nipah_analysis.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "38881d81",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "pandas 1.3.4\n",
      "biopython 1.79\n"
     ]
    }
   ],
   "source": [
    "import pandas\n",
    "import Bio\n",
    "from Bio.Seq import Seq\n",
    "print('pandas',pandas.__version__)\n",
    "print('biopython',Bio.__version__)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "260d52f7",
   "metadata": {},
   "outputs": [],
   "source": [
    "# accession id : NC_002728 Nipah virus, complete genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d4d95f19",
   "metadata": {},
   "outputs": [],
   "source": [
    "## entrez search for nucleotide"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "b1fc3875",
   "metadata": {},
   "outputs": [],
   "source": [
    "from Bio import Entrez, SeqIO\n",
    "Entrez.email = \"\" \n",
    "handle = Entrez.efetch(db=\"nucleotide\", id=\"NC_002728\", rettype=\"gb\", retmode=\"text\")\n",
    "recs = list(SeqIO.parse(handle, 'gb'))\n",
    "handle.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "6c8194e3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[SeqRecord(seq=Seq('ACCAAACAAGGGAGAATATGGATACGTTAAAATATATAACGTATTTTTAAAACT...GGT'), id='NC_002728.1', name='NC_002728', description='Nipah virus, complete genome', dbxrefs=['Project:15443', 'BioProject:PRJNA485481'])]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "recs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "c33ad811",
   "metadata": {},
   "outputs": [],
   "source": [
    "nipah_dna = recs[0].seq"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "d58ccbc9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('ACCAAACAAGGGAGAATATGGATACGTTAAAATATATAACGTATTTTTAAAACT...GGT')"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "nipah_dna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "a4b11627",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The genome of Nipah consists of 18246 nucleotides.\n"
     ]
    }
   ],
   "source": [
    "print(f'The genome of Nipah consists of {len(nipah_dna)} nucleotides.')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "46652788",
   "metadata": {},
   "outputs": [],
   "source": [
    "## chemical and physical property of the nucleotide molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "219c88e8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "5647061.569500455"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# molecular weight\n",
    "from Bio.SeqUtils import molecular_weight\n",
    "molecular_weight(nipah_dna)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "53229ea2",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "38.16726953852899"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# GC content - higher GC content implies more stable molecule due to G and C forming triple hydrogen bonds\n",
    "from Bio.SeqUtils import GC\n",
    "GC(nipah_dna)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3098fe63",
   "metadata": {},
   "source": [
    "## nucleotide distribution"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "25ca1e10",
   "metadata": {},
   "outputs": [],
   "source": [
    "count_nucleotides = {\n",
    "    'A': nipah_dna.count('A'),\n",
    "    'T': nipah_dna.count('T'),\n",
    "    'C': nipah_dna.count('C'),\n",
    "    'G': nipah_dna.count('G')\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "ac10d2ed",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'A': 6176, 'T': 5106, 'C': 3326, 'G': 3638}"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "count_nucleotides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4a3d127f",
   "metadata": {},
   "outputs": [],
   "source": [
    "##plotting of nucleotides"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "229ea8f3",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 1.0, 'Nucleotide Frequency')"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "width = 0.5\n",
    "plt.bar(count_nucleotides.keys(), count_nucleotides.values(), width, color=['b', 'r', 'm', 'c'])\n",
    "plt.xlabel('Nucleotide')\n",
    "plt.ylabel('Frequency')\n",
    "plt.title('Nucleotide Frequency')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "14e90c87",
   "metadata": {},
   "outputs": [],
   "source": [
    "## transcription of dna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "bb63b9f0",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('ACCAAACAAGGGAGAAUAUGGAUACGUUAAAAUAUAUAACGUAUUUUUAAAACU...GGU')"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## nipah dna to mrna\n",
    "nipah_mrna = nipah_dna.transcribe()\n",
    "nipah_mrna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d9156c68",
   "metadata": {},
   "outputs": [],
   "source": [
    "## transaltion of mrna"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "5194b22d",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('TKQGRIWIR*NI*RIFKT*EPRQTLLVLVLDPQEIYHHE*YL*RGG*F*ELSI*...LFG')"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## nipah mrna to amino acid\n",
    "nipah_aa = nipah_mrna.translate()\n",
    "nipah_aa"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "05e474e8",
   "metadata": {},
   "outputs": [],
   "source": [
    "## counting aminoacids in the total aminoacids coded by genome"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "9b30923c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('L', 720),\n",
       " ('S', 504),\n",
       " ('*', 483),\n",
       " ('I', 463),\n",
       " ('R', 382),\n",
       " ('T', 364),\n",
       " ('K', 359),\n",
       " ('Q', 322),\n",
       " ('N', 266),\n",
       " ('V', 245)]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "#most common amino acids\n",
    "from collections import Counter\n",
    "common_amino = Counter(nipah_aa)\n",
    "common_amino.most_common(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e6039404",
   "metadata": {},
   "outputs": [],
   "source": [
    "## amino acid distribution is plotted"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ea32feb8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Text(0.5, 1.0, 'Protein Sequence Frequency')"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {
      "needs_background": "light"
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "del common_amino['*']\n",
    "\n",
    "width = 0.5\n",
    "plt.bar(common_amino.keys(), common_amino.values(), width, color=['b', 'r', 'm', 'c'])\n",
    "plt.xlabel('Amino Acid')\n",
    "plt.ylabel('Frequency')\n",
    "plt.title('Protein Sequence Frequency')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "db59c5c2",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "nipah's genome has 5599 amino acids\n"
     ]
    }
   ],
   "source": [
    "print(f\"nipah's genome has {sum(common_amino.values())} amino acids\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "4ef6fde6",
   "metadata": {},
   "outputs": [],
   "source": [
    "## splitting of amino acid chains"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "e66f3f4f",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Seq('TKQGRIWIR'),\n",
       " Seq('NI'),\n",
       " Seq('RIFKT'),\n",
       " Seq('EPRQTLLVLVLDPQEIYHHE'),\n",
       " Seq('YL')]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proteins = nipah_aa.split('*')\n",
    "proteins[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "31bd3736",
   "metadata": {},
   "outputs": [],
   "source": [
    "## removing aminoacid chain which is less than 20 amino acid"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "e38ad583",
   "metadata": {},
   "outputs": [],
   "source": [
    "for protein in proteins:\n",
    "    if len(protein) < 20:\n",
    "        proteins.remove(protein)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "547c6c66",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "We have 271 proteins with more than 20 amino acids in the covid-19 genome\n"
     ]
    }
   ],
   "source": [
    "print(f'We have {len(proteins)} proteins with more than 20 amino acids in the covid-19 genome')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0e0dbd5e",
   "metadata": {},
   "outputs": [],
   "source": [
    "##sorting protein based on length"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "aa4475e3",
   "metadata": {},
   "outputs": [],
   "source": [
    "top_5_proteins = sorted(proteins, key = len)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "f0b4caf8",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq(''),\n",
       " Seq('N'),\n",
       " Seq('Y'),\n",
       " Seq('G'),\n",
       " Seq('I'),\n",
       " Seq('A'),\n",
       " Seq('Y'),\n",
       " Seq('G'),\n",
       " Seq('K'),\n",
       " Seq('Y'),\n",
       " Seq('R'),\n",
       " Seq('T'),\n",
       " Seq('I'),\n",
       " Seq('G'),\n",
       " Seq('L'),\n",
       " Seq('NI'),\n",
       " Seq('TP'),\n",
       " Seq('RC'),\n",
       " Seq('HL'),\n",
       " Seq('FF'),\n",
       " Seq('PV'),\n",
       " Seq('IL'),\n",
       " Seq('KT'),\n",
       " Seq('GI'),\n",
       " Seq('MY'),\n",
       " Seq('AK'),\n",
       " Seq('FI'),\n",
       " Seq('LI'),\n",
       " Seq('ML'),\n",
       " Seq('LC'),\n",
       " Seq('RGG'),\n",
       " Seq('PRH'),\n",
       " Seq('PSL'),\n",
       " Seq('STL'),\n",
       " Seq('LVT'),\n",
       " Seq('TIQ'),\n",
       " Seq('LVN'),\n",
       " Seq('FQP'),\n",
       " Seq('TRN'),\n",
       " Seq('EED'),\n",
       " Seq('KME'),\n",
       " Seq('EHY'),\n",
       " Seq('PEL'),\n",
       " Seq('YQI'),\n",
       " Seq('PTT'),\n",
       " Seq('TII'),\n",
       " Seq('MRM'),\n",
       " Seq('SQS'),\n",
       " Seq('REG'),\n",
       " Seq('VCI'),\n",
       " Seq('QLH'),\n",
       " Seq('RGN'),\n",
       " Seq('RRY'),\n",
       " Seq('YPR'),\n",
       " Seq('LKK'),\n",
       " Seq('ELSI'),\n",
       " Seq('FRQS'),\n",
       " Seq('EETF'),\n",
       " Seq('ACCL'),\n",
       " Seq('TKLL'),\n",
       " Seq('EYLM'),\n",
       " Seq('IYHL'),\n",
       " Seq('NIPI'),\n",
       " Seq('HYMRQ'),\n",
       " Seq('LQRGA'),\n",
       " Seq('LDHPE'),\n",
       " Seq('VLSTQ'),\n",
       " Seq('ELERY'),\n",
       " Seq('LITVL'),\n",
       " Seq('IQLKA'),\n",
       " Seq('DNLYQ'),\n",
       " Seq('IPQQC'),\n",
       " Seq('TSEVV'),\n",
       " Seq('RKSCL'),\n",
       " Seq('LIWICA'),\n",
       " Seq('YRQLTR'),\n",
       " Seq('GNIWGQ'),\n",
       " Seq('KIKSFF'),\n",
       " Seq('HCLDLS'),\n",
       " Seq('RKCIKN'),\n",
       " Seq('KILGNL'),\n",
       " Seq('EKVLGA'),\n",
       " Seq('ISDRSS'),\n",
       " Seq('YTIIIRH'),\n",
       " Seq('LLNTTTD'),\n",
       " Seq('EKLRRQV'),\n",
       " Seq('LKIEEMK'),\n",
       " Seq('HLPFQII'),\n",
       " Seq('QRLTRMF'),\n",
       " Seq('IGQRGEV'),\n",
       " Seq('SRPQTCSK'),\n",
       " Seq('IPQQYRSL'),\n",
       " Seq('GLTLKIES'),\n",
       " Seq('CSQGLSER'),\n",
       " Seq('VKLDLSKE'),\n",
       " Seq('QVKSSMLI'),\n",
       " Seq('LSGFIFLF'),\n",
       " Seq('YQLLNMLN'),\n",
       " Seq('ERVDFSQS'),\n",
       " Seq('ISELREKR'),\n",
       " Seq('TLTITSTA'),\n",
       " Seq('SCKITILYY'),\n",
       " Seq('QFIQWINWN'),\n",
       " Seq('KAKKFLVLC'),\n",
       " Seq('YTCETKVLK'),\n",
       " Seq('PTKCVHVKS'),\n",
       " Seq('QTNRMGQLYS'),\n",
       " Seq('FIQRLSFILV'),\n",
       " Seq('GYRYWKVNSD'),\n",
       " Seq('TGVTSRNPPF'),\n",
       " Seq('MEIIYQVKEN'),\n",
       " Seq('IQRYAINLISA'),\n",
       " Seq('FIQNGDPGKPR'),\n",
       " Seq('EHCNYKIRSCK'),\n",
       " Seq('TFTGKERVYTY'),\n",
       " Seq('SRAQMGTNIVCT'),\n",
       " Seq('PQFPLQTIYPID'),\n",
       " Seq('KLMITTGYITYT'),\n",
       " Seq('LTYMQITINLLG'),\n",
       " Seq('IILMTTDHLHTT'),\n",
       " Seq('IYRIEKLKSGGR'),\n",
       " Seq('VIMTLKPCVKSRF'),\n",
       " Seq('RSTKTTLMTLSVM'),\n",
       " Seq('EHWVTLQKTLMIF'),\n",
       " Seq('LTTPPVLQPYSVM'),\n",
       " Seq('SSKITQDQQTIRP'),\n",
       " Seq('QSTLWLSIGVITR'),\n",
       " Seq('YNSETGLINNLDR'),\n",
       " Seq('KSHSKHTISLVRK'),\n",
       " Seq('WRQQSNRISSTNL'),\n",
       " Seq('FLHYSNSRMRLGS'),\n",
       " Seq('YHQILAQLTWHEH'),\n",
       " Seq('TFLYGQLRNFMMS'),\n",
       " Seq('RGKICCRRCAHWRQ'),\n",
       " Seq('RTLSMTSLTVIFDH'),\n",
       " Seq('YTSLGRGRKVLLTY'),\n",
       " Seq('LIPCSLSWETEFTI'),\n",
       " Seq('KMGCQEMSAIASIF'),\n",
       " Seq('KVYFMTNLLMKILN'),\n",
       " Seq('KWQYDSKIQDLYPRS'),\n",
       " Seq('LTHPVPLLSQLTLGC'),\n",
       " Seq('DLVFSARMLNLIVHT'),\n",
       " Seq('FSSFSYQLSLVLTRH'),\n",
       " Seq('FLKSRIHSLSSSTMI'),\n",
       " Seq('QASSSENIFSQYHKAQ'),\n",
       " Seq('KFNKKLRTQVHNSLDT'),\n",
       " Seq('WCPYSMEDQKQHGSGI'),\n",
       " Seq('CSNCYFDNQDKDICTSY'),\n",
       " Seq('LKNLSALDRKTQSFGSC'),\n",
       " Seq('VQEKQCHCLQSSSVLED'),\n",
       " Seq('DEIAVFTGFHRRTKSPH'),\n",
       " Seq('YTVLRYQMHLRLWWEGI'),\n",
       " Seq('AYVFQTRPKISTSPCWRN'),\n",
       " Seq('ASTMIIQNGSVLSQISYW'),\n",
       " Seq('WTGGLYYLEPLMRYWIIH'),\n",
       " Seq('IVSKGKMLSLHIIGASRGQ'),\n",
       " Seq('YQGKGKEKERGKIILSLNQ'),\n",
       " Seq('QYRENSKGLNRILLKFNQS'),\n",
       " Seq('RIRFGAYHWLRYMTQETMS'),\n",
       " Seq('EPRQTLLVLVLDPQEIYHHE'),\n",
       " Seq('ICPWRLPIIVELCHGCGYYY'),\n",
       " Seq('YFILIINDIMTNKDSNWIMI'),\n",
       " Seq('KIKLYLQSKTNGTVYTHVKC'),\n",
       " Seq('PQVSVNILRRTGWLRMSTNF'),\n",
       " Seq('SRHLLEDSITLICLEFLLEI'),\n",
       " Seq('HTPLDSQSQDYLTCTDHISD'),\n",
       " Seq('ENCVWIIWPSKSPRSVEESTD'),\n",
       " Seq('FRMCRTCLSAQGVSWKIIKHD'),\n",
       " Seq('VLHVSVKQQAGQSHNQENKLC'),\n",
       " Seq('SLRTMISYSSSSDNQFFICTL'),\n",
       " Seq('VNLNGMSVFCFGLLSKQRCEQ'),\n",
       " Seq('VSVVLQIRRFGLCLLMIFYPF'),\n",
       " Seq('KDLLSMLQTLIAPLILTNIWN'),\n",
       " Seq('QRLYLKGCKREEKKTVSKKFG'),\n",
       " Seq('LIKKNLGSKRFTLGSPIKLSSH'),\n",
       " Seq('ENPRDRETQEDQDNCCLPSGCW'),\n",
       " Seq('SKMRCRVSNSRSKGLLTKSAQR'),\n",
       " Seq('RNSCILRTLNAITFYSPSHPKA'),\n",
       " Seq('PLMTVSRIGNHSVGFNLIVSWS'),\n",
       " Seq('EINPHNLSLQGVYSTEFLDMLT'),\n",
       " Seq('NSMGQKFLRVKSVMISVQISIH'),\n",
       " Seq('DPNYSRLRYQSNVHKNQPHNLMD'),\n",
       " Seq('LNKSSAEYFFKISNSMFFQLLDS'),\n",
       " Seq('MGIGIDTEEPGLLFTSPHMHLNI'),\n",
       " Seq('PQHHQKLDATLQRNWPKSPLYGAS'),\n",
       " Seq('FITKPQIKTGCKSSKRSRLIQCNR'),\n",
       " Seq('RQNLHYIFKDYFLSFQWYLVMKVS'),\n",
       " Seq('ISPYNSLRTISKRLNDSLILLIHH'),\n",
       " Seq('FHTTIAFRPRKYPYNYTMYLTVNM'),\n",
       " Seq('KSTNVTFLVLTHSLLESIGHRQKG'),\n",
       " Seq('TGTKFRSSCRTRCCSSGNISRKARE'),\n",
       " Seq('RGRTYRTEWQTVSYLQKGDEYFIPC'),\n",
       " Seq('RWLQGCLLHATLGELCPSCREVLLC'),\n",
       " Seq('IRILSAFSNQTKLERSVIILHPKWF'),\n",
       " Seq('SAKFVSRETRCMGGSLYLGIPNWIR'),\n",
       " Seq('TQNQHQKRSLILIVGRQWRIINIEG'),\n",
       " Seq('ECLSSPRSSGGTLFPQSYCEKNSWIN'),\n",
       " Seq('IWHYQSTSLICFLYLAPTFKTQFLIQ'),\n",
       " Seq('IIILKALLSVLQSLQIKLIYQVRYPA'),\n",
       " Seq('RHSSNCLFPQFLEGTVRVMILNPSII'),\n",
       " Seq('KKLLKMIYSFIILKAVLKDIAKKHGL'),\n",
       " Seq('TLSCLSQNILKWITIILYMIQTPFQK'),\n",
       " Seq('TVACYCLHRVLTFINKILKSCLKTFL'),\n",
       " Seq('RIGESDLQAVGISTTLGHSVFRLMKLC'),\n",
       " Seq('RSTIRLTNLFLYQLKSLVMNKYFSKQG'),\n",
       " Seq('LSTHLSSSRTPKAQNFITSKITSEEKF'),\n",
       " Seq('SDTYLLSDLTFQIQDQLITYVDLRFSY'),\n",
       " Seq('ISECCRVNESWSCFHTHLYVFRETRGSH'),\n",
       " Seq('CNFYHHRVIKILLYKLVQIFGHELHTTL'),\n",
       " Seq('TTTTHLMINTSCLQMISQTLSSRTTLIA'),\n",
       " Seq('GQKFCFSNPLAFVKEDTSNGAGHQEYFK'),\n",
       " Seq('LYLSKLSHIKGEIECFFGDLDHYYMCLL'),\n",
       " Seq('YQDPGNHNALDSIHVQRSAGKEFIMMHS'),\n",
       " Seq('KLNTKKQKWPMNYQYPTSFTLNVIWIVL'),\n",
       " Seq('QPSLRPTDNRHEHPGLCSYHHRGPDLDTDR'),\n",
       " Seq('MMKTLIHTTCWNMSYPVLISRMNNSMFLIA'),\n",
       " Seq('RDRLRSVLESWLFHHMFPDLHYLTGFCLPIA'),\n",
       " Seq('ISIIYICWQSSFLSFVRLAILFLRLKLLQKK'),\n",
       " Seq('EKILFFLNLILRRQMHLNLFLWQMIHPEMLSRH'),\n",
       " Seq('SFEDLTMMSTFIPKHNNIKWSICIVDLSRILVS'),\n",
       " Seq('RMLTTSTNSKAALNQLMKLSLNFKRLQKRQSMC'),\n",
       " Seq('VPMRQTRGLLQLSKETMNQLLSLKKFILIFPTR'),\n",
       " Seq('THKKKYVYCVTLFLNLGMWTRPPDHGILLTWIL'),\n",
       " Seq('IRPTKESQSVLCSNSAMANRNEESALPESISKEVHG'),\n",
       " Seq('IKIRIKLIPSEDSFQEVIKSKRLADLPIIYHKTRQW'),\n",
       " Seq('GMSKDQLRPCVLLSELRQYILGPMGTMKSVGMKLGT'),\n",
       " Seq('PMSGPHQIQTPFTTVVLYTTMNSIMYFVQCQLLETLF'),\n",
       " Seq('GINHIKVTNRFNYINQMILFYGQTEEPMSTCKLSFGIAI'),\n",
       " Seq('DQWCNQQTAVCSNGIPKKPLFLFDGHQSLAQQIDLEQQL'),\n",
       " Seq('SVKVVPVSQTHCWLWTRAILHIATWKESDHVQEGSPNKE'),\n",
       " Seq('IKNLVMRVSWTGPVIHTRATCLTHKASLKQLKISQQGLY'),\n",
       " Seq('ITLKNKLKRSQRSSISLSPLTEFWPRLTPHSQPLKDTWFP'),\n",
       " Seq('VFDLKLDNYYKKLRSQALASFRRLNKHSYHWINKRIGFIV'),\n",
       " Seq('ARVYSLTAIRPQKILFLLYSKIMKYFIGHNWLLRTPMHKKQ'),\n",
       " Seq('VHFLQLILRNSVSIGDTNQWLYLLNVWMRYTVYLDFLIGCTND'),\n",
       " Seq('RQSSRNNLRHRKLCRGNWYGRILRNHQIRVGDKVSSTCTQRIPE'),\n",
       " Seq('IKKNLGPRSLIMPIFSRNHSIDHRLKALLPSSSEEILLELIYMI'),\n",
       " Seq('ELKSKTLALRLAEMSIWTASNCTHQMTKRQISLNSKMSLQEAQVK'),\n",
       " Seq('QQSPTSRQWFQVNNNNLNTNLSHKHYSFQPSDDNTILDTCLLKCM'),\n",
       " Seq('NPRVMVGVTININLPYEVSRKGGMIKLCRMDLQASNRVTPCIFLL'),\n",
       " Seq('DFWSGQSLNTMIQIVPSRSVNTVNLKIAGYLWGLDQTAIISFDLDY'),\n",
       " Seq('SCNNRCWINGQRNTSNGEERRQGSGGDGRLDENPQNCSRQQQGKNTFC'),\n",
       " Seq('ATVFALEYTIPLTSFLTLISCYFFDKSLNLTKVYQVMLAQVNCNLNLD'),\n",
       " Seq('NTIYQMGRTPKLYSLKYLIKDYLLDLLAKSMILWVNLFSTKRHFHGIL'),\n",
       " Seq('YWCVSQYIVIQILLKYIFFAYRRRSRLLFPRKKSLSTLICTMKSMTRE'),\n",
       " Seq('NGPLKFIIGVLEEDILWSTYCQILYQIHQSTLTKCCQMPCHILEYSRDL'),\n",
       " Seq('LICLSQIISHNNSRKCRQKTRKLDSKILLQTKGKFLVKLLRATTEPWTLRK'),\n",
       " Seq('SAFLLKMKSLQVLAENPMNPLDVQSKANQSETTFKPRTTNQQMYQEQDRKIQQ'),\n",
       " Seq('EPSATILKLQKLSSVHIFLFIRRKFIMMVLCCLRHSNQCQDVAFGQRLWWMKLD...ALQ'),\n",
       " Seq('ARIKLRSSTVLCKLLTGKDQELRCQSPEVFPLKRAQTRNIHLLGRKTCLGRRVV...MSN'),\n",
       " Seq('KTKRITLLIRLNLLSIIRAKLTESIITCHPIHEIVISVVIQVSLFSIIIPSLIL...LIQ'),\n",
       " Seq('SMMASILLTLFRRTKKKYRRHTDDQVFNNPASKIKQKPGKIFCSAPVENLNKLR...KLI')]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top_5_proteins"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fa822bf5",
   "metadata": {},
   "outputs": [],
   "source": [
    "# finding longest amino acid chain"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "0e938402",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "167"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(top_5_proteins[-1])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "4705ceed",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Seq('SMMASILLTLFRRTKKKYRRHTDDQVFNNPASKIKQKPGKIFCSAPVENLNKLR...KLI')"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top_5_proteins[-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d05dd9cc",
   "metadata": {},
   "outputs": [],
   "source": [
    "## writing this to a fasta file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "bdccb452",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open(\"nipah_protein_seq.fasta\", \"w\") as file:\n",
    "    file.write(f\">covid protein\\n{top_5_proteins[-1]}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "e4ac2728",
   "metadata": {},
   "outputs": [],
   "source": [
    "## using  blast to search the pdb database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "4c9a88c6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<_io.StringIO at 0x7ff3902f1550>"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from Bio.Blast import NCBIWWW\n",
    "\n",
    "result_handle2 = NCBIWWW.qblast(\"blastp\", \"pdb\", top_5_proteins[-1])\n",
    "result_handle2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "65547384",
   "metadata": {},
   "outputs": [],
   "source": [
    "## saving its result as xml file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "e510d93b",
   "metadata": {},
   "outputs": [],
   "source": [
    "with open('nipah_results.xml', 'w') as save_file:\n",
    "    nipah_blast_results = result_handle2.read()\n",
    "    save_file.write(nipah_blast_results)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "1f48e726",
   "metadata": {},
   "outputs": [
    {
     "ename": "AttributeError",
     "evalue": "'str' object has no attribute 'read'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m/tmp/ipykernel_11786/3561643587.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mblast_records\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mNCBIXML\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mparse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'nipah_results.xml'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 5\u001b[0;31m \u001b[0mblast_records\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mblast_records\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      6\u001b[0m \u001b[0mblast_records\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m~/anaconda3/lib/python3.9/site-packages/Bio/Blast/NCBIXML.py\u001b[0m in \u001b[0;36mparse\u001b[0;34m(handle, debug)\u001b[0m\n\u001b[1;32m    787\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    788\u001b[0m     \u001b[0mpending\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 789\u001b[0;31m     \u001b[0mtext\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhandle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mBLOCK\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    790\u001b[0m     \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtext\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbytes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    791\u001b[0m         \u001b[0;31m# Not a text handle, raw bytes mode\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mAttributeError\u001b[0m: 'str' object has no attribute 'read'"
     ]
    }
   ],
   "source": [
    "from Bio.Blast import NCBIXML\n",
    "\n",
    "blast_records = NCBIXML.parse('nipah_results.xml')\n",
    "    \n",
    "blast_records = list(blast_records)\n",
    "blast_records\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "a62bc57f",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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