Genome De-coder.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# All data can be pulled from https://www.ncbi.nlm.nih.gov/genbank/\n",
    "# Coded by Ian Finn"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2732"
      ]
     },
     "execution_count": 37,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "import lzma\n",
    "lzc =lzma.compress(cc.encode(\"utf-8\"))\n",
    "len(lzc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# DNA Codons\n",
    "# DO NOT ALTER \n",
    "\n",
    "tt = \"\"\"Ala / A\tGCT, GCC, GCA, GCG\n",
    "Ile / I\tATT, ATC, ATA\n",
    "Arg / R\tCGT, CGC, CGA, CGG; AGA, AGG\n",
    "Leu / L\tCTT, CTC, CTA, CTG; TTA, TTG\n",
    "Asn / N\tAAT, AAC\n",
    "Lys / K\tAAA, AAG\n",
    "Asp / D\tGAT, GAC\n",
    "Met / M\tATG\n",
    "Phe / F\tTTT, TTC\n",
    "Cys / C\tTGT, TGC\n",
    "Pro / P\tCCT, CCC, CCA, CCG\n",
    "Gln / Q\tCAA, CAG\n",
    "Ser / S\tTCT, TCC, TCA, TCG; AGT, AGC\n",
    "Glu / E\tGAA, GAG\n",
    "Thr / T\tACT, ACC, ACA, ACG\n",
    "Trp / W\tTGG\n",
    "Gly / G\tGGT, GGC, GGA, GGG\n",
    "Tyr / Y\tTAT, TAC\n",
    "His / H\tCAT, CAC\n",
    "Val / V\tGTT, GTC, GTA, GTG\n",
    "STOP\tTAA, TGA, TAG\n",
    "\"\"\".strip()\n",
    "dec = {}\n",
    "for t in tt.split(\"\\n\"):\n",
    "    k,v = t.split(\"\\x09\")\n",
    "    if '/' in k:\n",
    "        k = k.split(\"/\")[-1].strip()\n",
    "    k = k.replace(\"STOP\", \"#\")\n",
    "    v = v.replace(\",\", \"\").replace(\";\", \"\").lower().replace(\"u\", \"t\").split(\" \")\n",
    "    for vv in v:\n",
    "        if vv in dec:\n",
    "            print (\"dup\", vv)\n",
    "        dec[vv] = k\n",
    "#dec\n",
    "len(set(dec.values()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Insert Genome here \n",
    "# Genome of Human immunodeficiency virus 1 (HIV-1) used for example. \n",
    "cc = \"\"\"1 ggtctctctg gttagaccag atctgagcct gggagctctc tggctaacta gggaacccac\n",
    "       61 tgcttaagcc tcaataaagc ttgccttgag tgcttcaagt agtgtgtgcc cgtctgttgt\n",
    "      121 gtgactctgg taactagaga tccctcagac ccttttagtc agtgtggaaa atctctagca\n",
    "      181 gtggcgcccg aacagggacc tgaaagcgaa agggaaacca gaggagctct ctcgacgcag\n",
    "      241 gactcggctt gctgaagcgc gcacggcaag aggcgagggg cggcgactgg tgagtacgcc\n",
    "      301 aaaaattttg actagcggag gctagaagga gagagatggg tgcgagagcg tcagtattaa\n",
    "      361 gcgggggaga attagatcga tgggaaaaaa ttcggttaag gccaggggga aagaaaaaat\n",
    "      421 ataaattaaa acatatagta tgggcaagca gggagctaga acgattcgca gttaatcctg\n",
    "      481 gcctgttaga aacatcagaa ggctgtagac aaatactggg acagctacaa ccatcccttc\n",
    "      541 agacaggatc agaagaactt agatcattat ataatacagt agcaaccctc tattgtgtgc\n",
    "      601 atcaaaggat agagataaaa gacaccaagg aagctttaga caagatagag gaagagcaaa\n",
    "      661 acaaaagtaa gaaaaaagca cagcaagcag cagctgacac aggacacagc aatcaggtca\n",
    "      721 gccaaaatta ccctatagtg cagaacatcc aggggcaaat ggtacatcag gccatatcac\n",
    "      781 ctagaacttt aaatgcatgg gtaaaagtag tagaagagaa ggctttcagc ccagaagtga\n",
    "      841 tacccatgtt ttcagcatta tcagaaggag ccaccccaca agatttaaac accatgctaa\n",
    "      901 acacagtggg gggacatcaa gcagccatgc aaatgttaaa agagaccatc aatgaggaag\n",
    "      961 ctgcagaatg ggatagagtg catccagtgc atgcagggcc tattgcacca ggccagatga\n",
    "     1021 gagaaccaag gggaagtgac atagcaggaa ctactagtac ccttcaggaa caaataggat\n",
    "     1081 ggatgacaaa taatccacct atcccagtag gagaaattta taaaagatgg ataatcctgg\n",
    "     1141 gattaaataa aatagtaaga atgtatagcc ctaccagcat tctggacata agacaaggac\n",
    "     1201 caaaggaacc ctttagagac tatgtagacc ggttctataa aactctaaga gccgagcaag\n",
    "     1261 cttcacagga ggtaaaaaat tggatgacag aaaccttgtt ggtccaaaat gcgaacccag\n",
    "     1321 attgtaagac tattttaaaa gcattgggac cagcggctac actagaagaa atgatgacag\n",
    "     1381 catgtcaggg agtaggagga cccggccata aggcaagagt tttggctgaa gcaatgagcc\n",
    "     1441 aagtaacaaa ttcagctacc ataatgatgc agagaggcaa ttttaggaac caaagaaaga\n",
    "     1501 ttgttaagtg tttcaattgt ggcaaagaag ggcacacagc cagaaattgc agggccccta\n",
    "     1561 ggaaaaaggg ctgttggaaa tgtggaaagg aaggacacca aatgaaagat tgtactgaga\n",
    "     1621 gacaggctaa ttttttaggg aagatctggc cttcctacaa gggaaggcca gggaattttc\n",
    "     1681 ttcagagcag accagagcca acagccccac cagaagagag cttcaggtct ggggtagaga\n",
    "     1741 caacaactcc ccctcagaag caggagccga tagacaagga actgtatcct ttaacttccc\n",
    "     1801 tcaggtcact ctttggcaac gacccctcgt cacaataaag ataggggggc aactaaagga\n",
    "     1861 agctctatta gatacaggag cagatgatac agtattagaa gaaatgagtt tgccaggaag\n",
    "     1921 atggaaacca aaaatgatag ggggaattgg aggttttatc aaagtaagac agtatgatca\n",
    "     1981 gatactcata gaaatctgtg gacataaagc tataggtaca gtattagtag gacctacacc\n",
    "     2041 tgtcaacata attggaagaa atctgttgac tcagattggt tgcactttaa attttcccat\n",
    "     2101 tagccctatt gagactgtac cagtaaaatt aaagccagga atggatggcc caaaagttaa\n",
    "     2161 acaatggcca ttgacagaag aaaaaataaa agcattagta gaaatttgta cagagatgga\n",
    "     2221 aaaggaaggg aaaatttcaa aaattgggcc tgaaaatcca tacaatactc cagtatttgc\n",
    "     2281 cataaagaaa aaagacagta ctaaatggag aaaattagta gatttcagag aacttaataa\n",
    "     2341 gagaactcaa gacttctggg aagttcaatt aggaatacca catcccgcag ggttaaaaaa\n",
    "     2401 gaaaaaatca gtaacagtac tggatgtggg tgatgcatat ttttcagttc ccttagatga\n",
    "     2461 agacttcagg aagtatactg catttaccat acctagtata aacaatgaga caccagggat\n",
    "     2521 tagatatcag tacaatgtgc ttccacaggg atggaaagga tcaccagcaa tattccaaag\n",
    "     2581 tagcatgaca aaaatcttag agccttttag aaaacaaaat ccagacatag ttatctatca\n",
    "     2641 atacatggat gatttgtatg taggatctga cttagaaata gggcagcata gaacaaaaat\n",
    "     2701 agaggagctg agacaacatc tgttgaggtg gggacttacc acaccagaca aaaaacatca\n",
    "     2761 gaaagaacct ccattccttt ggatgggtta tgaactccat cctgataaat ggacagtaca\n",
    "     2821 gcctatagtg ctgccagaaa aagacagctg gactgtcaat gacatacaga agttagtggg\n",
    "     2881 gaaattgaat tgggcaagtc agatttaccc agggattaaa gtaaggcaat tatgtaaact\n",
    "     2941 ccttagagga accaaagcac taacagaagt aataccacta acagaagaag cagagctaga\n",
    "     3001 actggcagaa aacagagaga ttctaaaaga accagtacat ggagtgtatt atgacccatc\n",
    "     3061 aaaagactta atagcagaaa tacagaagca ggggcaaggc caatggacat atcaaattta\n",
    "     3121 tcaagagcca tttaaaaatc tgaaaacagg aaaatatgca agaatgaggg gtgcccacac\n",
    "     3181 taatgatgta aaacaattaa cagaggcagt gcaaaaaata accacagaaa gcatagtaat\n",
    "     3241 atggggaaag actcctaaat ttaaactgcc catacaaaag gaaacatggg aaacatggtg\n",
    "     3301 gacagagtat tggcaagcca cctggattcc tgagtgggag tttgttaata cccctccctt\n",
    "     3361 agtgaaatta tggtaccagt tagagaaaga acccatagta ggagcagaaa ccttctatgt\n",
    "     3421 agatggggca gctaacaggg agactaaatt aggaaaagca ggatatgtta ctaatagagg\n",
    "     3481 aagacaaaaa gttgtcaccc taactgacac aacaaatcag aagactgagt tacaagcaat\n",
    "     3541 ttatctagct ttgcaggatt cgggattaga agtaaacata gtaacagact cacaatatgc\n",
    "     3601 attaggaatc attcaagcac aaccagatca aagtgaatca gagttagtca atcaaataat\n",
    "     3661 agagcagtta ataaaaaagg aaaaggtcta tctggcatgg gtaccagcac acaaaggaat\n",
    "     3721 tggaggaaat gaacaagtag ataaattagt cagtgctgga atcaggaaag tactattttt\n",
    "     3781 agatggaata gataaggccc aagatgaaca tgagaaatat cacagtaatt ggagagcaat\n",
    "     3841 ggctagtgat tttaacctgc cacctgtagt agcaaaagaa atagtagcca gctgtgataa\n",
    "     3901 atgtcagcta aaaggagaag ccatgcatgg acaagtagac tgtagtccag gaatatggca\n",
    "     3961 actagattgt acacatttag aaggaaaagt tatcctggta gcagttcatg tagccagtgg\n",
    "     4021 atatatagaa gcagaagtta ttccagcaga aacagggcag gaaacagcat attttctttt\n",
    "     4081 aaaattagca ggaagatggc cagtaaaaac aatacatact gacaatggca gcaatttcac\n",
    "     4141 cggtgctacg gttagggccg cctgttggtg ggcgggaatc aagcaggaat ttggaattcc\n",
    "     4201 ctacaatccc caaagtcaag gagtagtaga atctatgaat aaagaattaa agaaaattat\n",
    "     4261 aggacaggta agagatcagg ctgaacatct taagacagca gtacaaatgg cagtattcat\n",
    "     4321 ccacaatttt aaaagaaaag gggggattgg ggggtacagt gcaggggaaa gaatagtaga\n",
    "     4381 cataatagca acagacatac aaactaaaga attacaaaaa caaattacaa aaattcaaaa\n",
    "     4441 ttttcgggtt tattacaggg acagcagaaa tccactttgg aaaggaccag caaagctcct\n",
    "     4501 ctggaaaggt gaaggggcag tagtaataca agataatagt gacataaaag tagtgccaag\n",
    "     4561 aagaaaagca aagatcatta gggattatgg aaaacagatg gcaggtgatg attgtgtggc\n",
    "     4621 aagtagacag gatgaggatt agaacatgga aaagtttagt aaaacaccat atgtatgttt\n",
    "     4681 cagggaaagc taggggatgg ttttatagac atcactatga aagccctcat ccaagaataa\n",
    "     4741 gttcagaagt acacatccca ctaggggatg ctagattggt aataacaaca tattggggtc\n",
    "     4801 tgcatacagg agaaagagac tggcatttgg gtcagggagt ctccatagaa tggaggaaaa\n",
    "     4861 agagatatag cacacaagta gaccctgaac tagcagacca actaattcat ctgtattact\n",
    "     4921 ttgactgttt ttcagactct gctataagaa aggccttatt aggacacata gttagcccta\n",
    "     4981 ggtgtgaata tcaagcagga cataacaagg taggatctct acaatacttg gcactagcag\n",
    "     5041 cattaataac accaaaaaag ataaagccac ctttgcctag tgttacgaaa ctgacagagg\n",
    "     5101 atagatggaa caagccccag aagaccaagg gccacagagg gagccacaca atgaatggac\n",
    "     5161 actagagctt ttagaggagc ttaagaatga agctgttaga cattttccta ggatttggct\n",
    "     5221 ccatggctta gggcaacata tctatgaaac ttatggggat acttgggcag gagtggaagc\n",
    "     5281 cataataaga attctgcaac aactgctgtt tatccatttt cagaattggg tgtcgacata\n",
    "     5341 gcagaatagg cgttactcga cagaggagag caagaaatgg agccagtaga tcctagacta\n",
    "     5401 gagccctgga agcatccagg aagtcagcct aaaactgctt gtaccaattg ctattgtaaa\n",
    "     5461 aagtgttgct ttcattgcca agtttgtttc ataacaaaag ccttaggcat ctcctatggc\n",
    "     5521 aggaagaagc ggagacagcg acgaagagct catcagaaca gtcagactca tcaagcttct\n",
    "     5581 ctatcaaagc agtaagtagt acatgtaatg caacctatac caatagtagc aatagtagca\n",
    "     5641 ttagtagtag caataataat agcaatagtt gtgtggtcca tagtaatcat agaatatagg\n",
    "     5701 aaaatattaa gacaaagaaa aatagacagg ttaattgata gactaataga aagagcagaa\n",
    "     5761 gacagtggca atgagagtga aggagaaata tcagcacttg tggagatggg ggtggagatg\n",
    "     5821 gggcaccatg ctccttggga tgttgatgat ctgtagtgct acagaaaaat tgtgggtcac\n",
    "     5881 agtctattat ggggtacctg tgtggaagga agcaaccacc actctatttt gtgcatcaga\n",
    "     5941 tgctaaagca tatgatacag aggtacataa tgtttgggcc acacatgcct gtgtacccac\n",
    "     6001 agaccccaac ccacaagaag tagtattggt aaatgtgaca gaaaatttta acatgtggaa\n",
    "     6061 aaatgacatg gtagaacaga tgcatgagga tataatcagt ttatgggatc aaagcctaaa\n",
    "     6121 gccatgtgta aaattaaccc cactctgtgt tagtttaaag tgcactgatt tgaagaatga\n",
    "     6181 tactaatacc aatagtagta gcgggagaat gataatggag aaaggagaga taaaaaactg\n",
    "     6241 ctctttcaat atcagcacaa gcataagagg taaggtgcag aaagaatatg cattttttta\n",
    "     6301 taaacttgat ataataccaa tagataatga tactaccagc tataagttga caagttgtaa\n",
    "     6361 cacctcagtc attacacagg cctgtccaaa ggtatccttt gagccaattc ccatacatta\n",
    "     6421 ttgtgccccg gctggttttg cgattctaaa atgtaataat aagacgttca atggaacagg\n",
    "     6481 accatgtaca aatgtcagca cagtacaatg tacacatgga attaggccag tagtatcaac\n",
    "     6541 tcaactgctg ttaaatggca gtctagcaga agaagaggta gtaattagat ctgtcaattt\n",
    "     6601 cacggacaat gctaaaacca taatagtaca gctgaacaca tctgtagaaa ttaattgtac\n",
    "     6661 aagacccaac aacaatacaa gaaaaagaat ccgtatccag agaggaccag ggagagcatt\n",
    "     6721 tgttacaata ggaaaaatag gaaatatgag acaagcacat tgtaacatta gtagagcaaa\n",
    "     6781 atggaataac actttaaaac agatagctag caaattaaga gaacaatttg gaaataataa\n",
    "     6841 aacaataatc tttaagcaat cctcaggagg ggacccagaa attgtaacgc acagttttaa\n",
    "     6901 ttgtggaggg gaatttttct actgtaattc aacacaactg tttaatagta cttggtttaa\n",
    "     6961 tagtacttgg agtactgaag ggtcaaataa cactgaagga agtgacacaa tcaccctccc\n",
    "     7021 atgcagaata aaacaaatta taaacatgtg gcagaaagta ggaaaagcaa tgtatgcccc\n",
    "     7081 tcccatcagt ggacaaatta gatgttcatc aaatattaca gggctgctat taacaagaga\n",
    "     7141 tggtggtaat agcaacaatg agtccgagat cttcagacct ggaggaggag atatgaggga\n",
    "     7201 caattggaga agtgaattat ataaatataa agtagtaaaa attgaaccat taggagtagc\n",
    "     7261 acccaccaag gcaaagagaa gagtggtgca gagagaaaaa agagcagtgg gaataggagc\n",
    "     7321 tttgttcctt gggttcttgg gagcagcagg aagcactatg ggcgcagcct caatgacgct\n",
    "     7381 gacggtacag gccagacaat tattgtctgg tatagtgcag cagcagaaca atttgctgag\n",
    "     7441 ggctattgag gcgcaacagc atctgttgca actcacagtc tggggcatca agcagctcca\n",
    "     7501 ggcaagaatc ctggctgtgg aaagatacct aaaggatcaa cagctcctgg ggatttgggg\n",
    "     7561 ttgctctgga aaactcattt gcaccactgc tgtgccttgg aatgctagtt ggagtaataa\n",
    "     7621 atctctggaa cagatttgga atcacacgac ctggatggag tgggacagag aaattaacaa\n",
    "     7681 ttacacaagc ttaatacact ccttaattga agaatcgcaa aaccagcaag aaaagaatga\n",
    "     7741 acaagaatta ttggaattag ataaatgggc aagtttgtgg aattggttta acataacaaa\n",
    "     7801 ttggctgtgg tatataaaat tattcataat gatagtagga ggcttggtag gtttaagaat\n",
    "     7861 agtttttgct gtactttcta tagtgaatag agttaggcag ggatattcac cattatcgtt\n",
    "     7921 tcagacccac ctcccaaccc cgaggggacc cgacaggccc gaaggaatag aagaagaagg\n",
    "     7981 tggagagaga gacagagaca gatccattcg attagtgaac ggatccttgg cacttatctg\n",
    "     8041 ggacgatctg cggagcctgt gcctcttcag ctaccaccgc ttgagagact tactcttgat\n",
    "    ban 8101 tgtaacgagg attgtggaac ttctgggacg cagggggtgg gaagccctca aatattggtg\n",
    "     8161 gaatctccta cagtattgga gtcaggaact aaagaatagt gctgttagct tgctcaatgc\n",
    "     8221 cacagccata gcagtagctg aggggacaga tagggttata gaagtagtac aaggagcttg\n",
    "     8281 tagagctatt cgccacatac ctagaagaat aagacagggc ttggaaagga ttttgctata\n",
    "     8341 agatgggtgg caagtggtca aaaagtagtg tgattggatg gcctactgta agggaaagaa\n",
    "     8401 tgagacgagc tgagccagca gcagataggg tgggagcagc atctcgagac ctggaaaaac\n",
    "     8461 atggagcaat cacaagtagc aatacagcag ctaccaatgc tgcttgtgcc tggctagaag\n",
    "     8521 cacaagagga ggaggaggtg ggttttccag tcacacctca ggtaccttta agaccaatga\n",
    "     8581 cttacaaggc agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc\n",
    "     8641 taattcactc ccaaagaaga caagatatcc ttgatctgtg gatctaccac acacaaggct\n",
    "     8701 acttccctga ttagcagaac tacacaccag ggccaggggt cagatatcca ctgacctttg\n",
    "     8761 gatggtgcta caagctagta ccagttgagc cagataagat agaagaggcc aataaaggag\n",
    "     8821 agaacaccag cttgttacac cctgtgagcc tgcatgggat ggatgacccg gagagagaag\n",
    "     8881 tgttagagtg gaggtttgac agccgcctag catttcatca cgtggcccga gagctgcatc\n",
    "     8941 cggagtactt caagaactgc tgacatcgag cttgctacaa gggactttcc gctggggact\n",
    "     9001 ttccagggag gcgtggcctg ggcgggactg gggagtggcg agccctcaga tcctgcatat\n",
    "     9061 aagcagctgc tttttgcctg tactgggtct ctctggttag accagatctg agcctgggag\n",
    "     9121 ctctctggct aactagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt\n",
    "     9181 c\n",
    "\"\"\"\n",
    "\n",
    "\n",
    "for s in \" \\n0123456789\":\n",
    "    cc = cc.replace(s, \"\")\n",
    "    cc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['FFREDLAFLQGKAREFSSEQTRANSPTRRELQVWGRDNNSPSEAGADRQGTVSFNFPQVTLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNFPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLCKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSAGIRKVLFLDGIDKAQDEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTGATVRAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRNPLWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED',\n",
       " 'KEQKTVAMRVKEKYQHLWRWGWRWGTMLLGMLMICSATEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKCTDLKNDTNTNSSSGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDTTSYKLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTRPNNNTRKRIRIQRGPGRAFVTIGKIGNMRQAHCNISRAKWNNTLKQIASKLREQFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTEGSNNTEGSDTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGALFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQLLGIWGCSGKLICTTAVPWNASWSNKSLEQIWNHTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELLELDKWASLWNWFNITNWLWYIKLFIMIVGGLVGLRIVFAVLSIVNRVRQGYSPLSFQTHLPTPRGPDRPEGIEEEGGERDRDRSIRLVNGSLALIWDDLRSLCLFSYHRLRDLLLIVTRIVELLGRRGWEALKYWWNLLQYWSQELKNSAVSLLNATAIAVAEGTDRVIEVVQGACRAIRHIPRRIRQGLERILL',\n",
       " 'LAEARRREMGARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQPSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVSQNYPIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQGVGGPGHKARVLAEAMSQVTNSATIMMQRGNFRNQRKIVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWPSYKGRPGNFLQSRPEPTAPPEESFRSGVETTTPPQKQEPIDKELYPLTSLRSLFGNDPSSQ',\n",
       " 'CQEEKQRSLGIMENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLGDARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAIRKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKTKGHRGSHTMNGH',\n",
       " 'DRAWKGFCYKMGGKWSKSSVIGWPTVRERMRRAEPAADRVGAASRDLEKHGAITSSNTAATNAACAWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPD']"
      ]
     },
     "execution_count": 40,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "def decode(x):\n",
    "    aa = []\n",
    "    for i in range(0, len(x)-2, 3):\n",
    "        aa.append(dec[x[i:i+3]])\n",
    "    aa = ''.join(aa)\n",
    "    return aa\n",
    "\n",
    "aa = decode(cc[0:]) + decode(cc[1:]) +decode(cc[2:])\n",
    "# aa\n",
    "decode(cc[266-1:13483])\n",
    "list(filter(lambda x: len(x) > 100, aa.split(\"#\")))\n",
    "\n",
    "# Check to see if the Decoding matched on https://www.ncbi.nlm.nih.gov/\n",
    "# 'https://www.ncbi.nlm.nih.gov/nuccore/4558520'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.4"
  }
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