Get Protein Names i.e. Synonyms.ipynb

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    "### Get UniProt Protein Names/Synonyms"
   ]
  },
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   "id": "67d915a2",
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   "source": [
    "import pandas as pd, requests\n",
    "# IDs = ... whatever the list of your proteins' UniProt IDs are"
   ]
  },
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   "source": [
    "def get_short_full_names(names, section_key, section_values):\n",
    "    '''\n",
    "    FUNCTION:\n",
    "    - Get all names from an entry\n",
    "    \n",
    "    PARAMS:\n",
    "    - names (list)\n",
    "    '''\n",
    "    # Full name\n",
    "    if section_key == 'fullName':\n",
    "        name = section_values['value']\n",
    "        names.append(name)\n",
    "\n",
    "    # Short names\n",
    "    if section_key == 'shortNames':\n",
    "        for entry in section_values:\n",
    "            name = entry['value']\n",
    "            names.append(name)  \n",
    "            \n",
    "    # EC Numbers\n",
    "    if section_key == 'ecNumbers':\n",
    "         for entry in section_values:\n",
    "            name = entry['value']\n",
    "            names.append(name) \n",
    "            \n",
    "    return names\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "id2syns = dict()\n",
    "\n",
    "SIZE = str(500)\n",
    "\n",
    "# For each ID, get the protein names (one protein at a time)\n",
    "for index, ID in enumerate(IDs):\n",
    "    print(index+1,'/',len(IDs),end='\\r')\n",
    "    names = list()\n",
    "    \n",
    "    # Get data via UniProt API \n",
    "    url = 'https://rest.uniprot.org/uniprotkb/search?fields=accession,protein_name,ec&format=json&query='\\\n",
    "           +ID+'&size='+SIZE\n",
    "    res = requests.get(url).json()\n",
    "    r = res['results'][0]['proteinDescription']\n",
    "\n",
    "    \n",
    "    \n",
    "    ### Recommended name ###\n",
    "    try:\n",
    "        # Find sections\n",
    "        rec_name_section = r['recommendedName']\n",
    "        for section_key, section_values in rec_name_section.items():\n",
    "            \n",
    "            # Get names\n",
    "            names = get_short_full_names(names, section_key, section_values)\n",
    "            \n",
    "        print(ID, rec_name_section)\n",
    "        print(names)\n",
    "    except:\n",
    "        pass\n",
    "    \n",
    "    \n",
    "    ### Alternative Names ###\n",
    "    try:\n",
    "        # Find sections\n",
    "        alt_name_section = r['alternativeNames']\n",
    "        for entry in alt_name_section:\n",
    "            for section_key, section_values in entry.items():\n",
    "                \n",
    "                # Get names\n",
    "                names = get_short_full_names(names, section_key, section_values)\n",
    "    except:\n",
    "        pass\n",
    "    \n",
    "    \n",
    "    ### Submitted Names ###\n",
    "    try:\n",
    "        # Find sections\n",
    "        sub_name_section = r['submissionNames']\n",
    "        for entry in sub_name_section:\n",
    "            for section_key, section_values in entry.items():\n",
    "\n",
    "                # Get names\n",
    "                names = get_short_full_names(names, section_key, section_values)     \n",
    "    except:\n",
    "        pass\n",
    "    \n",
    "    \n",
    "    id2syns[ID] = names\n",
    "    \n",
    "json.dump(id2syns, open('input/id2names_not_case_varied.json','w'))"
   ]
  }
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