       "      <td>GO:0005862</td>\n",
       "      <td>muscle thin filament tropomyosin</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0005862</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>muscle thin filament tropomyosin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30417</th>\n",
       "      <td>GO:0033178</td>\n",
       "      <td>proton-transporting two-sector ATPase complex ...</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0098796</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>membrane protein complex</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30468</th>\n",
       "      <td>GO:0090637</td>\n",
       "      <td>inner dense plaque of desmosome</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0090637</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>inner dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30471</th>\n",
       "      <td>GO:0090636</td>\n",
       "      <td>outer dense plaque of desmosome</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0090636</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>outer dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30499</th>\n",
       "      <td>GO:0055087</td>\n",
       "      <td>Ski complex</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0055087</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>Ski complex</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1378 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          gene_id                                        information  \\\n",
       "0      GO:0097440                                    apical dendrite   \n",
       "1      GO:0030424                                               axon   \n",
       "2      GO:0097441                                     basal dendrite   \n",
       "3      GO:0042995                                    cell projection   \n",
       "4      GO:0005856                                       cytoskeleton   \n",
       "...           ...                                                ...   \n",
       "30253  GO:0005862                   muscle thin filament tropomyosin   \n",
       "30417  GO:0033178  proton-transporting two-sector ATPase complex ...   \n",
       "30468  GO:0090637                    inner dense plaque of desmosome   \n",
       "30471  GO:0090636                    outer dense plaque of desmosome   \n",
       "30499  GO:0055087                                        Ski complex   \n",
       "\n",
       "       ancestor_1  ancestor_2  ancestor_3     ancestor_1_info  \\\n",
       "0      GO:0005575  GO:0110165  GO:0042995  cellular_component   \n",
       "1      GO:0005575  GO:0110165  GO:0042995  cellular_component   \n",
       "2      GO:0005575  GO:0110165  GO:0042995  cellular_component   \n",
       "3      GO:0005575  GO:0110165  GO:0042995  cellular_component   \n",
       "4      GO:0005575  GO:0110165  GO:0005622  cellular_component   \n",
       "...           ...         ...         ...                 ...   \n",
       "30253  GO:0005575  GO:0032991  GO:0005862  cellular_component   \n",
       "30417  GO:0005575  GO:0032991  GO:0098796  cellular_component   \n",
       "30468  GO:0005575  GO:0110165  GO:0090637  cellular_component   \n",
       "30471  GO:0005575  GO:0110165  GO:0090636  cellular_component   \n",
       "30499  GO:0005575  GO:0032991  GO:0055087  cellular_component   \n",
       "\n",
       "                  ancestor_2_info                     ancestor_3_info  \n",
       "0      cellular anatomical entity                     cell projection  \n",
       "1      cellular anatomical entity                     cell projection  \n",
       "2      cellular anatomical entity                     cell projection  \n",
       "3      cellular anatomical entity                     cell projection  \n",
       "4      cellular anatomical entity  intracellular anatomical structure  \n",
       "...                           ...                                 ...  \n",
       "30253  protein-containing complex    muscle thin filament tropomyosin  \n",
       "30417  protein-containing complex            membrane protein complex  \n",
       "30468  cellular anatomical entity     inner dense plaque of desmosome  \n",
       "30471  cellular anatomical entity     outer dense plaque of desmosome  \n",
       "30499  protein-containing complex                         Ski complex  \n",
       "\n",
       "[1378 rows x 8 columns]"
      ]
     },
     "execution_count": 180,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_cellular_component"
   ]
  },
  {
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   "execution_count": 181,
   "metadata": {},
   "outputs": [
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       "      <th>0</th>\n",
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       "      <td>GO:0110165</td>\n",
       "      <td>GO:0042995</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
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       "      gene_id      information  ancestor_1  ancestor_2  ancestor_3  \\\n",
       "0  GO:0097440  apical dendrite  GO:0005575  GO:0110165  GO:0042995   \n",
       "\n",
       "      ancestor_1_info             ancestor_2_info  ancestor_3_info  \n",
       "0  cellular_component  cellular anatomical entity  cell projection  "
      ]
     },
     "execution_count": 181,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_cellular_component.drop_duplicates(subset=['ancestor_1'])"
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  {
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   "execution_count": 182,
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   "outputs": [
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       "      <th>gene_id</th>\n",
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       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
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       "      <td>GO:0005875</td>\n",
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       "      <th>6851</th>\n",
       "      <td>GO:0044216</td>\n",
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       "      <td>cellular_component</td>\n",
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       "         gene_id                     information  ancestor_1  ancestor_2  \\\n",
       "0     GO:0097440                 apical dendrite  GO:0005575  GO:0110165   \n",
       "11    GO:0005875  microtubule associated complex  GO:0005575  GO:0032991   \n",
       "6851  GO:0044216             other organism cell  GO:0005575  GO:0044217   \n",
       "\n",
       "      ancestor_3     ancestor_1_info             ancestor_2_info  \\\n",
       "0     GO:0042995  cellular_component  cellular anatomical entity   \n",
       "11    GO:0005875  cellular_component  protein-containing complex   \n",
       "6851  GO:0044216  cellular_component         other organism part   \n",
       "\n",
       "                     ancestor_3_info  \n",
       "0                    cell projection  \n",
       "11    microtubule associated complex  \n",
       "6851             other organism cell  "
      ]
     },
     "execution_count": 182,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_cellular_component.drop_duplicates(subset=['ancestor_2'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 183,
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "      <th>ancestor_1</th>\n",
       "      <th>ancestor_2</th>\n",
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       "      <td>GO:0110165</td>\n",
       "      <td>GO:0005829</td>\n",
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       "      <td>GO:0098794</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>GO:0030426</td>\n",
       "      <td>growth cone</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0030427</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>site of polarized growth</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>29599</th>\n",
       "      <td>GO:0032311</td>\n",
       "      <td>angiogenin-PRI complex</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0032311</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>angiogenin-PRI complex</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30253</th>\n",
       "      <td>GO:0005862</td>\n",
       "      <td>muscle thin filament tropomyosin</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0005862</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>muscle thin filament tropomyosin</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30468</th>\n",
       "      <td>GO:0090637</td>\n",
       "      <td>inner dense plaque of desmosome</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0090637</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>inner dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30471</th>\n",
       "      <td>GO:0090636</td>\n",
       "      <td>outer dense plaque of desmosome</td>\n",
       "      <td>GO:0005575</td>\n",
       "      <td>GO:0110165</td>\n",
       "      <td>GO:0090636</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>cellular anatomical entity</td>\n",
       "      <td>outer dense plaque of desmosome</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30499</th>\n",
       "      <td>GO:0055087</td>\n",
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       "      <td>GO:0005575</td>\n",
       "      <td>GO:0032991</td>\n",
       "      <td>GO:0055087</td>\n",
       "      <td>cellular_component</td>\n",
       "      <td>protein-containing complex</td>\n",
       "      <td>Ski complex</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>306 rows × 8 columns</p>\n",
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      ],
      "text/plain": [
       "          gene_id                       information  ancestor_1  ancestor_2  \\\n",
       "0      GO:0097440                   apical dendrite  GO:0005575  GO:0110165   \n",
       "4      GO:0005856                      cytoskeleton  GO:0005575  GO:0110165   \n",
       "5      GO:0005829                           cytosol  GO:0005575  GO:0110165   \n",
       "7      GO:0043197                   dendritic spine  GO:0005575  GO:0110165   \n",
       "8      GO:0030426                       growth cone  GO:0005575  GO:0110165   \n",
       "...           ...                               ...         ...         ...   \n",
       "29599  GO:0032311            angiogenin-PRI complex  GO:0005575  GO:0032991   \n",
       "30253  GO:0005862  muscle thin filament tropomyosin  GO:0005575  GO:0032991   \n",
       "30468  GO:0090637   inner dense plaque of desmosome  GO:0005575  GO:0110165   \n",
       "30471  GO:0090636   outer dense plaque of desmosome  GO:0005575  GO:0110165   \n",
       "30499  GO:0055087                       Ski complex  GO:0005575  GO:0032991   \n",
       "\n",
       "       ancestor_3     ancestor_1_info             ancestor_2_info  \\\n",
       "0      GO:0042995  cellular_component  cellular anatomical entity   \n",
       "4      GO:0005622  cellular_component  cellular anatomical entity   \n",
       "5      GO:0005829  cellular_component  cellular anatomical entity   \n",
       "7      GO:0098794  cellular_component  cellular anatomical entity   \n",
       "8      GO:0030427  cellular_component  cellular anatomical entity   \n",
       "...           ...                 ...                         ...   \n",
       "29599  GO:0032311  cellular_component  protein-containing complex   \n",
       "30253  GO:0005862  cellular_component  protein-containing complex   \n",
       "30468  GO:0090637  cellular_component  cellular anatomical entity   \n",
       "30471  GO:0090636  cellular_component  cellular anatomical entity   \n",
       "30499  GO:0055087  cellular_component  protein-containing complex   \n",
       "\n",
       "                          ancestor_3_info  \n",
       "0                         cell projection  \n",
       "4      intracellular anatomical structure  \n",
       "5                                 cytosol  \n",
       "7                             postsynapse  \n",
       "8                site of polarized growth  \n",
       "...                                   ...  \n",
       "29599              angiogenin-PRI complex  \n",
       "30253    muscle thin filament tropomyosin  \n",
       "30468     inner dense plaque of desmosome  \n",
       "30471     outer dense plaque of desmosome  \n",
       "30499                         Ski complex  \n",
       "\n",
       "[306 rows x 8 columns]"
      ]
     },
     "execution_count": 183,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ancestors_cellular_component.drop_duplicates(subset=['ancestor_3'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 189,
   "metadata": {},
   "outputs": [],
   "source": [
    "ancestors_cellular_component.to_excel('ancestors cellular component.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
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       "      <th>8</th>\n",
       "      <td>P14873</td>\n",
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       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>P14873</td>\n",
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       "      <td>GO:0097457</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>P14873</td>\n",
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       "      <td>GO:0005874</td>\n",
       "      <td>microtubule</td>\n",
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       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0005875</td>\n",
       "      <td>microtubule associated complex</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0043025</td>\n",
       "      <td>neuronal cell body</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0043204</td>\n",
       "      <td>perikaryon</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0048471</td>\n",
       "      <td>perinuclear region of cytoplasm</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0001750</td>\n",
       "      <td>photoreceptor outer segment</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0005886</td>\n",
       "      <td>plasma membrane</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0014069</td>\n",
       "      <td>postsynaptic density</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0036477</td>\n",
       "      <td>somatodendritic compartment</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0045202</td>\n",
       "      <td>synapse</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0043196</td>\n",
       "      <td>varicosity</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   AC_uniprot   ID_uniprot     gene_id                      information\n",
       "0      P14873  MAP1B_MOUSE  GO:0097440                  apical dendrite\n",
       "1      P14873  MAP1B_MOUSE  GO:0030424                             axon\n",
       "2      P14873  MAP1B_MOUSE  GO:0097441                   basal dendrite\n",
       "3      P14873  MAP1B_MOUSE  GO:0042995                  cell projection\n",
       "4      P14873  MAP1B_MOUSE  GO:0005856                     cytoskeleton\n",
       "5      P14873  MAP1B_MOUSE  GO:0005829                          cytosol\n",
       "6      P14873  MAP1B_MOUSE  GO:0030425                         dendrite\n",
       "7      P14873  MAP1B_MOUSE  GO:0043197                  dendritic spine\n",
       "8      P14873  MAP1B_MOUSE  GO:0030426                      growth cone\n",
       "9      P14873  MAP1B_MOUSE  GO:0097457          hippocampal mossy fiber\n",
       "10     P14873  MAP1B_MOUSE  GO:0005874                      microtubule\n",
       "11     P14873  MAP1B_MOUSE  GO:0005875   microtubule associated complex\n",
       "12     P14873  MAP1B_MOUSE  GO:0043025               neuronal cell body\n",
       "13     P14873  MAP1B_MOUSE  GO:0043204                       perikaryon\n",
       "14     P14873  MAP1B_MOUSE  GO:0048471  perinuclear region of cytoplasm\n",
       "15     P14873  MAP1B_MOUSE  GO:0001750      photoreceptor outer segment\n",
       "16     P14873  MAP1B_MOUSE  GO:0005886                  plasma membrane\n",
       "17     P14873  MAP1B_MOUSE  GO:0014069             postsynaptic density\n",
       "18     P14873  MAP1B_MOUSE  GO:0036477      somatodendritic compartment\n",
       "19     P14873  MAP1B_MOUSE  GO:0045202                          synapse\n",
       "20     P14873  MAP1B_MOUSE  GO:0043196                       varicosity"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cellular_component[cellular_component[\"AC_uniprot\"]==\"P14873\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true
   },
   "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>AC_uniprot</th>\n",
       "      <th>ID_uniprot</th>\n",
       "      <th>gene_id</th>\n",
       "      <th>information</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>P14873</td>\n",
       "      <td>MAP1B_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>P20357</td>\n",
       "      <td>MTAP2_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>Q62261</td>\n",
       "      <td>SPTB2_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>51</th>\n",
       "      <td>Q9WV92</td>\n",
       "      <td>E41L3_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>106</th>\n",
       "      <td>Q9QYR6</td>\n",
       "      <td>MAP1A_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19906</th>\n",
       "      <td>Q8CC35</td>\n",
       "      <td>SYNPO_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19913</th>\n",
       "      <td>O55042</td>\n",
       "      <td>SYUA_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20069</th>\n",
       "      <td>Q9JKK7</td>\n",
       "      <td>TMOD2_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20083</th>\n",
       "      <td>P58771</td>\n",
       "      <td>TPM1_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20204</th>\n",
       "      <td>O88342</td>\n",
       "      <td>WDR1_MOUSE</td>\n",
       "      <td>GO:0003779</td>\n",
       "      <td>actin binding</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>160 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      AC_uniprot   ID_uniprot     gene_id    information\n",
       "0         P14873  MAP1B_MOUSE  GO:0003779  actin binding\n",
       "6         P20357  MTAP2_MOUSE  GO:0003779  actin binding\n",
       "12        Q62261  SPTB2_MOUSE  GO:0003779  actin binding\n",
       "51        Q9WV92  E41L3_MOUSE  GO:0003779  actin binding\n",
       "106       Q9QYR6  MAP1A_MOUSE  GO:0003779  actin binding\n",
       "...          ...          ...         ...            ...\n",
       "19906     Q8CC35  SYNPO_MOUSE  GO:0003779  actin binding\n",
       "19913     O55042   SYUA_MOUSE  GO:0003779  actin binding\n",
       "20069     Q9JKK7  TMOD2_MOUSE  GO:0003779  actin binding\n",
       "20083     P58771   TPM1_MOUSE  GO:0003779  actin binding\n",
       "20204     O88342   WDR1_MOUSE  GO:0003779  actin binding\n",
       "\n",
       "[160 rows x 4 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "molecular_function[molecular_function[\"information\"]==\"actin binding\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Collecting goatools\n",
      "  Downloading goatools-1.0.15.tar.gz (15.1 MB)\n",
      "\u001b[K     |████████████████████████████████| 15.1 MB 5.0 MB/s eta 0:00:01    |█████████████████▏              | 8.1 MB 4.7 MB/s eta 0:00:02\n",
      "\u001b[?25hRequirement already satisfied: pandas in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.0.1)\n",
      "Requirement already satisfied: numpy in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.18.5)\n",
      "Requirement already satisfied: scipy in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.5.0)\n",
      "Requirement already satisfied: xlsxwriter in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.2.9)\n",
      "Collecting statsmodels\n",
      "  Downloading statsmodels-0.12.1-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB)\n",
      "\u001b[K     |████████████████████████████████| 9.5 MB 89 kB/s  eta 0:00:01\n",
      "\u001b[?25hRequirement already satisfied: xlrd==1.2.0 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.2.0)\n",
      "Requirement already satisfied: docopt in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (0.6.2)\n",
      "Requirement already satisfied: pydot in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (1.4.1)\n",
      "Requirement already satisfied: requests in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from goatools) (2.24.0)\n",
      "Collecting wget\n",
      "  Downloading wget-3.2.zip (10 kB)\n",
      "Requirement already satisfied: pytz>=2017.2 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from pandas->goatools) (2020.1)\n",
      "Requirement already satisfied: python-dateutil>=2.6.1 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from pandas->goatools) (2.8.1)\n",
      "Collecting patsy>=0.5\n",
      "  Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB)\n",
      "\u001b[K     |████████████████████████████████| 231 kB 4.7 MB/s eta 0:00:01\n",
      "\u001b[?25hRequirement already satisfied: pyparsing>=2.1.4 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from pydot->goatools) (2.4.7)\n",
      "Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from requests->goatools) (1.25.9)\n",
      "Requirement already satisfied: chardet<4,>=3.0.2 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from requests->goatools) (3.0.4)\n",
      "Requirement already satisfied: idna<3,>=2.5 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from requests->goatools) (2.10)\n",
      "Requirement already satisfied: certifi>=2017.4.17 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from requests->goatools) (2020.12.5)\n",
      "Requirement already satisfied: six>=1.5 in /home/user/anaconda3/envs/tensorflow/lib/python3.7/site-packages (from python-dateutil>=2.6.1->pandas->goatools) (1.15.0)\n",
      "Building wheels for collected packages: goatools, wget\n",
      "  Building wheel for goatools (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for goatools: filename=goatools-1.0.15-py3-none-any.whl size=15762722 sha256=f4d32784d6d8ca47d6c451e604c3824f2ffc9196bcaffc1c237e38d2fff8a8fd\n",
      "  Stored in directory: /home/user/.cache/pip/wheels/45/b5/70/37665e37cb3dff31128c3b5361080d896dbee9167e3dbf7df8\n",
      "  Building wheel for wget (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25h  Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9681 sha256=b73e6e1511a9b7c6c5f571968191f06765f17de8fd28f64dd13eab7825d1ddc0\n",
      "  Stored in directory: /home/user/.cache/pip/wheels/a1/b6/7c/0e63e34eb06634181c63adacca38b79ff8f35c37e3c13e3c02\n",
      "Successfully built goatools wget\n",
      "Installing collected packages: patsy, statsmodels, wget, goatools\n",
      "Successfully installed goatools-1.0.15 patsy-0.5.1 statsmodels-0.12.1 wget-3.2\n",
      "Note: you may need to restart the kernel to use updated packages.\n"
     ]
    }
   ],
   "source": [
    "pip install goatools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "go-basic.obo: fmt(1.2) rel(2021-01-01) 47,285 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('go-basic.obo',\n",
    "              optional_attrs={'relationship'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 75,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6\n"
     ]
    }
   ],
   "source": [
    "#Create a set\n",
    "seta = set([5, 10, 3, 15, 2, 20])\n",
    "#Find the length use len()\n",
    "print(len(seta))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "ename": "KeyError",
     "evalue": "'GO:0003674'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-9-a956e0b3dbe5>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     34\u001b[0m             \u001b[0mGO_ID\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgo2parents_isa\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mGO_ID\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     35\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 36\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfind_ancestors\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"GO:0003714\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m<ipython-input-9-a956e0b3dbe5>\u001b[0m in \u001b[0;36mfind_ancestors\u001b[0;34m(GO_ID)\u001b[0m\n\u001b[1;32m     28\u001b[0m             \u001b[0mancestor_2\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgo2parents_isa\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mancestor_3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     29\u001b[0m \u001b[0;31m#             print(ancestor_2)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 30\u001b[0;31m             \u001b[0mancestor_1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgo2parents_isa\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mancestor_2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     31\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mancestor_1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mancestor_2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mancestor_3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     32\u001b[0m             \u001b[0mnot_root\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyError\u001b[0m: 'GO:0003674'"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "from goatools.godag.go_tasks import get_go2parents\n",
    "\n",
    " \n",
    "\n",
    "\n",
    "def find_ancestors(GO_ID):\n",
    "    optional_relationships = set()\n",
    "    go2parents_isa = get_go2parents(godag, optional_relationships)\n",
    "\n",
    "    \n",
    "    not_root = True\n",
    "    while(not_root):\n",
    "        gosubdag_r0 = GoSubDag([GO_ID], godag, prt=None)\n",
    "#         print(list(gosubdag_r0.rcntobj.go2ancestors[GO_ID]))\n",
    "        if len(list(gosubdag_r0.rcntobj.go2ancestors[GO_ID]))==1:\n",
    "            ancestor_1 = go2parents_isa[GO_ID]\n",
    "            return (list(ancestor_1)[0],GO_ID,\"\")\n",
    "            not_root = False \n",
    "        if len(list(gosubdag_r0.rcntobj.go2ancestors[GO_ID]))==2:\n",
    "            ancestor_2 = go2parents_isa[GO_ID]\n",
    "            ancestor_1 = go2parents_isa[list(ancestor_2)[0]]\n",
    "            return (list(ancestor_1)[0],list(ancestor_2)[0],GO_ID)\n",
    "            not_root = False\n",
    "        if len(list(gosubdag_r0.rcntobj.go2ancestors[GO_ID]))==3:\n",
    "            ancestor_3 = go2parents_isa[GO_ID]\n",
    "#             print(ancestor_3)\n",
    "            ancestor_2 = go2parents_isa[list(ancestor_3)[0]]\n",
    "#             print(ancestor_2)\n",
    "            ancestor_1 = go2parents_isa[list(ancestor_2)[0]]\n",
    "            return (list(ancestor_1)[0],list(ancestor_2)[0],list(ancestor_3)[0])\n",
    "            not_root = False\n",
    "        else:\n",
    "            GO_ID = list(go2parents_isa[GO_ID])[0]\n",
    "        \n",
    "print(find_ancestors(\"GO:0003714\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "('GO:0008150', 'GO:0009987', 'GO:0060352')\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "from goatools.godag.go_tasks import get_go2parents\n",
    "\n",
    " \n",
    "\n",
    "\n",
    "def find_ancestors1(GO_ID):\n",
    "    optional_relationships = set()\n",
    "    go2parents_isa = get_go2parents(godag, optional_relationships)\n",
    "    ancestor_1 = \"\"\n",
    "    ancestor_2 = \"\"\n",
    "    ancestor_3 = \"\"\n",
    "    try:\n",
    "        gosubdag_r0 = GoSubDag([GO_ID], godag, prt=None)\n",
    "        ancestors = list(gosubdag_r0.rcntobj.go2ancestors[GO_ID])\n",
    "#         print(ancestors)\n",
    "        levels = []\n",
    "        for n in gosubdag_r0.rcntobj.go2ancestors[GO_ID]:\n",
    "            levels.append(godag[n].level)\n",
    "#         print(levels)   \n",
    "\n",
    "    #     print(levels.index(0))\n",
    "        ancestor_1 = ancestors[levels.index(0)]\n",
    "        if 2 in levels:\n",
    "            ancestor_3 = ancestors[levels.index(2)]\n",
    "            ancestor_2 = ancestors[levels.index(1)]\n",
    "        elif 1 in levels:\n",
    "            ancestor_2 = ancestors[levels.index(1)]\n",
    "            ancestor_3 = GO_ID\n",
    "        else:\n",
    "            ancestor_2 = GO_ID\n",
    "            ancestor_3 = \"\"    \n",
    "        return ancestor_1,ancestor_2,ancestor_3\n",
    "    except KeyError as e:\n",
    "        print ('I got a KeyError - reason' + str(e))\n",
    "        return ancestor_1,ancestor_2,ancestor_3\n",
    "        \n",
    "print(find_ancestors1(\"GO:0060352\"))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 213,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "IOPub data rate exceeded.\n",
      "The notebook server will temporarily stop sending output\n",
      "to the client in order to avoid crashing it.\n",
      "To change this limit, set the config variable\n",
      "`--NotebookApp.iopub_data_rate_limit`.\n",
      "\n",
      "Current values:\n",
      "NotebookApp.iopub_data_rate_limit=1000000.0 (bytes/sec)\n",
      "NotebookApp.rate_limit_window=3.0 (secs)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "\n",
    "# Choose a deep leaf-level GO ID associated with \"bacteria\"\n",
    "DESC = 'nucleus'            # GO Term name contains this\n",
    "NSPC = 'cellular_component'  # Desired namespace\n",
    "\n",
    "# Create a chooser function which returns True or False\n",
    "def chooser(goterm):\n",
    "    \"\"\"Choose a leaf-level GO term based on its name\"\"\"\n",
    "    b_match = DESC in goterm.name\n",
    "    # True if GO term is leaf-level (has no children)\n",
    "    b_leaf = not goterm.children\n",
    "    # True if GO term is in 'cellular_component' namespace (nspc)\n",
    "    b_nspc = goterm.namespace == NSPC\n",
    "    return b_match and b_leaf and b_nspc\n",
    "\n",
    "# Get GO terms with desired name in desired GO DAG branch\n",
    "go_ids_selected = set(o.item_id for o in godag.values() if chooser(o))\n",
    "print(godag.values())\n",
    "print('{N} {desc} GO terms'.format(N=len(go_ids_selected), desc=DESC))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 250,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "3\n"
     ]
    }
   ],
   "source": [
    "# for o in godag.values():\n",
    "#     print(o)\n",
    "print(godag[\"GO:0003714\"].level)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 246,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n"
     ]
    }
   ],
   "source": [
    "print((godag[\"GO:0003674\"].level))\n",
    "\n",
    "# for n in ....:\n",
    "#     if godag[n]."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 241,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      " GoSubDag:  19 sources in  36 GOs rcnt(True). 0 alt GO IDs\n",
      " GoSubDag: namedtuple fields: NS level depth GO alt GO_name dcnt D1 id\n",
      " GoSubDag: relationships: set()\n"
     ]
    }
   ],
   "source": [
    "from goatools.gosubdag.gosubdag import GoSubDag\n",
    "gosubdag = GoSubDag(go_ids_selected, godag)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 204,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0014808 release of sequestered calcium ion into cytosol by sarcoplasmic reticulum\n"
     ]
    }
   ],
   "source": [
    "go_id, go_term = max(gosubdag.go2obj.items(), key=lambda t: t[1].depth)\n",
    "\n",
    "# Print GO ID, using print format in gosubdag\n",
    "print(go_id, go_term.name)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 205,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "48 ancestors for GO:0014808 \"release of sequestered calcium ion into cytosol by sarcoplasmic reticulum\"\n"
     ]
    }
   ],
   "source": [
    "go_ids_chosen = go_term.get_all_parents()\n",
    "print('{N} ancestors for {GO} \"{name}\"'.format(\n",
    "    N=len(go_ids_chosen), GO=go_term.item_id, name=go_term.name))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 206,
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'str' object has no attribute 'children'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-206-87467ad86709>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mppp\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"GO:0014808\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 2\u001b[0;31m \u001b[0mppp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mchildren\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m: 'str' object has no attribute 'children'"
     ]
    }
   ],
   "source": [
    "ppp = \"GO:0014808\"\n",
    "ppp.children"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 168,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'protein-containing complex'"
      ]
     },
     "execution_count": 168,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "godag[\"GO:0032991\"].name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 169,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "GO:0019222 ancestors: {'GO:0008150', 'GO:0050789', 'GO:0065007'}\n"
     ]
    }
   ],
   "source": [
    "\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": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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