{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# UniProt Demo\n",
    "\n",
    "This demo shows how to create and query a UniProt dataset.\n",
    "\n",
    "![UniPort](http://www.uniprot.org/images/logos/uniprot-rgb-optimized.svg)\n",
    "\n",
    "\n",
    "### Binder can't fetch FTP, this filter will only work locally\n",
    "\n",
    "## Imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pyspark import SparkConf, SparkContext, SQLContext\n",
    "from mmtfPyspark.datasets import uniProt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Configure Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "conf = SparkConf().setMaster(\"local[*]\") \\\n",
    "                      .setAppName(\"UniprotDemo\")\n",
    "sc = SparkContext(conf = conf)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Get UniProt Datasets"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "ds = uniProt.get_dataset(uniProt.SWISS_PROT)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Display UniProt Dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|db |uniqueIdentifier|entryName |proteinName                               |organismName                         |geneName |proteinExistence|sequenceVersion|sequence                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |\n",
      "+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "|>sp|Q6GZX4          |001R_FRG3G|Putativetranscriptionfactor001R           |Frogvirus3(isolateGoorha)OX=654924   |FV3-001R |4               |1              |MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWKFTPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |\n",
      "|>sp|Q6GZX3          |002L_FRG3G|Uncharacterizedprotein002L                |Frogvirus3(isolateGoorha)OX=654924   |FV3-002L |4               |1              |MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRKVMFFVAGAVLVAILISTVRW                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |\n",
      "|>sp|Q197F8          |002R_IIV3 |Uncharacterizedprotein002R                |Invertebrateiridescentvirus3OX=345201|IIV3-002R|4               |1              |MASNTVSAQGGSNRPVRDFSNIQDVAQFLLFDPIWNEQPGSIVPWKMNREQALAERYPELQTSEPSEDYSGPVESLELLPLEIKLDIMQYLSWEQISWCKHPWLWTRWYKDNVVRVSAITFEDFQREYAFPEKIQEIHFTDTRAEEIKAILETTPNVTRLVIRRIDDMNYNTHGDLGLDDLEFLTHLMVEDACGFTDFWAPSLTHLTIKNLDMHPRWFGPVMDGIKSMQSTLKYLYIFETYGVNKPFVQWCTDNIETFYCTNSYRYENVPRPIYVWVLFQEDEWHGYRVEDNKFHRRYMYSTILHKRDTDWVENNPLKTPAQVEMYKFLLRISQLNRDGTGYESDSDPENEHFDDESFSSGEEDSSDEDDPTWAPDSDDSDWETETEEEPSVAARILEKGKLTITNLMKSLGFKPKPKKIQSIDRYFCSLDSNYNSEDEDFEYDSDSEDDDSDSEDDC                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |\n",
      "|>sp|Q197F7          |003L_IIV3 |Uncharacterizedprotein003L                |Invertebrateiridescentvirus3OX=345201|IIV3-003L|4               |1              |MYQAINPCPQSWYGSPQLEREIVCKMSGAPHYPNYYPVHPNALGGAWFDTSLNARSLTTTPSLTTCTPPSLAACTPPTSLGMVDSPPHINPPRRIGTLCFDFGSAKSPQRCECVASDRPSTTSNTAPDTYRLLITNSKTRKNNYGTCRLEPLTYGI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |\n",
      "|>sp|Q6GZX2          |003R_FRG3G|Uncharacterizedprotein3R                  |Frogvirus3(isolateGoorha)OX=654924   |FV3-003R |3               |1              |MARPLLGKTSSVRRRLESLSACSIFFFLRKFCQKMASLVFLNSPVYQMSNILLTERRQVDRAMGGSDDDGVMVVALSPSDFKTVLGSALLAVERDMVHVVPKYLQTPGILHDMLVLLTPIFGEALSVDMSGATDVMVQQIATAGFVDVDPLHSSVSWKDNVSCPVALLAVSNAVRTMMGQPCQVTLIIDVGTQNILRDLVNLPVEMSGDLQVMAYTKDPLGKVPAVGVSVFDSGSVQKGDAHSVGAPDGLVSFHTHPVSSAVELNYHAGWPSNVDMSSLLTMKNLMHVVVAEEGLWTMARTLSMQRLTKVLTDAEKDVMRAAAFNLFLPLNELRVMGTKDSNNKSLKTYFEVFETFTIGALMKHSGVTPTAFVDRRWLDNTIYHMGFIPWGRDMRFVVEYDLDGTNPFLNTVPTLMSVKRKAKIQEMFDNMVSRMVTS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |\n",
      "|>sp|Q6GZX1          |004R_FRG3G|Uncharacterizedprotein004R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-004R |4               |1              |MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |\n",
      "|>sp|Q197F5          |005L_IIV3 |Uncharacterizedprotein005L                |Invertebrateiridescentvirus3OX=345201|IIV3-005L|3               |1              |MRYTVLIALQGALLLLLLIDDGQGQSPYPYPGMPCNSSRQCGLGTCVHSRCAHCSSDGTLCSPEDPTMVWPCCPESSCQLVVGLPSLVNHYNCLPNQCTDSSQCPGGFGCMTRRSKCELCKADGEACNSPYLDWRKDKECCSGYCHTEARGLEGVCIDPKKIFCTPKNPWQLAPYPPSYHQPTTLRPPTSLYDSWLMSGFLVKSTTAPSTQEEEDDY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |\n",
      "|>sp|Q6GZX0          |005R_FRG3G|Uncharacterizedprotein005R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-005R |4               |1              |MQNPLPEVMSPEHDKRTTTPMSKEANKFIRELDKKPGDLAVVSDFVKRNTGKRLPIGKRSNLYVRICDLSGTIYMGETFILESWEELYLPEPTKMEVLGTLESCCGIPPFPEWIVMVGEDQCVYAYGDEEILLFAYSVKQLVEEGIQETGISYKYPDDISDVDEEVLQQDEEIQKIRKKTREFVDKDAQEFQDFLNSLDASLLS                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |\n",
      "|>sp|Q91G88          |006L_IIV6 |PutativeKilA-Ndomain-containingprotein006L|Invertebrateiridescentvirus6OX=176652|IIV6-006L|3               |1              |MDSLNEVCYEQIKGTFYKGLFGDFPLIVDKKTGCFNATKLCVLGGKRFVDWNKTLRSKKLIQYYETRCDIKTESLLYEIKGDNNDEITKQITGTYLPKEFILDIASWISVEFYDKCNNIIINYFVNEYKTMDKKTLQSKINEVEEKMQKLLNEKEEELQEKNDKIDELILFSKRMEEDRKKDREMMIKQEKMLRELGIHLEDVSSQNNELIEKVDEQVEQNAVLNFKIDNIQNKLEIAVEDRAPQPKQNLKRERFILLKRNDDYYPYYTIRAQDINARSALKRQKNLYNEVSVLLDLTCHPNSKTLYVRVKDELKQKGVVFNLCKVSISNSKINEEELIKAMETINDEKRDV                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |\n",
      "|>sp|Q6GZW9          |006R_FRG3G|Uncharacterizedprotein006R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-006R |4               |1              |MYKMYFLKDQKFSLSGTIRINDKTQSEYGSVWCPGLSITGLHHDAIDHNMFEEMETEIIEYLGPWVQAEYRRIKG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |\n",
      "|>sp|Q6GZW8          |007R_FRG3G|Uncharacterizedprotein007R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-007R |4               |1              |MRSIKPLRCCNAHGRHVSQEYGRCTLLLFREKLFLQTGLVCNKQCNAPNNDGAESKHHGIHHGSRGALALRGAGVHLLASAALGPRVLAGLVPTGRSVQGSVGQCGRVAQIGRARDVAARKQESYCEK                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |\n",
      "|>sp|Q197F3          |007R_IIV3 |Uncharacterizedprotein007R                |Invertebrateiridescentvirus3OX=345201|IIV3-007R|4               |1              |MEAKNITIDNTTYNFFKFYNINQPLTNLKYLNSERLCFSNAVMGKIVDDASTITITYHRVYFGISGPKPRQVADLGEYYDVNELLNYDTYTKTQEFAQKYNSLVKPTIDAKNWSGNELVLLVGNEWYCKTFGKAGSKNVFLYNMIPTIYRDEPQHQEQILKKFMFFNATKNVEQNPNFLDNVPEEYYHLLLPKSWVEKNLSDKYRKIMETEHKPLVFSCEPAFSFGLCRNTQDKNESYQLSLCLYEREKPRDAEIVWAAKYDELAAMVRDYLKKTPEFKKYRSFISCMKGLSWKNNEIGDKDGPKLYPKVIFNRKKGEFVTIFTKDDDVEPETIEDPRTILDRRCVVQAALRLESVFVHNKVAIQLRINDVLISEWKEASSKPQPLILRRHRFTKPSSSVAKSTSPSLRNSGSDESDLNQSDSDKEDERVVPVPKTKRIVKTVKLPN                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |\n",
      "|>sp|Q197F2          |008L_IIV3 |Uncharacterizedprotein008L                |Invertebrateiridescentvirus3OX=345201|IIV3-008L|4               |1              |MSFKVYDPIAELIATQFPTSNPDLQIINNDVLVVSPHKITLPMGPQNAGDVTNKAYVDQAVMSAAVPVASSTTVGTIQMAGDLEGSSGTNPIIAANKITLNKLQKIGPKMVIGNPNSDWNNTQEIELDSSFRIVDNRLNAGIVPISSTDPNKSNTVIPAPQQNGLFYLDSSGRVWVWAEHYYKCITPSRYISKWMGVGDFQELTVGQSVMWDSGRPSIETVSTQGLEVEWISSTNFTLSSLYLIPIVVKVTICIPLLGQPDQMAKFVLYSVSSAQQPRTGIVLTTDSSRSSAPIVSEYITVNWFEPKSYSVQLKEVNSDSGTTVTICSDKWLANPFLDCWITIEEVG                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |\n",
      "|>sp|Q6GZW6          |009L_FRG3G|Putativehelicase009L                      |Frogvirus3(isolateGoorha)OX=654924   |FV3-009L |4               |1              |MDTSPYDFLKLYPWLSRGEADKGTLLDAFPGETFEQSLASDVAMRRAVQDDPAFGHQKLVETFLSEDTPYRELLLFHAPGTGKTCTVVSVAERAKEKGLTRGCIVLARGAALLRNFLHELVFNCGTGGRYIPEGYADMGDQERTRKMRKAVSSYYQFRTYETFAKSVATMSAEAIRARYDRFVIVMDEVHHLRSVQAEGVNTYSAISRFLRTVRGCVKMLLTGTPMTNEPGELADVLNLILPQDKTIRPEDGIFSNSGDLLKPDELAERVRGRVSYLKAARPDAGLTFAGEVLGGTGMTHLRLVRLEMSAFQSDAYASAWDQDAGDRNIFSNSRQCSLAVMPDRRWGSAAEARNPSQVRRMAGQNLAEYSVKYDYLVRVASSSPKTFAYCEYVNGSGLSLLSDILLANGWRRATGRETTPGKRFALLTASQKNIHKIVQRFNHEDNVDGAYISLLLGSRVVAEGLTFKEVRHTVILTPHWNYTETAQAIARSWRAGSHDRLKARGEAVAVTVHRLVAVPRGRDTPRSIDSDMYAVSEVKDKRIKAVERILMTSAADCSLLRSRNLYPSEFDGSRECEYGRCAYRCSNVSVEPGPLPALLGASAAEAVAQVRLDGGGDPAIMKVDMSTLWAEVTAGRRYVNRWGDGAVLRAEGGRLELSAPYGSSEEGRWGDFYKTRNLCYAKMDQDHLRADDLRDSLPQEVEELLTVSPVETIGETASAMPQEVATAILMACVQARADGKTLNVVRRDALLDFYKGFYAMGPSGWTVWLHARGANAKVYDGRRWNPADEDTLEFLAARSAKFTDTRIGYYGLYNPNLKDFCIRDVTQGKRDKVDLRKLTVGRRCVDWDQRTLVHIVARLMKIDGRRDFMPHATLREMRELAEQDPLHEPSDLTSKEACRRFLFWTQKGDNKFRRQDICKAMEKWFIENDLMEDNFDCGHQHKRRGKFA|\n",
      "|>sp|Q91G85          |009R_IIV6 |Uncharacterizedprotein009R                |Invertebrateiridescentvirus6OX=176652|IIV6-009R|3               |1              |MIKLFCVLAAFISINSACQSSHQQREEFTVATYHSSSICTTYCYSNCVVASQHKGLNVESYTCDKPDPYGRETVCKCTLIKCHDI                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |\n",
      "|>sp|Q6GZW5          |010R_FRG3G|Uncharacterizedprotein010R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-010R |4               |1              |MKMDTDCRHWIVLASVPVLTVLAFKGEGALALAGLLVMAAVAMYRDRTEKKYSAARAPSPIAGHKTAYVTDPSAFAAGTVPVYPAPSNMGSDRFEGWVGGVLTGVGSSHLDHRKFAERQLVDRREKMVGYGWTKSFF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |\n",
      "|>sp|Q197E9          |011L_IIV3 |Uncharacterizedprotein011L                |Invertebrateiridescentvirus3OX=345201|IIV3-011L|4               |1              |MMESPKYKKSTCSVTNLGGTCILPQKGATAPKAKDVSPELLVNKMDNLCQDWARTRNEYNKVHIEQAPTDSYFGVVHSHTPKKKYTSRDSDSEPEATSTRRSATAQRAANLKSSPVDQWSTTPPQPQPQPAAPTVKKTCASSPPAALSVKRTCTSPPPPPVLIDDDTGEDAFYDTNDPDIFYDIENGVSELETEGPKRPVYYQRNIRYPIDGSVPQESEQWYDPIDDEFLASSGDVVSLEPSPIAAFQPTPPKTVQFVPMPEEIIVPPPPPPKTVVDEGVQAMPYTVDQMIQTDFEESPLLANVNLRTIPIEEVNPNFSPVLMQDMVRDSFVFGTVAQRVMASQRVKQFFKELIEQDVSLAGRMCMDSGSPQLNLYNSLMGVKLLYRWRSSTTFYRAIVPEIDEPVQVMQDVLSSSEWAKFDSQAGIPPKMVYIHYKLLNDLVKTLICPNFQLTHAALVCVDCRPEAVGSDGLQDGRQRRCSNLVSEYHEMTLEDLFNTIKPADLNAKNIILSVLFQMLYAVATVQKQFGMGGLFANADSVHVRRIQPGGFWHYTVNGLRYSVPNYGYLVILTNFTDVVNYRPDFATTRYFGRRQAKVVPTRNWYKFVPFTTRYRPFVTVDPITQAKTTAYAPNPPTEGITINEFYKDSSDLRPSVPVDLNDMITFPVPEFHLTICRLFSFFSKFYDSNFIGNDPFVRNLVDRYSQPFEFPDVYWPEDGVSRVLACYTIEEIYPNWVDGDTDYVIESYNLD                                                                                                                                                                                                     |\n",
      "|>sp|Q6GZW4          |011R_FRG3G|Uncharacterizedprotein011R                |Frogvirus3(isolateGoorha)OX=654924   |FV3-011R |4               |1              |MTSVKTIAMLAMLVIVAALIYMGYRTFTSMQSKLNELESRVNAPQLRPPVMSPIVPLNFIESEDLDKELD                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |\n",
      "|>sp|Q6GZW3          |012L_FRG3G|Uncharacterizedprotein012L                |Frogvirus3(isolateGoorha)OX=654924   |FV3-012L |4               |1              |MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVPAQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTAHTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAMEAAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEEETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADPTLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |\n",
      "|>sp|Q197E7          |013L_IIV3 |UncharacterizedproteinIIV3-013L           |Invertebrateiridescentvirus3OX=345201|IIV3-013L|4               |1              |MYYRDQYGNVKYAPEGMGPHHAASSSHHSAQHHHMTKENFSMDDVHSWFEKYKMWFLYALILALIFGVFMWWSKYNHDKKRSLNTASIFY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |\n",
      "+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n",
      "only showing top 20 rows\n",
      "\n"
     ]
    }
   ],
   "source": [
    "ds.show(20, False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": true
   },
   "source": [
    "## Terminate Spark"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "sc.stop()"
   ]
  }
 ],
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   "file_extension": ".py",
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   "nbconvert_exporter": "python",
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