Gene Classification.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Enzymes: MFO 'Catalytic activity', GO:0003824 \n",
    "#         OR\n",
    "#         any EC term\n",
    "\n",
    "# Metabolic Enzymes: BPO 'primary metabolic process', GO:0044238 \n",
    "#                   AND \n",
    "#           MFO 'Catalytic activity', GO:0003824 OR any EC term \n",
    "\n",
    "# Kinases: MFO 'protein kinase activity', GO:0004672 \n",
    "#         OR \n",
    "#         EC: 2.7.10/11/12/13/99.-\n",
    "#         OR \n",
    "#         text search \"protein kinase\" in Uniprot protein name field\n",
    "\n",
    "# TFs: MFO GO:0044212 transcription regulatory region DNA binding \n",
    "#     OR \n",
    "#     BPO GO:0006355 regulation of transcription, DNA-templated\n",
    "#     OR\n",
    "#     text search \"transcription factor\" in Uniprot protein name field\n",
    "\n",
    "# Nucleic-Acid Binding Proteins: MFO GO:0003676 nucleic-acid binding\n",
    "\n",
    "# Signaling Proteins: BPO GO:0023052 signaling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>AADAC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>AARS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>AASDHPPT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>AASS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>ABCB5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>500</td>\n",
       "      <td>YRDC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>501</td>\n",
       "      <td>YWHAG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>502</td>\n",
       "      <td>ZIC1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>503</td>\n",
       "      <td>ZIC4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>504</td>\n",
       "      <td>ZMPSTE24</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>505 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Genes\n",
       "0       AADAC\n",
       "1        AARS\n",
       "2    AASDHPPT\n",
       "3        AASS\n",
       "4       ABCB5\n",
       "..        ...\n",
       "500      YRDC\n",
       "501     YWHAG\n",
       "502      ZIC1\n",
       "503      ZIC4\n",
       "504  ZMPSTE24\n",
       "\n",
       "[505 rows x 1 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load genelist of genes for matrix to be created \n",
    "\n",
    "Genelist = pd.read_csv('Genelist.csv', names = ['Genes'])\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "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_Names</th>\n",
       "      <th>GO</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  \n",
       "0                                     Gene ontology (GO)  \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...  \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...  \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...  \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...  \n",
       "...                                                  ...  \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...  \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...  \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...  \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...  \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...  \n",
       "\n",
       "[20350 rows x 2 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load uniprot data of all genes and all GO terms \n",
    "# use the uniprot frame to add on gene conditions and use the uniprot_start frame as a dummy blank frame\n",
    "\n",
    "Uniprot = pd.read_csv('uniprot_20200225_key.csv', names = ['Gene_Names', 'GO'])\n",
    "Uniprot_start = pd.read_csv('uniprot_20200225_key.csv', names = ['Gene_Names', 'GO'])\n",
    "\n",
    "Uniprot_start"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot = pd.read_csv('uniprot_20200225_key.csv', names = ['Gene_Names', 'GO'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Enzymes: MFO 'Catalytic activity', GO:0003824 \n",
    "#         OR\n",
    "#         any EC term\n",
    "\n",
    "# first add in MFO Catalytic acivity\n",
    "\n",
    "\n",
    "Uniprot_Enzyme = Uniprot_start.copy()\n",
    "\n",
    "infile = open('MFO_catalytic_activity_GO-0003824_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Enzyme['GO'].str.contains(GO_test)\n",
    "    Uniprot_Enzyme[GO_test] = a\n",
    "\n",
    "###Uniprot_Enzyme"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add in the any EC term \n",
    "\n",
    "Any_EC = pd.read_csv('EC_Genes_All.csv', names = ['EC Genes'])\n",
    "\n",
    "###Any_EC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "EC_genes = (Uniprot['Gene_Names']).isin(Any_EC['EC Genes'])\n",
    "\n",
    "###EC_genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot_Enzyme['EC'] = EC_genes\n",
    "\n",
    "###Uniprot_Enzyme"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# filter the matrix down so that it only contains a column of whether any row contains a true value\n",
    "# note you have to drop Gene_Names and GO otherwise they get counted as true....\n",
    "\n",
    "Uniprot_Enzyme = Uniprot_Enzyme.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Enzyme_Cond = Uniprot_Enzyme.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Enzyme'] = Enzyme_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  \n",
       "0                                     Gene ontology (GO)   False  \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False  \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False  \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False  \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True  \n",
       "...                                                  ...     ...  \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False  \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False  \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True  \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False  \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False  \n",
       "\n",
       "[20350 rows x 3 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5589"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Enzyme'].sum()"
   ]
  },
  {
   "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": 14,
   "metadata": {},
   "outputs": [
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     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Gene_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>GO:0000012</th>\n",
       "      <th>GO:0000018</th>\n",
       "      <th>GO:0000019</th>\n",
       "      <th>GO:0045950</th>\n",
       "      <th>GO:0000023</th>\n",
       "      <th>GO:0000024</th>\n",
       "      <th>GO:0000025</th>\n",
       "      <th>GO:0000038</th>\n",
       "      <th>...</th>\n",
       "      <th>GO:2001301</th>\n",
       "      <th>GO:2001302</th>\n",
       "      <th>GO:2001303</th>\n",
       "      <th>GO:2001304</th>\n",
       "      <th>GO:2001306</th>\n",
       "      <th>GO:2001311</th>\n",
       "      <th>GO:2001312</th>\n",
       "      <th>GO:2001313</th>\n",
       "      <th>GO:2001314</th>\n",
       "      <th>GO:2001315</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>...</td>\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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 6772 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO GO:0000012  \\\n",
       "0                                     Gene ontology (GO)      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...      False   \n",
       "...                                                  ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...      False   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...      False   \n",
       "\n",
       "      GO:0000018 GO:0000019 GO:0045950 GO:0000023 GO:0000024 GO:0000025  \\\n",
       "0          False      False      False      False      False      False   \n",
       "1          False      False      False      False      False      False   \n",
       "2          False      False      False      False      False      False   \n",
       "3          False      False      False      False      False      False   \n",
       "4          False      False      False      False      False      False   \n",
       "...          ...        ...        ...        ...        ...        ...   \n",
       "20345      False      False      False      False      False      False   \n",
       "20346      False      False      False      False      False      False   \n",
       "20347      False      False      False      False      False      False   \n",
       "20348      False      False      False      False      False      False   \n",
       "20349      False      False      False      False      False      False   \n",
       "\n",
       "      GO:0000038  ... GO:2001301 GO:2001302 GO:2001303 GO:2001304 GO:2001306  \\\n",
       "0          False  ...      False      False      False      False      False   \n",
       "1          False  ...      False      False      False      False      False   \n",
       "2          False  ...      False      False      False      False      False   \n",
       "3          False  ...      False      False      False      False      False   \n",
       "4          False  ...      False      False      False      False      False   \n",
       "...          ...  ...        ...        ...        ...        ...        ...   \n",
       "20345      False  ...      False      False      False      False      False   \n",
       "20346      False  ...      False      False      False      False      False   \n",
       "20347      False  ...      False      False      False      False      False   \n",
       "20348      False  ...      False      False      False      False      False   \n",
       "20349      False  ...      False      False      False      False      False   \n",
       "\n",
       "      GO:2001311 GO:2001312 GO:2001313 GO:2001314 GO:2001315  \n",
       "0          False      False      False      False      False  \n",
       "1          False      False      False      False      False  \n",
       "2          False      False      False      False      False  \n",
       "3          False      False      False      False      False  \n",
       "4          False      False      False      False      False  \n",
       "...          ...        ...        ...        ...        ...  \n",
       "20345      False      False      False      False      False  \n",
       "20346      False      False      False      False      False  \n",
       "20347      False      False      False      False      False  \n",
       "20348      False      False      False      False      False  \n",
       "20349      False      False      False      False      False  \n",
       "\n",
       "[20350 rows x 6772 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Metabolic Enzymes: BPO 'primary metabolic process', GO:0044238 \n",
    "#                   AND \n",
    "#           MFO 'Catalytic activity', GO:0003824 OR any EC term \n",
    "# Note we split out these two terms into two matrixes then combine them in the end to check both conidtions are true\n",
    "\n",
    "Uniprot_Metabolic_1 = Uniprot_start.copy()\n",
    "\n",
    "infile = open('BPO_primary_metabolic_process_GO-0044238_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Metabolic_1['GO'].str.contains(GO_test)\n",
    "    Uniprot_Metabolic_1[GO_test] = a\n",
    "\n",
    "Uniprot_Metabolic_1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot_Metabolic_1 = Uniprot_Metabolic_1.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Metabolic_1_Cond = Uniprot_Metabolic_1.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0        False\n",
       "1         True\n",
       "2         True\n",
       "3        False\n",
       "4         True\n",
       "         ...  \n",
       "20345     True\n",
       "20346     True\n",
       "20347     True\n",
       "20348    False\n",
       "20349    False\n",
       "Length: 20350, dtype: bool"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Metabolic_1_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "9809"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Metabolic_1_Cond.sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>GO:0003756</th>\n",
       "      <th>GO:0015036</th>\n",
       "      <th>GO:0000009</th>\n",
       "      <th>GO:0000010</th>\n",
       "      <th>GO:0000014</th>\n",
       "      <th>GO:0000016</th>\n",
       "      <th>GO:0000026</th>\n",
       "      <th>GO:0000030</th>\n",
       "      <th>...</th>\n",
       "      <th>GO:1990883</th>\n",
       "      <th>GO:1990886</th>\n",
       "      <th>GO:1990887</th>\n",
       "      <th>GO:1990888</th>\n",
       "      <th>GO:1990929</th>\n",
       "      <th>GO:1990930</th>\n",
       "      <th>GO:1990931</th>\n",
       "      <th>GO:1990939</th>\n",
       "      <th>GO:1990965</th>\n",
       "      <th>GO:1990984</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>...</td>\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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 7003 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO GO:0003756  \\\n",
       "0                                     Gene ontology (GO)      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...      False   \n",
       "...                                                  ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...      False   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...      False   \n",
       "\n",
       "      GO:0015036 GO:0000009 GO:0000010 GO:0000014 GO:0000016 GO:0000026  \\\n",
       "0          False      False      False      False      False      False   \n",
       "1          False      False      False      False      False      False   \n",
       "2          False      False      False      False      False      False   \n",
       "3          False      False      False      False      False      False   \n",
       "4          False      False      False      False      False      False   \n",
       "...          ...        ...        ...        ...        ...        ...   \n",
       "20345      False      False      False      False      False      False   \n",
       "20346      False      False      False      False      False      False   \n",
       "20347      False      False      False      False      False      False   \n",
       "20348      False      False      False      False      False      False   \n",
       "20349      False      False      False      False      False      False   \n",
       "\n",
       "      GO:0000030  ... GO:1990883 GO:1990886 GO:1990887 GO:1990888 GO:1990929  \\\n",
       "0          False  ...      False      False      False      False      False   \n",
       "1          False  ...      False      False      False      False      False   \n",
       "2          False  ...      False      False      False      False      False   \n",
       "3          False  ...      False      False      False      False      False   \n",
       "4          False  ...      False      False      False      False      False   \n",
       "...          ...  ...        ...        ...        ...        ...        ...   \n",
       "20345      False  ...      False      False      False      False      False   \n",
       "20346      False  ...      False      False      False      False      False   \n",
       "20347      False  ...      False      False      False      False      False   \n",
       "20348      False  ...      False      False      False      False      False   \n",
       "20349      False  ...      False      False      False      False      False   \n",
       "\n",
       "      GO:1990930 GO:1990931 GO:1990939 GO:1990965 GO:1990984  \n",
       "0          False      False      False      False      False  \n",
       "1          False      False      False      False      False  \n",
       "2          False      False      False      False      False  \n",
       "3          False      False      False      False      False  \n",
       "4          False      False      False      False      False  \n",
       "...          ...        ...        ...        ...        ...  \n",
       "20345      False      False      False      False      False  \n",
       "20346      False      False      False      False      False  \n",
       "20347      False      False      False      False      False  \n",
       "20348      False      False      False      False      False  \n",
       "20349      False      False      False      False      False  \n",
       "\n",
       "[20350 rows x 7003 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot_Metabolic_2 = Uniprot_start.copy()\n",
    "\n",
    "infile = open('MFO_catalytic_activity_GO-0003824_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Metabolic_2['GO'].str.contains(GO_test)\n",
    "    Uniprot_Metabolic_2[GO_test] = a\n",
    "\n",
    "Uniprot_Metabolic_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>GO:0003756</th>\n",
       "      <th>GO:0015036</th>\n",
       "      <th>GO:0000009</th>\n",
       "      <th>GO:0000010</th>\n",
       "      <th>GO:0000014</th>\n",
       "      <th>GO:0000016</th>\n",
       "      <th>GO:0000026</th>\n",
       "      <th>GO:0000030</th>\n",
       "      <th>...</th>\n",
       "      <th>GO:1990886</th>\n",
       "      <th>GO:1990887</th>\n",
       "      <th>GO:1990888</th>\n",
       "      <th>GO:1990929</th>\n",
       "      <th>GO:1990930</th>\n",
       "      <th>GO:1990931</th>\n",
       "      <th>GO:1990939</th>\n",
       "      <th>GO:1990965</th>\n",
       "      <th>GO:1990984</th>\n",
       "      <th>EC</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
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       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
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       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>...</td>\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",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 7004 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO GO:0003756  \\\n",
       "0                                     Gene ontology (GO)      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...      False   \n",
       "...                                                  ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...      False   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...      False   \n",
       "\n",
       "      GO:0015036 GO:0000009 GO:0000010 GO:0000014 GO:0000016 GO:0000026  \\\n",
       "0          False      False      False      False      False      False   \n",
       "1          False      False      False      False      False      False   \n",
       "2          False      False      False      False      False      False   \n",
       "3          False      False      False      False      False      False   \n",
       "4          False      False      False      False      False      False   \n",
       "...          ...        ...        ...        ...        ...        ...   \n",
       "20345      False      False      False      False      False      False   \n",
       "20346      False      False      False      False      False      False   \n",
       "20347      False      False      False      False      False      False   \n",
       "20348      False      False      False      False      False      False   \n",
       "20349      False      False      False      False      False      False   \n",
       "\n",
       "      GO:0000030  ... GO:1990886 GO:1990887 GO:1990888 GO:1990929 GO:1990930  \\\n",
       "0          False  ...      False      False      False      False      False   \n",
       "1          False  ...      False      False      False      False      False   \n",
       "2          False  ...      False      False      False      False      False   \n",
       "3          False  ...      False      False      False      False      False   \n",
       "4          False  ...      False      False      False      False      False   \n",
       "...          ...  ...        ...        ...        ...        ...        ...   \n",
       "20345      False  ...      False      False      False      False      False   \n",
       "20346      False  ...      False      False      False      False      False   \n",
       "20347      False  ...      False      False      False      False      False   \n",
       "20348      False  ...      False      False      False      False      False   \n",
       "20349      False  ...      False      False      False      False      False   \n",
       "\n",
       "      GO:1990931 GO:1990939 GO:1990965 GO:1990984     EC  \n",
       "0          False      False      False      False  False  \n",
       "1          False      False      False      False  False  \n",
       "2          False      False      False      False  False  \n",
       "3          False      False      False      False  False  \n",
       "4          False      False      False      False   True  \n",
       "...          ...        ...        ...        ...    ...  \n",
       "20345      False      False      False      False  False  \n",
       "20346      False      False      False      False  False  \n",
       "20347      False      False      False      False   True  \n",
       "20348      False      False      False      False  False  \n",
       "20349      False      False      False      False  False  \n",
       "\n",
       "[20350 rows x 7004 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# add in the any EC term \n",
    "\n",
    "Any_EC = pd.read_csv('EC_Genes_All.csv', names = ['EC Genes'])\n",
    "EC_genes = (Uniprot['Gene_Names']).isin(Any_EC['EC Genes'])\n",
    "Uniprot_Metabolic_2['EC'] = EC_genes\n",
    "\n",
    "Uniprot_Metabolic_2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0        False\n",
       "1        False\n",
       "2        False\n",
       "3        False\n",
       "4         True\n",
       "         ...  \n",
       "20345    False\n",
       "20346    False\n",
       "20347     True\n",
       "20348    False\n",
       "20349    False\n",
       "Length: 20350, dtype: bool"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot_Metabolic_2 = Uniprot_Metabolic_2.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Metabolic_2_Cond = Uniprot_Metabolic_2.any(axis=1, bool_only = True)\n",
    "\n",
    "Metabolic_2_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\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>Cond_1</th>\n",
       "      <th>Cond_2</th>\n",
       "      <th>Final</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       Cond_1  Cond_2  Final\n",
       "0       False   False  False\n",
       "1        True   False  False\n",
       "2        True   False  False\n",
       "3       False   False  False\n",
       "4        True    True   True\n",
       "...       ...     ...    ...\n",
       "20345    True   False  False\n",
       "20346    True   False  False\n",
       "20347    True    True   True\n",
       "20348   False   False  False\n",
       "20349   False   False  False\n",
       "\n",
       "[20350 rows x 3 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Metabolic_Cross_Ref = pd.DataFrame()\n",
    "\n",
    "Metabolic_Cross_Ref['Cond_1'] = Metabolic_1_Cond\n",
    "Metabolic_Cross_Ref['Cond_2'] = Metabolic_2_Cond\n",
    "\n",
    "Metabolic_Cross_Ref['Final'] = Metabolic_Cross_Ref['Cond_1'] & Metabolic_Cross_Ref['Cond_2']\n",
    "\n",
    "Metabolic_Cross_Ref"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Metabolic'] = Metabolic_Cross_Ref['Final']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \n",
       "0                                     Gene ontology (GO)   False      False  \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False  \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False  \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False  \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True  \n",
       "...                                                  ...     ...        ...  \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False  \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False  \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True  \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False  \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False  \n",
       "\n",
       "[20350 rows x 4 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "4316"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Metabolic'].sum()"
   ]
  },
  {
   "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": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Kinases: MFO 'protein kinase activity', GO:0004672 \n",
    "#         OR \n",
    "#         EC: 2.7.10/11/12/13/99.-\n",
    "#         OR \n",
    "#         text search \"protein kinase\" in Uniprot protein name field\n",
    "\n",
    "Uniprot_Kinase = Uniprot_start.copy()\n",
    "\n",
    "infile = open('MFO_protein_kinase_activity_GO-0004672_descendants.csv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Kinase['GO'].str.contains(GO_test)\n",
    "    Uniprot_Kinase[GO_test] = a\n",
    "\n",
    "###Uniprot_Kinase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add in the kinase EC terms \n",
    "\n",
    "Kinase_EC = pd.read_csv('EC_Genes_Kinase.csv', names = ['EC Genes'])\n",
    "\n",
    "###Kinase_EC"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "EC_genes = (Uniprot['Gene_Names']).isin(Kinase_EC['EC Genes'])\n",
    "\n",
    "###EC_genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot_Kinase['EC'] = EC_genes\n",
    "\n",
    "###Uniprot_Kinase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add in the kinase text search terms\n",
    "\n",
    "Kinase_Name = pd.read_csv('text_search_protein_kinase.csv', names = ['Name Genes'])\n",
    "\n",
    "###Kinase_Name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "Name_genes = (Uniprot['Gene_Names']).isin(Kinase_Name['Name Genes'])\n",
    "\n",
    "###Name_genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot_Kinase['Name'] = Name_genes\n",
    "\n",
    "###Uniprot_Kinase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "# filter the matrix down so that it only contains a column of whether any row contains a true value\n",
    "# note you have to drop Gene_Names and GO otherwise they get counted as true....\n",
    "\n",
    "Uniprot_Kinase = Uniprot_Kinase.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Kinase_Cond = Uniprot_Kinase.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Kinase'] = Kinase_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  \n",
       "0       False  \n",
       "1       False  \n",
       "2       False  \n",
       "3       False  \n",
       "4       False  \n",
       "...       ...  \n",
       "20345   False  \n",
       "20346   False  \n",
       "20347   False  \n",
       "20348   False  \n",
       "20349   False  \n",
       "\n",
       "[20350 rows x 5 columns]"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "624"
      ]
     },
     "execution_count": 35,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Kinase'].sum()"
   ]
  },
  {
   "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": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "# TFs: MFO GO:0044212 transcription regulatory region DNA binding \n",
    "#     OR \n",
    "#     BPO GO:0006355 regulation of transcription, DNA-templated\n",
    "#     OR\n",
    "#     text search \"transcription factor\" in Uniprot protein name field\n",
    "\n",
    "Uniprot_TF = Uniprot_start.copy()\n",
    "\n",
    "infile = open('MFO_TF_regulatory_binding_GO-0044212_descendants.csv', 'r')\n",
    "infile2  = open('BPO_TF_regulation_GO-0006355_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_TF['GO'].str.contains(GO_test)\n",
    "    Uniprot_TF[GO_test] = a\n",
    "\n",
    "for line in infile2: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_TF['GO'].str.contains(GO_test)\n",
    "    Uniprot_TF[GO_test] = a\n",
    "    \n",
    "\n",
    "###Uniprot_TF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add in the TF text search terms\n",
    "\n",
    "TF_Name = pd.read_csv('text_search_transcription_factor.csv', names = ['Name Genes'])\n",
    "\n",
    "###TF_Name"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [],
   "source": [
    "Name_genes = (Uniprot['Gene_Names']).isin(TF_Name['Name Genes'])\n",
    "\n",
    "###Name_genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot_TF['Name'] = Name_genes\n",
    "\n",
    "###Uniprot_TF"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "# filter the matrix down so that it only contains a column of whether any row contains a true value\n",
    "# note you have to drop Gene_Names and GO otherwise they get counted as true....\n",
    "\n",
    "Uniprot_TF = Uniprot_TF.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "TF_Cond = Uniprot_TF.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Transcription Factor'] = TF_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  Transcription Factor  \n",
       "0       False                 False  \n",
       "1       False                 False  \n",
       "2       False                  True  \n",
       "3       False                 False  \n",
       "4       False                 False  \n",
       "...       ...                   ...  \n",
       "20345   False                 False  \n",
       "20346   False                 False  \n",
       "20347   False                 False  \n",
       "20348   False                 False  \n",
       "20349   False                 False  \n",
       "\n",
       "[20350 rows x 6 columns]"
      ]
     },
     "execution_count": 42,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2803"
      ]
     },
     "execution_count": 43,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Transcription Factor'].sum()"
   ]
  },
  {
   "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": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Nucleic-Acid Binding Proteins: MFO GO:0003676 nucleic-acid binding\n",
    "# create a matrix to test whether each gene has contains any of the nucleic-acid binding GO terms\n",
    "\n",
    "Uniprot_Nucleic = Uniprot_start.copy()\n",
    "\n",
    "infile = open('MFO_nucleicacid_binding_GO-0003676_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Nucleic['GO'].str.contains(GO_test)\n",
    "    Uniprot_Nucleic[GO_test] = a\n",
    "\n",
    "###Uniprot_Nucleic"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [],
   "source": [
    "# filter the matrix down so that it only contains a column of whether any row contains a true value\n",
    "# note you have to drop Gene_Names and GO otherwise they get counted as true....\n",
    "\n",
    "Uniprot_Nucleic = Uniprot_Nucleic.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Nucleic_Cond = Uniprot_Nucleic.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Nucleic-Acid Binding'] = Nucleic_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "    }\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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  Transcription Factor  Nucleic-Acid Binding  \n",
       "0       False                 False                 False  \n",
       "1       False                 False                 False  \n",
       "2       False                  True                 False  \n",
       "3       False                 False                 False  \n",
       "4       False                 False                 False  \n",
       "...       ...                   ...                   ...  \n",
       "20345   False                 False                 False  \n",
       "20346   False                 False                 False  \n",
       "20347   False                 False                 False  \n",
       "20348   False                 False                 False  \n",
       "20349   False                 False                 False  \n",
       "\n",
       "[20350 rows x 7 columns]"
      ]
     },
     "execution_count": 47,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "3849"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Nucleic-Acid Binding'].sum()"
   ]
  },
  {
   "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": 49,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Signaling Proteins: BPO GO:0023052 signaling\n",
    "# create a matrix to test whether each gene has contains any of the signalling GO terms\n",
    "\n",
    "Uniprot_Signalling = Uniprot_start.copy()\n",
    "\n",
    "infile = open('BPO_signaling_GO-0023052_descendants.tsv', 'r')\n",
    "\n",
    "for line in infile: \n",
    "    GO_test = str(line[:-1])\n",
    "    a = Uniprot_Signalling['GO'].str.contains(GO_test)\n",
    "    Uniprot_Signalling[GO_test] = a\n",
    "\n",
    "###Uniprot_Signalling"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "# filter the matrix down so that it only contains a column of whether any row contains a true value\n",
    "# note you have to drop Gene_Names and GO otherwise they get counted as true....\n",
    "\n",
    "Uniprot_Signalling = Uniprot_Signalling.drop(['Gene_Names', 'GO'], axis=1)\n",
    "\n",
    "Signalling_Cond = Uniprot_Signalling.any(axis=1, bool_only = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot['Signalling'] = Signalling_Cond"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "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_Names</th>\n",
       "      <th>GO</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>Gene names  (primary )</td>\n",
       "      <td>Gene ontology (GO)</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>PLAA</td>\n",
       "      <td>cell [GO:0005623]; cell junction [GO:0030054];...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>NACC1</td>\n",
       "      <td>cell junction [GO:0030054]; cytoplasm [GO:0005...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>MTSS1</td>\n",
       "      <td>actin cytoskeleton [GO:0015629]; cytoplasm [GO...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>PNPLA8</td>\n",
       "      <td>endoplasmic reticulum membrane [GO:0005789]; G...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20345</td>\n",
       "      <td>GPRC5B</td>\n",
       "      <td>cell surface [GO:0009986]; cytoplasmic vesicle...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20346</td>\n",
       "      <td>DNAJB12</td>\n",
       "      <td>endoplasmic reticulum [GO:0005783]; endoplasmi...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20347</td>\n",
       "      <td>GCNT3</td>\n",
       "      <td>extracellular exosome [GO:0070062]; Golgi memb...</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20348</td>\n",
       "      <td>DLEC1</td>\n",
       "      <td>cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>20349</td>\n",
       "      <td>DLG5</td>\n",
       "      <td>cell junction [GO:0030054]; cell-cell adherens...</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>20350 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                   Gene_Names  \\\n",
       "0      Gene names  (primary )   \n",
       "1                        PLAA   \n",
       "2                       NACC1   \n",
       "3                       MTSS1   \n",
       "4                      PNPLA8   \n",
       "...                       ...   \n",
       "20345                  GPRC5B   \n",
       "20346                 DNAJB12   \n",
       "20347                   GCNT3   \n",
       "20348                   DLEC1   \n",
       "20349                    DLG5   \n",
       "\n",
       "                                                      GO  Enzyme  Metabolic  \\\n",
       "0                                     Gene ontology (GO)   False      False   \n",
       "1      cell [GO:0005623]; cell junction [GO:0030054];...   False      False   \n",
       "2      cell junction [GO:0030054]; cytoplasm [GO:0005...   False      False   \n",
       "3      actin cytoskeleton [GO:0015629]; cytoplasm [GO...   False      False   \n",
       "4      endoplasmic reticulum membrane [GO:0005789]; G...    True       True   \n",
       "...                                                  ...     ...        ...   \n",
       "20345  cell surface [GO:0009986]; cytoplasmic vesicle...   False      False   \n",
       "20346  endoplasmic reticulum [GO:0005783]; endoplasmi...   False      False   \n",
       "20347  extracellular exosome [GO:0070062]; Golgi memb...    True       True   \n",
       "20348  cytoplasm [GO:0005737]; cytosol [GO:0005829]; ...   False      False   \n",
       "20349  cell junction [GO:0030054]; cell-cell adherens...   False      False   \n",
       "\n",
       "       Kinase  Transcription Factor  Nucleic-Acid Binding  Signalling  \n",
       "0       False                 False                 False       False  \n",
       "1       False                 False                 False        True  \n",
       "2       False                  True                 False       False  \n",
       "3       False                 False                 False        True  \n",
       "4       False                 False                 False       False  \n",
       "...       ...                   ...                   ...         ...  \n",
       "20345   False                 False                 False        True  \n",
       "20346   False                 False                 False       False  \n",
       "20347   False                 False                 False       False  \n",
       "20348   False                 False                 False       False  \n",
       "20349   False                 False                 False        True  \n",
       "\n",
       "[20350 rows x 8 columns]"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "6222"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Uniprot['Signalling'].sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " Enzyme Genes:  5589 28.00 % \n",
      " Metabolic Enzyme Genes:  4316 21.00 % \n",
      " Kinase Genes:  624 3.00 % \n",
      " Transcription Factor Genes:  2803 14.00 % \n",
      " Nucleic Acid Binding Genes:  3849 19.00 % \n",
      " Signalling Genes:  6222 27.00 % \n",
      "\n"
     ]
    }
   ],
   "source": [
    "print('\\n', 'Enzyme Genes: ', Uniprot['Enzyme'].sum(),  \"{0:.2f}\".format(round(Uniprot['Enzyme'].sum()/Uniprot['Gene_Names'].count(),2)*100), '%', '\\n',\n",
    "      'Metabolic Enzyme Genes: ', Uniprot['Metabolic'].sum(), \"{0:.2f}\".format(round(Uniprot['Metabolic'].sum()/Uniprot['Gene_Names'].count(),2)*100), '%', '\\n',\n",
    "      'Kinase Genes: ', Uniprot['Kinase'].sum(), \"{0:.2f}\".format(round(Uniprot['Kinase'].sum()/Uniprot['Gene_Names'].count(),2)*100), '%', '\\n',\n",
    "      'Transcription Factor Genes: ', Uniprot['Transcription Factor'].sum(), \"{0:.2f}\".format(round(Uniprot['Transcription Factor'].sum()/Uniprot['Gene_Names'].count(),2)*100), '%', '\\n',\n",
    "      'Nucleic Acid Binding Genes: ', Uniprot['Nucleic-Acid Binding'].sum(), \"{0:.2f}\".format(round(Uniprot['Nucleic-Acid Binding'].sum()/Uniprot['Gene_Names'].count(),2)*100), '%', '\\n',\n",
    "     'Signalling Genes: ', Uniprot['Signalling'].sum(), \"{0:.2f}\".format(round(Uniprot['Enzyme'].sum()/Uniprot['Signalling'].count(),2)*100), '%', '\\n',\n",
    "     )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [],
   "source": [
    "Uniprot.to_csv(r'Uniprot_Classification.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "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>Genes</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>AADAC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>AARS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>AASDHPPT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>AASS</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>ABCB5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>500</td>\n",
       "      <td>YRDC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>501</td>\n",
       "      <td>YWHAG</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>502</td>\n",
       "      <td>ZIC1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>503</td>\n",
       "      <td>ZIC4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>504</td>\n",
       "      <td>ZMPSTE24</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>505 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Genes\n",
       "0       AADAC\n",
       "1        AARS\n",
       "2    AASDHPPT\n",
       "3        AASS\n",
       "4       ABCB5\n",
       "..        ...\n",
       "500      YRDC\n",
       "501     YWHAG\n",
       "502      ZIC1\n",
       "503      ZIC4\n",
       "504  ZMPSTE24\n",
       "\n",
       "[505 rows x 1 columns]"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# load genelist of genes for matrix to be created \n",
    "\n",
    "Genelist = pd.read_csv('Genelist.csv', names = ['Genes'])\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "\n",
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       "        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>Genes</th>\n",
       "      <th>Enzyme</th>\n",
       "      <th>Metabolic</th>\n",
       "      <th>Kinase</th>\n",
       "      <th>Transcription Factor</th>\n",
       "      <th>Nucleic-Acid Binding</th>\n",
       "      <th>Signalling</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <td>0</td>\n",
       "      <td>AADAC</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>1</td>\n",
       "      <td>AARS</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>2</td>\n",
       "      <td>AASDHPPT</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>3</td>\n",
       "      <td>AASS</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>4</td>\n",
       "      <td>ABCB5</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\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",
       "      <td>500</td>\n",
       "      <td>YRDC</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>501</td>\n",
       "      <td>YWHAG</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>502</td>\n",
       "      <td>ZIC1</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>503</td>\n",
       "      <td>ZIC4</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <td>504</td>\n",
       "      <td>ZMPSTE24</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>505 rows × 7 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Genes Enzyme Metabolic Kinase Transcription Factor  \\\n",
       "0       AADAC   True      True  False                False   \n",
       "1        AARS   True      True  False                False   \n",
       "2    AASDHPPT   True      True  False                False   \n",
       "3        AASS   True      True  False                False   \n",
       "4       ABCB5   True     False  False                False   \n",
       "..        ...    ...       ...    ...                  ...   \n",
       "500      YRDC   True      True  False                False   \n",
       "501     YWHAG  False     False   True                False   \n",
       "502      ZIC1  False     False  False                 True   \n",
       "503      ZIC4  False     False  False                 True   \n",
       "504  ZMPSTE24   True      True  False                 True   \n",
       "\n",
       "    Nucleic-Acid Binding Signalling  \n",
       "0                  False      False  \n",
       "1                   True      False  \n",
       "2                  False      False  \n",
       "3                  False      False  \n",
       "4                  False      False  \n",
       "..                   ...        ...  \n",
       "500                 True      False  \n",
       "501                 True       True  \n",
       "502                 True       True  \n",
       "503                 True      False  \n",
       "504                 True       True  \n",
       "\n",
       "[505 rows x 7 columns]"
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "factors = [\"Enzyme\", \"Metabolic\", \"Kinase\", \"Transcription Factor\", \"Nucleic-Acid Binding\", \"Signalling\"]\n",
    "\n",
    "for item in factors: \n",
    "    count_dict = Uniprot.set_index('Gene_Names')[item].to_dict()\n",
    "    Genelist[item] = Genelist['Genes'].map(count_dict)\n",
    "\n",
    "Genelist"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      " Enzyme Genes:  279 55.00 % \n",
      " Metabolic Enzyme Genes:  241 48.0 % \n",
      " Kinase Genes:  52 10.00 % \n",
      " Transcription Factor Genes:  101 20.0 % \n",
      " Nucleic Acid Binding Genes:  131 26.0 % \n",
      " Signalling Genes:  221 44.0 % \n",
      "\n"
     ]
    }
   ],
   "source": [
    "print('\\n', 'Enzyme Genes: ', Genelist['Enzyme'].sum(), \"{0:.2f}\".format(round(Genelist['Enzyme'].sum()/Genelist['Genes'].count(),2)*100), '%', '\\n',\n",
    "      'Metabolic Enzyme Genes: ', Genelist['Metabolic'].sum(), round(Genelist['Metabolic'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "      'Kinase Genes: ', Genelist['Kinase'].sum(), \"{0:.2f}\".format(round(Genelist['Kinase'].sum()/Genelist['Genes'].count(),2)*100), '%', '\\n',\n",
    "      'Transcription Factor Genes: ', Genelist['Transcription Factor'].sum(), round(Genelist['Transcription Factor'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "      'Nucleic Acid Binding Genes: ', Genelist['Nucleic-Acid Binding'].sum(), round(Genelist['Nucleic-Acid Binding'].sum()/Genelist['Genes'].count(),2)*100, '%','\\n',\n",
    "     'Signalling Genes: ', Genelist['Signalling'].sum(), round(Genelist['Signalling'].sum()/Genelist['Genes'].count(),2)*100, '%', '\\n',\n",
    "     )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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