{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Retrieve Uniprot data using python \n",
    "\n",
    "In this Mini-tool I will show you to retrieve data from Uniprot using a PDB ID or an Uniprot ID directly on python. I wrote this function based on the Uniprot [programmatic access for python](https://www.uniprot.org/help/api_idmapping). Despite in essence is the same idea, I did minor modifications to retrieve the data as a plain text from which would be easier to extract useful data.\n",
    "\n",
    "Let's put the hands on it."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## The python funtion"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import urllib\n",
    "from bs4 import BeautifulSoup\n",
    "\n",
    "def get_uniprot (query='',query_type='PDB_ID'):\n",
    "    #query_type must be: \"PDB_ID\" or \"ACC\"\n",
    "    url = 'https://www.uniprot.org/uploadlists/' #This is the webser to retrieve the Uniprot data\n",
    "    params = {\n",
    "    'from':query_type,\n",
    "    'to':'ACC',\n",
    "    'format':'txt',\n",
    "    'query':query\n",
    "    }\n",
    "\n",
    "    data = urllib.parse.urlencode(params)\n",
    "    data = data.encode('ascii')\n",
    "    request = urllib.request.Request(url, data)\n",
    "    with urllib.request.urlopen(request) as response:\n",
    "        res = response.read()\n",
    "        page=BeautifulSoup(res).get_text()\n",
    "        page=page.splitlines()\n",
    "    return page"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This very simple function will allow us to save Uniprot data for a PDB entry or Uniprot entry into a list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### PDB entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ID   ACES_TETCF              Reviewed;         586 AA.',\n",
       " 'AC   P04058;',\n",
       " 'DT   01-NOV-1986, integrated into UniProtKB/Swiss-Prot.',\n",
       " 'DT   01-JUN-1994, sequence version 2.',\n",
       " 'DT   16-OCT-2019, entry version 170.',\n",
       " 'DE   RecName: Full=Acetylcholinesterase;',\n",
       " 'DE            Short=AChE;',\n",
       " 'DE            EC=3.1.1.7;',\n",
       " 'DE   Flags: Precursor;',\n",
       " 'GN   Name=ache;']"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x=get_uniprot(query='1eve',query_type='PDB_ID')\n",
    "x[:10] #Just get the first 10 lines of data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Uniprot entry"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['ID   ACES_TETCF              Reviewed;         586 AA.',\n",
       " 'AC   P04058;',\n",
       " 'DT   01-NOV-1986, integrated into UniProtKB/Swiss-Prot.',\n",
       " 'DT   01-JUN-1994, sequence version 2.',\n",
       " 'DT   16-OCT-2019, entry version 170.',\n",
       " 'DE   RecName: Full=Acetylcholinesterase;',\n",
       " 'DE            Short=AChE;',\n",
       " 'DE            EC=3.1.1.7;',\n",
       " 'DE   Flags: Precursor;',\n",
       " 'GN   Name=ache;']"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "y=get_uniprot(query='P04058',query_type='ACC')\n",
    "y[:10] #Just get the first 10 lines of data"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Another examples\n",
    "\n",
    "Because all the data info is available through a list, it is very easy to find the info that we are interested in, the annotated Gene Ontology for instance."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DR   GO; GO:0031225; C:anchored component of membrane; IEA:UniProtKB-KW.\n",
      "DR   GO; GO:0030054; C:cell junction; IEA:UniProtKB-KW.\n",
      "DR   GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.\n",
      "DR   GO; GO:0043083; C:synaptic cleft; IEA:GOC.\n",
      "DR   GO; GO:0003990; F:acetylcholinesterase activity; IEA:UniProtKB-EC.\n",
      "DR   GO; GO:0001507; P:acetylcholine catabolic process in synaptic cleft; IEA:InterPro.\n"
     ]
    }
   ],
   "source": [
    "for line in y:\n",
    "    if 'DR   GO;' in line:\n",
    "        print (line)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Or all reported PDB's for desired protein including experimental methodology, resolution, and length."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "DR   PDB; 1ACJ; X-ray; 2.80 A; A=22-556.\n",
      "DR   PDB; 1ACL; X-ray; 2.80 A; A=22-556.\n",
      "DR   PDB; 1AMN; X-ray; 2.80 A; A=22-558.\n",
      "DR   PDB; 1AX9; X-ray; 2.80 A; A=22-558.\n",
      "DR   PDB; 1CFJ; X-ray; 2.60 A; A=22-558.\n",
      "DR   PDB; 1DX6; X-ray; 2.30 A; A=22-564.\n",
      "DR   PDB; 1E3Q; X-ray; 2.85 A; A=22-564.\n",
      "DR   PDB; 1E66; X-ray; 2.10 A; A=22-564.\n",
      "DR   PDB; 1EA5; X-ray; 1.80 A; A=22-558.\n",
      "DR   PDB; 1EEA; X-ray; 4.50 A; A=22-555.\n",
      "DR   PDB; 1EVE; X-ray; 2.50 A; A=22-564.\n",
      "DR   PDB; 1FSS; X-ray; 3.00 A; A=22-558.\n",
      "DR   PDB; 1GPK; X-ray; 2.10 A; A=22-558.\n",
      "DR   PDB; 1GPN; X-ray; 2.35 A; A=22-558.\n",
      "DR   PDB; 1GQR; X-ray; 2.20 A; A=25-556.\n",
      "DR   PDB; 1GQS; X-ray; 3.00 A; A=25-556.\n",
      "DR   PDB; 1H22; X-ray; 2.15 A; A=22-564.\n",
      "DR   PDB; 1H23; X-ray; 2.15 A; A=22-564.\n",
      "DR   PDB; 1HBJ; X-ray; 2.50 A; A=22-564.\n",
      "DR   PDB; 1JGA; Model; -; A=1-586.\n",
      "DR   PDB; 1JGB; Model; -; A=1-586.\n",
      "DR   PDB; 1JJB; X-ray; 2.30 A; A=25-556.\n",
      "DR   PDB; 1OCE; X-ray; 2.70 A; A=22-558.\n",
      "DR   PDB; 1ODC; X-ray; 2.20 A; A=22-564.\n",
      "DR   PDB; 1QID; X-ray; 2.05 A; A=22-558.\n",
      "DR   PDB; 1QIE; X-ray; 2.10 A; A=22-558.\n",
      "DR   PDB; 1QIF; X-ray; 2.10 A; A=22-558.\n",
      "DR   PDB; 1QIG; X-ray; 2.30 A; A=22-558.\n",
      "DR   PDB; 1QIH; X-ray; 2.50 A; A=22-558.\n",
      "DR   PDB; 1QII; X-ray; 2.65 A; A=22-558.\n",
      "DR   PDB; 1QIJ; X-ray; 2.80 A; A=22-558.\n",
      "DR   PDB; 1QIK; X-ray; 2.90 A; A=22-558.\n",
      "DR   PDB; 1QIM; X-ray; 3.00 A; A=22-558.\n",
      "DR   PDB; 1QTI; X-ray; 2.50 A; A=22-558.\n",
      "DR   PDB; 1SOM; X-ray; 2.20 A; A=22-564.\n",
      "DR   PDB; 1U65; X-ray; 2.61 A; A=22-564.\n",
      "DR   PDB; 1UT6; X-ray; 2.40 A; A=22-556.\n",
      "DR   PDB; 1VOT; X-ray; 2.50 A; A=22-558.\n",
      "DR   PDB; 1VXO; X-ray; 2.40 A; A=22-558.\n",
      "DR   PDB; 1VXR; X-ray; 2.20 A; A=22-558.\n",
      "DR   PDB; 1W4L; X-ray; 2.16 A; A=22-564.\n",
      "DR   PDB; 1W6R; X-ray; 2.05 A; A=22-564.\n",
      "DR   PDB; 1W75; X-ray; 2.40 A; A/B=22-564.\n",
      "DR   PDB; 1W76; X-ray; 2.30 A; A/B=22-564.\n",
      "DR   PDB; 1ZGB; X-ray; 2.30 A; A=22-564.\n",
      "DR   PDB; 1ZGC; X-ray; 2.10 A; A/B=22-564.\n",
      "DR   PDB; 2ACE; X-ray; 2.50 A; A=22-558.\n",
      "DR   PDB; 2ACK; X-ray; 2.40 A; A=22-558.\n",
      "DR   PDB; 2BAG; X-ray; 2.40 A; A=22-564.\n",
      "DR   PDB; 2C4H; X-ray; 2.15 A; A=22-558.\n",
      "DR   PDB; 2C58; X-ray; 2.30 A; A=22-558.\n",
      "DR   PDB; 2C5F; X-ray; 2.60 A; A=22-558.\n",
      "DR   PDB; 2C5G; X-ray; 1.95 A; A=22-558.\n",
      "DR   PDB; 2CEK; X-ray; 2.20 A; A=22-556.\n",
      "DR   PDB; 2CKM; X-ray; 2.15 A; A=22-564.\n",
      "DR   PDB; 2CMF; X-ray; 2.50 A; A=22-564.\n",
      "DR   PDB; 2DFP; X-ray; 2.30 A; A=23-556.\n",
      "DR   PDB; 2J3D; X-ray; 2.60 A; A=22-564.\n",
      "DR   PDB; 2J3Q; X-ray; 2.80 A; A=22-564.\n",
      "DR   PDB; 2J4F; X-ray; 2.80 A; A=22-564.\n",
      "DR   PDB; 2V96; X-ray; 2.40 A; A/B=22-558.\n",
      "DR   PDB; 2V97; X-ray; 2.40 A; A/B=22-558.\n",
      "DR   PDB; 2V98; X-ray; 3.00 A; A/B=22-558.\n",
      "DR   PDB; 2VA9; X-ray; 2.40 A; A/B=22-558.\n",
      "DR   PDB; 2VJA; X-ray; 2.30 A; A/B=22-558.\n",
      "DR   PDB; 2VJB; X-ray; 2.39 A; A/B=22-558.\n",
      "DR   PDB; 2VJC; X-ray; 2.20 A; A/B=22-558.\n",
      "DR   PDB; 2VJD; X-ray; 2.30 A; A/B=22-558.\n",
      "DR   PDB; 2VQ6; X-ray; 2.71 A; A=22-564.\n",
      "DR   PDB; 2VT6; X-ray; 2.40 A; A/B=22-558.\n",
      "DR   PDB; 2VT7; X-ray; 2.20 A; A/B=22-558.\n",
      "DR   PDB; 2W6C; X-ray; 2.69 A; X=1-586.\n",
      "DR   PDB; 2WFZ; X-ray; 1.95 A; A=22-558.\n",
      "DR   PDB; 2WG0; X-ray; 2.20 A; A=22-558.\n",
      "DR   PDB; 2WG1; X-ray; 2.20 A; A=22-558.\n",
      "DR   PDB; 2WG2; X-ray; 1.95 A; A=22-558.\n",
      "DR   PDB; 2XI4; X-ray; 2.30 A; A/B=22-558.\n",
      "DR   PDB; 3ACE; Model; -; A=22-558.\n",
      "DR   PDB; 3GEL; X-ray; 2.39 A; A=25-556.\n",
      "DR   PDB; 3I6M; X-ray; 2.26 A; A=23-556.\n",
      "DR   PDB; 3I6Z; X-ray; 2.19 A; A=23-556.\n",
      "DR   PDB; 3M3D; X-ray; 2.34 A; A=22-564.\n",
      "DR   PDB; 3ZV7; X-ray; 2.26 A; A=22-564.\n",
      "DR   PDB; 4ACE; Model; -; A=22-558.\n",
      "DR   PDB; 4TVK; X-ray; 2.30 A; A=23-556.\n",
      "DR   PDB; 4W63; X-ray; 2.80 A; A=23-556.\n",
      "DR   PDB; 4X3C; X-ray; 2.60 A; A=23-556.\n",
      "DR   PDB; 5BWB; X-ray; 2.57 A; A=22-558.\n",
      "DR   PDB; 5BWC; X-ray; 2.45 A; A=22-558.\n",
      "DR   PDB; 5DLP; X-ray; 2.70 A; A=22-564.\n",
      "DR   PDB; 5E2I; X-ray; 2.65 A; A=25-556.\n",
      "DR   PDB; 5E4J; X-ray; 2.54 A; A=25-556.\n",
      "DR   PDB; 5E4T; X-ray; 2.43 A; A=22-564.\n",
      "DR   PDB; 5EHX; X-ray; 2.10 A; A=25-556.\n",
      "DR   PDB; 5EI5; X-ray; 2.10 A; A=23-556.\n",
      "DR   PDB; 5IH7; X-ray; 2.40 A; A=23-556.\n",
      "DR   PDB; 5NAP; X-ray; 2.17 A; A=22-564.\n",
      "DR   PDB; 5NAU; X-ray; 2.25 A; A=22-564.\n",
      "DR   PDB; 5NUU; X-ray; 2.50 A; A=22-564.\n",
      "DR   PDB; 6EUC; X-ray; 2.22 A; A=25-556.\n",
      "DR   PDB; 6EUE; X-ray; 2.00 A; A=24-556.\n",
      "DR   PDB; 6EWK; X-ray; 2.22 A; A=25-556.\n",
      "DR   PDB; 6EZG; X-ray; 2.20 A; A/B=22-558.\n",
      "DR   PDB; 6EZH; X-ray; 2.60 A; A/B=22-558.\n",
      "DR   PDB; 6FLD; X-ray; 2.40 A; A=25-556.\n",
      "DR   PDB; 6FQN; X-ray; 2.30 A; A=25-556.\n",
      "DR   PDB; 6G17; X-ray; 2.20 A; A=22-558.\n",
      "DR   PDB; 6G1U; X-ray; 1.79 A; A/B=22-586.\n",
      "DR   PDB; 6G1V; X-ray; 1.82 A; A/B=22-586.\n",
      "DR   PDB; 6G1W; X-ray; 1.90 A; A/B=22-586.\n",
      "DR   PDB; 6G4M; X-ray; 2.63 A; A/B=22-558.\n",
      "DR   PDB; 6G4N; X-ray; 2.90 A; A/B=22-558.\n",
      "DR   PDB; 6G4O; X-ray; 2.78 A; A/B=22-558.\n",
      "DR   PDB; 6G4P; X-ray; 2.83 A; A/B=22-558.\n",
      "DR   PDB; 6H12; X-ray; 2.20 A; A/B=22-586.\n",
      "DR   PDB; 6H13; X-ray; 2.80 A; A/B=22-586.\n",
      "DR   PDB; 6H14; X-ray; 1.86 A; A/B=22-586.\n"
     ]
    }
   ],
   "source": [
    "for line in y:\n",
    "    if 'DR   PDB;' in line:\n",
    "        print (line)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The main use for which I created this function is to store data of a list of proteins (PDB entries or Uniprot entries) into a single table. For example:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd #To create our table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "prots=['P40926','O43175','Q9UM73']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "table=pd.DataFrame()\n",
    "for index,entry in enumerate(prots):\n",
    "    pdbs=[]\n",
    "    funtions=[]\n",
    "    process=[]\n",
    "    organism=[]\n",
    "    data=get_uniprot(query=entry,query_type='ACC')\n",
    "    \n",
    "    table.loc[index,'Uniprot_entry']=entry\n",
    "    \n",
    "    for line in data:\n",
    "        if 'OS   ' in line:\n",
    "            line=line.strip().replace('OS   ','').replace('.','')\n",
    "            organism.append(line)\n",
    "            table.loc[index,'Organism']=(\", \".join(list(set(organism))))\n",
    "\n",
    "        if 'DR   PDB;' in line:\n",
    "            line=line.strip().replace('DR   ','').replace(';','')\n",
    "            pdbs.append ((line.split()[1]+':'+line.split()[3]))\n",
    "            table.loc[index,'PDB:Resol']=(\", \".join(list(set(pdbs))))\n",
    "\n",
    "        if 'DR   GO; GO:' in line:\n",
    "            line=line.strip().replace('DR   GO; GO:','').replace(';','').split(':')\n",
    "            if 'F' in line[0]:\n",
    "                funtions.append(line[1])\n",
    "                table.loc[index,'GO_funtion']=(\", \".join(list(set(funtions))))\n",
    "            else:\n",
    "                process.append (line[1])\n",
    "                table.loc[index,'GO_process']=(\", \".join(list(set(process))))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "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>Uniprot_entry</th>\n",
       "      <th>Organism</th>\n",
       "      <th>PDB:Resol</th>\n",
       "      <th>GO_process</th>\n",
       "      <th>GO_funtion</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>P40926</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>2DFD:1.90, 4WLV:2.40, 4WLF:2.20, 4WLU:2.14, 4W...</td>\n",
       "      <td>tricarboxylic acid cycle IBA, aerobic respirat...</td>\n",
       "      <td>L-malate dehydrogenase activity IDA, malate de...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>O43175</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>6RJ5:1.89, 6RIH:2.15, 6RJ3:1.42, 6RJ2:2.00, 5N...</td>\n",
       "      <td>glycine metabolic process IEA, L-serine biosyn...</td>\n",
       "      <td>phosphoglycerate dehydrogenase activity IBA, e...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Q9UM73</td>\n",
       "      <td>Homo sapiens (Human)</td>\n",
       "      <td>3L9P:1.80, 4CMT:1.73, 4FNY:2.45, 5AAB:2.20, 2X...</td>\n",
       "      <td>activation of MAPK activity TAS, adult behavio...</td>\n",
       "      <td>ATP binding IEA, identical protein binding IPI...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Uniprot_entry              Organism  \\\n",
       "0        P40926  Homo sapiens (Human)   \n",
       "1        O43175  Homo sapiens (Human)   \n",
       "2        Q9UM73  Homo sapiens (Human)   \n",
       "\n",
       "                                           PDB:Resol  \\\n",
       "0  2DFD:1.90, 4WLV:2.40, 4WLF:2.20, 4WLU:2.14, 4W...   \n",
       "1  6RJ5:1.89, 6RIH:2.15, 6RJ3:1.42, 6RJ2:2.00, 5N...   \n",
       "2  3L9P:1.80, 4CMT:1.73, 4FNY:2.45, 5AAB:2.20, 2X...   \n",
       "\n",
       "                                          GO_process  \\\n",
       "0  tricarboxylic acid cycle IBA, aerobic respirat...   \n",
       "1  glycine metabolic process IEA, L-serine biosyn...   \n",
       "2  activation of MAPK activity TAS, adult behavio...   \n",
       "\n",
       "                                          GO_funtion  \n",
       "0  L-malate dehydrogenase activity IDA, malate de...  \n",
       "1  phosphoglycerate dehydrogenase activity IBA, e...  \n",
       "2  ATP binding IEA, identical protein binding IPI...  "
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "table"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Saving the table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "table.to_csv('Uniprot_search.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    ".. disqus::"
   ]
  }
 ],
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