annotate_v.ipynb

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    "# annotate_v\n",
    "\n",
    "A simple-to-use Python script annotating VH or VL sequences of an antibody. It utilizes the REST API interface of [Abnum](http://www.bioinf.org.uk/abs/abnum/) from Dr Andrew Martin's group at UCL\n",
    "\n",
    "# Description\n",
    "User provides a single-letter amino acid sequence of the VH or VL chain of an antibody, and specifies an annotation scheme (Kabat, Chothia, or Contact, or IMGT).  The script sends a request to [Abnum](http://www.bioinf.org.uk/abs/abnum/), which returns a string with each residue matched to its number. The script then identifies FR and CDR regions using definitions outlined [here](http://www.bioinf.org.uk/abs/info.html#kabatnum)<sup>1</sup>. It prints out the amino acid sequence of the FRs and CDRs, and returns a `list` of 2 `dict`. The first `dict` consists of `region: seq` pairs. The second `dict` consists of `number:residue` pairs. \n",
    "\n",
    "<sup>1</sup>Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table, except that for IMGT, H-CDR2 is defined as **H51-H57** in this script, as opposed to of **H51-H56** in the table. This slight revision generates result that matches that from [IMGT website](http://www.imgt.org/)\n",
    "\n",
    "# Dependencies\n",
    "- Imports `requests` module\n",
    "\n",
    "# Examples of Usage\n"
   ]
  },
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   "cell_type": "markdown",
   "source": [
    "# Limitations\n",
    "- Relies on internet connection to [Abnum](http://www.bioinf.org.uk/abs/abnum/) website\n",
    "- Currently it can only annotate using Kabat, Chothia, or Contact, or IMGT scheme. One scheme each time\n",
    "- Incomplete VH or VL sequence might not be annotated \n",
    "\n",
    "\n"
   ],
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   "source": [
    "import requests\n",
    "\n",
    "class annotate():\n",
    "    \"\"\"\n",
    "    class `annotate`. \n",
    "    \n",
    "    Initiator `__init__` has 2 parameters:\n",
    "    \n",
    "    :param aaseq: STRING: A single-letter, amino acid sequence corresponding to the complete VH or VL chain. Both uppercase and lowercase are accepted. \n",
    "    \n",
    "    :param scheme: STRING: \"kabat\", \"chothia\", \"contact\", or \"imgt\". Must be in lowercase\n",
    "    \n",
    "    Class has 3 methods. `retrieve()`: retrieves numbered seqs from Abnum website, then sends it to method `analyze` to determine the FR and CDR regions, and to `output() ` to print the result and return a list of 2 dictionaries, the first of which contains to region:seq pairs, the second of which contains number:residue pairs. \n",
    "    \n",
    "    \"\"\"\n",
    "    \n",
    "    def __init__(self, aaseq, scheme):\n",
    "        \n",
    "        self.aaseq=aaseq\n",
    "        self.scheme=scheme\n",
    "    \n",
    "    def __repr__(self):\n",
    "        return \"Annotation of VH or VL sequence using Kabat, Chothia, Contact, or IMGT scheme\"\n",
    "    \n",
    "    def output(self, chain, lst, regionlst):\n",
    "        \"\"\"\n",
    "        Prints the FR and CDR regions and their corresponding seq. It returns a `list` of 2 `dict`. \n",
    "        \n",
    "        :param chain: STRING, either \"H\" or \"L\" in uppercase\n",
    "        :param lst:  LIST, a list of residue and their corresponding numbers in kabat or chothia scheme\n",
    "        :param regionlst: LIST, a list of peptides, each corresponds to a FR or CDR region\n",
    "        :return: LIST, a list of 2 `dict`, The first dict consists of region: seq pairs. The second dict consists of number:residue pairs.\n",
    "        \n",
    "        \"\"\"\n",
    "        \n",
    "        self.chain=chain\n",
    "        self.lst=lst\n",
    "        self.regionlst=regionlst\n",
    "\n",
    "        self.regiondict, self.numberdict={}, {}\n",
    "        \n",
    "        for i in range (0, len(self.lst), 2):\n",
    "            self.numberdict[self.lst[i]]=self.lst[i+1]\n",
    "        \n",
    "        \n",
    "        if self.scheme==\"kabat\":\n",
    "            print(\"Annotation in Kabat scheme:\")\n",
    "        elif self.scheme==\"chothia\":\n",
    "            print(\"Annotation in Chothia scheme:\")\n",
    "        elif self.scheme==\"contact\":\n",
    "            print(\"Annotation in Contact scheme:\")\n",
    "        else:\n",
    "            print(\"Annotation in IMGT scheme:\")\n",
    "        \n",
    "        if self.chain==\"L\":\n",
    "            print(\"L-FR1:  \", self.regionlst[0])\n",
    "            print(\"L-CDR1: \", self.regionlst[1])\n",
    "            print(\"L-FR2:  \", self.regionlst[2])\n",
    "            print(\"L-CDR2: \", self.regionlst[3])\n",
    "            print(\"L-FR3:  \", self.regionlst[4])\n",
    "            print(\"L-CDR3: \", self.regionlst[5])\n",
    "            print(\"L-FR4:  \", self.regionlst[6])\n",
    "            \n",
    "            for region, seq in zip([\"L-FR1\", \"L-CDR1\", \"L-FR2\",\"L-CDR2\", \"L-FR3\", \"L-CDR3\", \"L-FR4\"], self.regionlst):\n",
    "                self.regiondict[region]=seq\n",
    "            \n",
    "            return [self.regiondict, self.numberdict]\n",
    "                \n",
    "        else:\n",
    "            print(\"H-FR1:  \", self.regionlst[0])\n",
    "            print(\"H-CDR1: \", self.regionlst[1])\n",
    "            print(\"H-FR2:  \", self.regionlst[2])\n",
    "            print(\"H-CDR2: \", self.regionlst[3])\n",
    "            print(\"H-FR3:  \", self.regionlst[4])\n",
    "            print(\"H-CDR3: \", self.regionlst[5])\n",
    "            print(\"H-FR4:  \", self.regionlst[6])\n",
    "            \n",
    "            for region, seq in zip([\"H-FR1\", \"H-CDR1\", \"H-FR2\",\"H-CDR2\", \"H-FR3\", \"H-CDR3\", \"H-FR4\"], self.regionlst):\n",
    "                self.regiondict[region]=seq\n",
    "            \n",
    "            return [self.regiondict, self.numberdict]\n",
    "            \n",
    "        \n",
    "        \n",
    "        \n",
    "\n",
    "    \n",
    "    def analyze(self,chain, lst):\n",
    "        \"\"\"\n",
    "        Define CDR and FR regions based on the numbered sequence returned from website\n",
    "        \n",
    "        :param chain: STRING, \"H\" or \"L\" in uppercase\n",
    "        :param lst: LIST, a list of residue and their corresponding numbers in kabat or chothia scheme\n",
    "        :return: LIST, a list of strings, where each string is a peptide corresponding to the a region, in the order of: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4\n",
    "        \n",
    "        :raises: `ValueError` if any of the FR or CDR region is missing\n",
    "        \n",
    "        \"\"\"\n",
    "        \n",
    "        self.chain=chain\n",
    "        self.lst=lst\n",
    "        if self.chain==\"L\":\n",
    "            self.L_FR1, self.L_CDR1, self.L_FR2, self.L_CDR2, self.L_FR3, self.L_CDR3, self.L_FR4=[\"\" for i in range (0, 7)]\n",
    "            \n",
    "            try:\n",
    "                if self.scheme in [\"kabat\", \"chothia\"]:\n",
    "                    self.L_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"L24\"), 2)])\n",
    "                    self.L_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L24\"), self.lst.index(\"L35\"), 2)])\n",
    "                    self.L_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L35\"), self.lst.index(\"L50\"), 2)])\n",
    "                    self.L_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L50\"), self.lst.index(\"L57\"), 2)])\n",
    "                    self.L_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L57\"), self.lst.index(\"L89\"), 2)])\n",
    "                    self.L_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L89\"), self.lst.index(\"L98\"), 2)])\n",
    "                    self.L_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L98\"), len(self.lst), 2)])\n",
    "                                    \n",
    "                elif self.scheme ==\"contact\": \n",
    "                    self.L_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"L30\"), 2)])\n",
    "                    self.L_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L30\"), self.lst.index(\"L37\"), 2)])\n",
    "                    self.L_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L37\"), self.lst.index(\"L46\"), 2)])\n",
    "                    self.L_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L46\"), self.lst.index(\"L56\"), 2)])\n",
    "                    self.L_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L56\"), self.lst.index(\"L89\"), 2)])\n",
    "                    self.L_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L89\"), self.lst.index(\"L97\"), 2)])\n",
    "                    self.L_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L97\"), len(self.lst), 2)])\n",
    "                                    \n",
    "                else: #IMGT scheme\n",
    "                    self.L_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"L27\"), 2)])\n",
    "                    self.L_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L27\"), self.lst.index(\"L33\"), 2)])\n",
    "                    self.L_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L33\"), self.lst.index(\"L50\"), 2)])\n",
    "                    self.L_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L50\"), self.lst.index(\"L52\"), 2)])\n",
    "                    self.L_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L52\"), self.lst.index(\"L89\"), 2)])\n",
    "                    self.L_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L89\"), self.lst.index(\"L98\"), 2)])\n",
    "                    self.L_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"L98\"), len(self.lst), 2)])\n",
    "                \n",
    "                return [self.L_FR1, self.L_CDR1, self.L_FR2, self.L_CDR2, self.L_FR3, self.L_CDR3, self.L_FR4] \n",
    "\n",
    "            except ValueError:\n",
    "                print(\"Unable to retrieve complete V region. Make sure the sequence has complete V region\")\n",
    "            except:\n",
    "                print(\"An error occured\")\n",
    "        else:\n",
    "            self.H_FR1, self.H_CDR1, self.H_FR2, self.H_CDR2, self.H_FR3, self.H_CDR3, self.H_FR4=[\"\" for i in range (0, 7)]\n",
    "            try:\n",
    "                if self.scheme==\"kabat\":\n",
    "                    self.H_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"H31\"), 2)])\n",
    "                    self.H_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H31\"), self.lst.index(\"H36\"), 2)])\n",
    "                    self.H_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H36\"), self.lst.index(\"H50\"), 2)])\n",
    "                    self.H_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H50\"), self.lst.index(\"H66\"), 2)])\n",
    "                    self.H_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H66\"), self.lst.index(\"H95\"), 2)])\n",
    "                    self.H_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H95\"), self.lst.index(\"H103\"), 2)])\n",
    "                    self.H_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H103\"), len(self.lst), 2)])            \n",
    "            \n",
    "                elif self.scheme==\"chothia\":\n",
    "                    self.H_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"H26\"), 2)])\n",
    "                    self.H_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H26\"), self.lst.index(\"H33\"), 2)])\n",
    "                    self.H_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H33\"), self.lst.index(\"H52\"), 2)])\n",
    "                    self.H_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H52\"), self.lst.index(\"H57\"), 2)])\n",
    "                    self.H_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H57\"), self.lst.index(\"H95\"), 2)])\n",
    "                    self.H_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H95\"), self.lst.index(\"H103\"), 2)])\n",
    "                    self.H_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H103\"), len(self.lst), 2)])\n",
    "\n",
    "                elif self.scheme==\"contact\":\n",
    "                    self.H_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"H30\"), 2)])\n",
    "                    self.H_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H30\"), self.lst.index(\"H36\"), 2)])\n",
    "                    self.H_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H36\"), self.lst.index(\"H47\"), 2)])\n",
    "                    self.H_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H47\"), self.lst.index(\"H59\"), 2)])\n",
    "                    self.H_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H59\"), self.lst.index(\"H93\"), 2)])\n",
    "                    self.H_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H93\"), self.lst.index(\"H102\"), 2)])\n",
    "                    self.H_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H102\"), len(self.lst), 2)])\n",
    "                                        \n",
    "                else: #IMGT scheme\n",
    "                    self.H_FR1=\"\".join([self.lst[i+1] for i in range (0, self.lst.index(\"H26\"), 2)])\n",
    "                    self.H_CDR1=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H26\"), self.lst.index(\"H34\"), 2)])\n",
    "                    self.H_FR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H34\"), self.lst.index(\"H51\"), 2)])\n",
    "                    self.H_CDR2=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H51\"), self.lst.index(\"H58\"), 2)]) #51>57 (instead of 56)\n",
    "                    self.H_FR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H58\"), self.lst.index(\"H93\"), 2)])\n",
    "                    self.H_CDR3=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H93\"), self.lst.index(\"H103\"), 2)])\n",
    "                    self.H_FR4=\"\".join([self.lst[i+1] for i in range (self.lst.index(\"H103\"), len(self.lst), 2)])                    \n",
    "                \n",
    "                return [self.H_FR1, self.H_CDR1, self.H_FR2, self.H_CDR2, self.H_FR3, self.H_CDR3, self.H_FR4]                    \n",
    "\n",
    "            except ValueError:\n",
    "                print(\"Unable to retrieve complete V region. Make sure the sequence has complete V region\")\n",
    "            except:\n",
    "                print(\"An error occured in the `analyze()` method\")\n",
    "        \n",
    "    def retrieve (self):\n",
    "        \"\"\"\n",
    "        Retrieve numbered residues from Abnum website\n",
    "        \n",
    "        :return: returns same object from the `output()` method. \n",
    "        \n",
    "        :raises: `ValueError` if input scheme is not among \"kabat\", \"chothia\", \"contact\", and \"imgt\"\n",
    "        \n",
    "        \"\"\"\n",
    "        \n",
    "        self.url=\"http://www.bioinf.org.uk/abs/abnum/abnum.cgi\"\n",
    "        \n",
    "        try: \n",
    "            if self.scheme not in [\"kabat\", \"chothia\", \"contact\", \"imgt\"]:\n",
    "                raise Exception\n",
    "            \n",
    "        except ValueError:\n",
    "            print(\"Incorrect scheme mode. Must be one of the following (lowercase): kabat, chothia, contact, imgt\")\n",
    "        \n",
    "        else:\n",
    "            if self.scheme==\"kabat\":\n",
    "                self.sche=\"-k\"\n",
    "            else:\n",
    "                self.sche=\"-c\"\n",
    "        \n",
    "        try:\n",
    "            self.d={\"plain\":1, \"scheme\":self.sche, \"aaseq\":self.aaseq}\n",
    "            self.myPage=requests.get(self.url, params=self.d)\n",
    "            self.text=self.myPage.text\n",
    "            self.lst=self.text.split()\n",
    "                \n",
    "            if len(self.lst)>1:\n",
    "                self.chain=self.lst[0][0]\n",
    "                self.result=self.output(self.chain, self.lst, self.analyze(self.chain, self.lst))\n",
    "                return self.result\n",
    "            else:\n",
    "                print(\"No annotation retrieved. Did you enter the complete VH or VL sequence?\")\n",
    "        except:\n",
    "            print(\"An error occured in the `retrieve()` method\")\n",
    "                "
   ],
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   "outputs": [
    {
     "name": "stdout",
     "text": [
      "Annotation in Chothia scheme:\n",
      "H-FR1:   QVQLVQPGAEVVKPGASVKLSCKTS\n",
      "H-CDR1:  GYTFTSN\n",
      "H-FR2:   WMHWVKQAPGQGLEWIGEI\n",
      "H-CDR2:  DPSDSY\n",
      "H-FR3:   TNYNQNFQGKAKLTVDKSTSTAYMEVSSLRSDDTAVYYCAR\n",
      "H-CDR3:  GSNPYYYAMDY\n",
      "H-FR4:   WGQGTSVTVSS\n",
      "{'H-FR1': 'QVQLVQPGAEVVKPGASVKLSCKTS', 'H-CDR1': 'GYTFTSN', 'H-FR2': 'WMHWVKQAPGQGLEWIGEI', 'H-CDR2': 'DPSDSY', 'H-FR3': 'TNYNQNFQGKAKLTVDKSTSTAYMEVSSLRSDDTAVYYCAR', 'H-CDR3': 'GSNPYYYAMDY', 'H-FR4': 'WGQGTSVTVSS'}\n",
      "{'H1': 'Q', 'H2': 'V', 'H3': 'Q', 'H4': 'L', 'H5': 'V', 'H6': 'Q', 'H7': 'P', 'H8': 'G', 'H9': 'A', 'H10': 'E', 'H11': 'V', 'H12': 'V', 'H13': 'K', 'H14': 'P', 'H15': 'G', 'H16': 'A', 'H17': 'S', 'H18': 'V', 'H19': 'K', 'H20': 'L', 'H21': 'S', 'H22': 'C', 'H23': 'K', 'H24': 'T', 'H25': 'S', 'H26': 'G', 'H27': 'Y', 'H28': 'T', 'H29': 'F', 'H30': 'T', 'H31': 'S', 'H32': 'N', 'H33': 'W', 'H34': 'M', 'H35': 'H', 'H36': 'W', 'H37': 'V', 'H38': 'K', 'H39': 'Q', 'H40': 'A', 'H41': 'P', 'H42': 'G', 'H43': 'Q', 'H44': 'G', 'H45': 'L', 'H46': 'E', 'H47': 'W', 'H48': 'I', 'H49': 'G', 'H50': 'E', 'H51': 'I', 'H52': 'D', 'H52A': 'P', 'H53': 'S', 'H54': 'D', 'H55': 'S', 'H56': 'Y', 'H57': 'T', 'H58': 'N', 'H59': 'Y', 'H60': 'N', 'H61': 'Q', 'H62': 'N', 'H63': 'F', 'H64': 'Q', 'H65': 'G', 'H66': 'K', 'H67': 'A', 'H68': 'K', 'H69': 'L', 'H70': 'T', 'H71': 'V', 'H72': 'D', 'H73': 'K', 'H74': 'S', 'H75': 'T', 'H76': 'S', 'H77': 'T', 'H78': 'A', 'H79': 'Y', 'H80': 'M', 'H81': 'E', 'H82': 'V', 'H82A': 'S', 'H82B': 'S', 'H82C': 'L', 'H83': 'R', 'H84': 'S', 'H85': 'D', 'H86': 'D', 'H87': 'T', 'H88': 'A', 'H89': 'V', 'H90': 'Y', 'H91': 'Y', 'H92': 'C', 'H93': 'A', 'H94': 'R', 'H95': 'G', 'H96': 'S', 'H97': 'N', 'H98': 'P', 'H99': 'Y', 'H100': 'Y', 'H100A': 'Y', 'H100B': 'A', 'H100C': 'M', 'H101': 'D', 'H102': 'Y', 'H103': 'W', 'H104': 'G', 'H105': 'Q', 'H106': 'G', 'H107': 'T', 'H108': 'S', 'H109': 'V', 'H110': 'T', 'H111': 'V', 'H112': 'S', 'H113': 'S'}\n"
     ],
     "output_type": "stream"
    }
   ],
   "source": [
    "aaseq=\"QVQLVQPGAEVVKPGASVKLSCKTSGYTFTSNWMHWVKQAPGQGLEWIGEIDPSDSYTNYNQNFQGKAKLTVDKSTSTAYMEVSSLRSDDTAVYYCARGSNPYYYAMDYWGQGTSVTVSS\"\n",
    "#aaseq=\"EIVLTQSPAIMSASPGERVTMTCSASSGVNYMHWYQQKPGTSPRRWIYDTSKLASGVPARFSGSGSGTDYSLTISSMEPEDAATYYCHQRGSYTFGGGTKLEIK\"\n",
    "scheme=\"chothia\"\n",
    "\n",
    "seq=annotate(aaseq,scheme)\n",
    "\n",
    "result=seq.retrieve()\n",
    "\n",
    "print(result[0])\n",
    "print(result[1])\n"
   ],
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