This demo shows how to create and query a UniProt dataset.
UniPort
In [1]:
from pyspark import SparkConf, SparkContext, SQLContext
from mmtfPyspark.datasets import uniProt
In [2]:
conf = SparkConf().setMaster("local[*]") \
.setAppName("UniprotDemo")
sc = SparkContext(conf = conf)
In [3]:
ds = uniProt.get_dataset(uniProt.SWISS_PROT)
In [4]:
ds.show(20, False)
+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|db |uniqueIdentifier|entryName |proteinName |organismName |geneName |proteinExistence|sequenceVersion|sequence |
+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
|>sp|Q6GZX4 |001R_FRG3G|Putativetranscriptionfactor001R |Frogvirus3(isolateGoorha)OX=654924 |FV3-001R |4 |1 |MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWKFTPL |
|>sp|Q6GZX3 |002L_FRG3G|Uncharacterizedprotein002L |Frogvirus3(isolateGoorha)OX=654924 |FV3-002L |4 |1 |MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRKVMFFVAGAVLVAILISTVRW |
|>sp|Q197F8 |002R_IIV3 |Uncharacterizedprotein002R |Invertebrateiridescentvirus3OX=345201|IIV3-002R|4 |1 |MASNTVSAQGGSNRPVRDFSNIQDVAQFLLFDPIWNEQPGSIVPWKMNREQALAERYPELQTSEPSEDYSGPVESLELLPLEIKLDIMQYLSWEQISWCKHPWLWTRWYKDNVVRVSAITFEDFQREYAFPEKIQEIHFTDTRAEEIKAILETTPNVTRLVIRRIDDMNYNTHGDLGLDDLEFLTHLMVEDACGFTDFWAPSLTHLTIKNLDMHPRWFGPVMDGIKSMQSTLKYLYIFETYGVNKPFVQWCTDNIETFYCTNSYRYENVPRPIYVWVLFQEDEWHGYRVEDNKFHRRYMYSTILHKRDTDWVENNPLKTPAQVEMYKFLLRISQLNRDGTGYESDSDPENEHFDDESFSSGEEDSSDEDDPTWAPDSDDSDWETETEEEPSVAARILEKGKLTITNLMKSLGFKPKPKKIQSIDRYFCSLDSNYNSEDEDFEYDSDSEDDDSDSEDDC |
|>sp|Q197F7 |003L_IIV3 |Uncharacterizedprotein003L |Invertebrateiridescentvirus3OX=345201|IIV3-003L|4 |1 |MYQAINPCPQSWYGSPQLEREIVCKMSGAPHYPNYYPVHPNALGGAWFDTSLNARSLTTTPSLTTCTPPSLAACTPPTSLGMVDSPPHINPPRRIGTLCFDFGSAKSPQRCECVASDRPSTTSNTAPDTYRLLITNSKTRKNNYGTCRLEPLTYGI |
|>sp|Q6GZX2 |003R_FRG3G|Uncharacterizedprotein3R |Frogvirus3(isolateGoorha)OX=654924 |FV3-003R |3 |1 |MARPLLGKTSSVRRRLESLSACSIFFFLRKFCQKMASLVFLNSPVYQMSNILLTERRQVDRAMGGSDDDGVMVVALSPSDFKTVLGSALLAVERDMVHVVPKYLQTPGILHDMLVLLTPIFGEALSVDMSGATDVMVQQIATAGFVDVDPLHSSVSWKDNVSCPVALLAVSNAVRTMMGQPCQVTLIIDVGTQNILRDLVNLPVEMSGDLQVMAYTKDPLGKVPAVGVSVFDSGSVQKGDAHSVGAPDGLVSFHTHPVSSAVELNYHAGWPSNVDMSSLLTMKNLMHVVVAEEGLWTMARTLSMQRLTKVLTDAEKDVMRAAAFNLFLPLNELRVMGTKDSNNKSLKTYFEVFETFTIGALMKHSGVTPTAFVDRRWLDNTIYHMGFIPWGRDMRFVVEYDLDGTNPFLNTVPTLMSVKRKAKIQEMFDNMVSRMVTS |
|>sp|Q6GZX1 |004R_FRG3G|Uncharacterizedprotein004R |Frogvirus3(isolateGoorha)OX=654924 |FV3-004R |4 |1 |MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY |
|>sp|Q197F5 |005L_IIV3 |Uncharacterizedprotein005L |Invertebrateiridescentvirus3OX=345201|IIV3-005L|3 |1 |MRYTVLIALQGALLLLLLIDDGQGQSPYPYPGMPCNSSRQCGLGTCVHSRCAHCSSDGTLCSPEDPTMVWPCCPESSCQLVVGLPSLVNHYNCLPNQCTDSSQCPGGFGCMTRRSKCELCKADGEACNSPYLDWRKDKECCSGYCHTEARGLEGVCIDPKKIFCTPKNPWQLAPYPPSYHQPTTLRPPTSLYDSWLMSGFLVKSTTAPSTQEEEDDY |
|>sp|Q6GZX0 |005R_FRG3G|Uncharacterizedprotein005R |Frogvirus3(isolateGoorha)OX=654924 |FV3-005R |4 |1 |MQNPLPEVMSPEHDKRTTTPMSKEANKFIRELDKKPGDLAVVSDFVKRNTGKRLPIGKRSNLYVRICDLSGTIYMGETFILESWEELYLPEPTKMEVLGTLESCCGIPPFPEWIVMVGEDQCVYAYGDEEILLFAYSVKQLVEEGIQETGISYKYPDDISDVDEEVLQQDEEIQKIRKKTREFVDKDAQEFQDFLNSLDASLLS |
|>sp|Q91G88 |006L_IIV6 |PutativeKilA-Ndomain-containingprotein006L|Invertebrateiridescentvirus6OX=176652|IIV6-006L|3 |1 |MDSLNEVCYEQIKGTFYKGLFGDFPLIVDKKTGCFNATKLCVLGGKRFVDWNKTLRSKKLIQYYETRCDIKTESLLYEIKGDNNDEITKQITGTYLPKEFILDIASWISVEFYDKCNNIIINYFVNEYKTMDKKTLQSKINEVEEKMQKLLNEKEEELQEKNDKIDELILFSKRMEEDRKKDREMMIKQEKMLRELGIHLEDVSSQNNELIEKVDEQVEQNAVLNFKIDNIQNKLEIAVEDRAPQPKQNLKRERFILLKRNDDYYPYYTIRAQDINARSALKRQKNLYNEVSVLLDLTCHPNSKTLYVRVKDELKQKGVVFNLCKVSISNSKINEEELIKAMETINDEKRDV |
|>sp|Q6GZW9 |006R_FRG3G|Uncharacterizedprotein006R |Frogvirus3(isolateGoorha)OX=654924 |FV3-006R |4 |1 |MYKMYFLKDQKFSLSGTIRINDKTQSEYGSVWCPGLSITGLHHDAIDHNMFEEMETEIIEYLGPWVQAEYRRIKG |
|>sp|Q6GZW8 |007R_FRG3G|Uncharacterizedprotein007R |Frogvirus3(isolateGoorha)OX=654924 |FV3-007R |4 |1 |MRSIKPLRCCNAHGRHVSQEYGRCTLLLFREKLFLQTGLVCNKQCNAPNNDGAESKHHGIHHGSRGALALRGAGVHLLASAALGPRVLAGLVPTGRSVQGSVGQCGRVAQIGRARDVAARKQESYCEK |
|>sp|Q197F3 |007R_IIV3 |Uncharacterizedprotein007R |Invertebrateiridescentvirus3OX=345201|IIV3-007R|4 |1 |MEAKNITIDNTTYNFFKFYNINQPLTNLKYLNSERLCFSNAVMGKIVDDASTITITYHRVYFGISGPKPRQVADLGEYYDVNELLNYDTYTKTQEFAQKYNSLVKPTIDAKNWSGNELVLLVGNEWYCKTFGKAGSKNVFLYNMIPTIYRDEPQHQEQILKKFMFFNATKNVEQNPNFLDNVPEEYYHLLLPKSWVEKNLSDKYRKIMETEHKPLVFSCEPAFSFGLCRNTQDKNESYQLSLCLYEREKPRDAEIVWAAKYDELAAMVRDYLKKTPEFKKYRSFISCMKGLSWKNNEIGDKDGPKLYPKVIFNRKKGEFVTIFTKDDDVEPETIEDPRTILDRRCVVQAALRLESVFVHNKVAIQLRINDVLISEWKEASSKPQPLILRRHRFTKPSSSVAKSTSPSLRNSGSDESDLNQSDSDKEDERVVPVPKTKRIVKTVKLPN |
|>sp|Q197F2 |008L_IIV3 |Uncharacterizedprotein008L |Invertebrateiridescentvirus3OX=345201|IIV3-008L|4 |1 |MSFKVYDPIAELIATQFPTSNPDLQIINNDVLVVSPHKITLPMGPQNAGDVTNKAYVDQAVMSAAVPVASSTTVGTIQMAGDLEGSSGTNPIIAANKITLNKLQKIGPKMVIGNPNSDWNNTQEIELDSSFRIVDNRLNAGIVPISSTDPNKSNTVIPAPQQNGLFYLDSSGRVWVWAEHYYKCITPSRYISKWMGVGDFQELTVGQSVMWDSGRPSIETVSTQGLEVEWISSTNFTLSSLYLIPIVVKVTICIPLLGQPDQMAKFVLYSVSSAQQPRTGIVLTTDSSRSSAPIVSEYITVNWFEPKSYSVQLKEVNSDSGTTVTICSDKWLANPFLDCWITIEEVG |
|>sp|Q6GZW6 |009L_FRG3G|Putativehelicase009L |Frogvirus3(isolateGoorha)OX=654924 |FV3-009L |4 |1 |MDTSPYDFLKLYPWLSRGEADKGTLLDAFPGETFEQSLASDVAMRRAVQDDPAFGHQKLVETFLSEDTPYRELLLFHAPGTGKTCTVVSVAERAKEKGLTRGCIVLARGAALLRNFLHELVFNCGTGGRYIPEGYADMGDQERTRKMRKAVSSYYQFRTYETFAKSVATMSAEAIRARYDRFVIVMDEVHHLRSVQAEGVNTYSAISRFLRTVRGCVKMLLTGTPMTNEPGELADVLNLILPQDKTIRPEDGIFSNSGDLLKPDELAERVRGRVSYLKAARPDAGLTFAGEVLGGTGMTHLRLVRLEMSAFQSDAYASAWDQDAGDRNIFSNSRQCSLAVMPDRRWGSAAEARNPSQVRRMAGQNLAEYSVKYDYLVRVASSSPKTFAYCEYVNGSGLSLLSDILLANGWRRATGRETTPGKRFALLTASQKNIHKIVQRFNHEDNVDGAYISLLLGSRVVAEGLTFKEVRHTVILTPHWNYTETAQAIARSWRAGSHDRLKARGEAVAVTVHRLVAVPRGRDTPRSIDSDMYAVSEVKDKRIKAVERILMTSAADCSLLRSRNLYPSEFDGSRECEYGRCAYRCSNVSVEPGPLPALLGASAAEAVAQVRLDGGGDPAIMKVDMSTLWAEVTAGRRYVNRWGDGAVLRAEGGRLELSAPYGSSEEGRWGDFYKTRNLCYAKMDQDHLRADDLRDSLPQEVEELLTVSPVETIGETASAMPQEVATAILMACVQARADGKTLNVVRRDALLDFYKGFYAMGPSGWTVWLHARGANAKVYDGRRWNPADEDTLEFLAARSAKFTDTRIGYYGLYNPNLKDFCIRDVTQGKRDKVDLRKLTVGRRCVDWDQRTLVHIVARLMKIDGRRDFMPHATLREMRELAEQDPLHEPSDLTSKEACRRFLFWTQKGDNKFRRQDICKAMEKWFIENDLMEDNFDCGHQHKRRGKFA|
|>sp|Q91G85 |009R_IIV6 |Uncharacterizedprotein009R |Invertebrateiridescentvirus6OX=176652|IIV6-009R|3 |1 |MIKLFCVLAAFISINSACQSSHQQREEFTVATYHSSSICTTYCYSNCVVASQHKGLNVESYTCDKPDPYGRETVCKCTLIKCHDI |
|>sp|Q6GZW5 |010R_FRG3G|Uncharacterizedprotein010R |Frogvirus3(isolateGoorha)OX=654924 |FV3-010R |4 |1 |MKMDTDCRHWIVLASVPVLTVLAFKGEGALALAGLLVMAAVAMYRDRTEKKYSAARAPSPIAGHKTAYVTDPSAFAAGTVPVYPAPSNMGSDRFEGWVGGVLTGVGSSHLDHRKFAERQLVDRREKMVGYGWTKSFF |
|>sp|Q197E9 |011L_IIV3 |Uncharacterizedprotein011L |Invertebrateiridescentvirus3OX=345201|IIV3-011L|4 |1 |MMESPKYKKSTCSVTNLGGTCILPQKGATAPKAKDVSPELLVNKMDNLCQDWARTRNEYNKVHIEQAPTDSYFGVVHSHTPKKKYTSRDSDSEPEATSTRRSATAQRAANLKSSPVDQWSTTPPQPQPQPAAPTVKKTCASSPPAALSVKRTCTSPPPPPVLIDDDTGEDAFYDTNDPDIFYDIENGVSELETEGPKRPVYYQRNIRYPIDGSVPQESEQWYDPIDDEFLASSGDVVSLEPSPIAAFQPTPPKTVQFVPMPEEIIVPPPPPPKTVVDEGVQAMPYTVDQMIQTDFEESPLLANVNLRTIPIEEVNPNFSPVLMQDMVRDSFVFGTVAQRVMASQRVKQFFKELIEQDVSLAGRMCMDSGSPQLNLYNSLMGVKLLYRWRSSTTFYRAIVPEIDEPVQVMQDVLSSSEWAKFDSQAGIPPKMVYIHYKLLNDLVKTLICPNFQLTHAALVCVDCRPEAVGSDGLQDGRQRRCSNLVSEYHEMTLEDLFNTIKPADLNAKNIILSVLFQMLYAVATVQKQFGMGGLFANADSVHVRRIQPGGFWHYTVNGLRYSVPNYGYLVILTNFTDVVNYRPDFATTRYFGRRQAKVVPTRNWYKFVPFTTRYRPFVTVDPITQAKTTAYAPNPPTEGITINEFYKDSSDLRPSVPVDLNDMITFPVPEFHLTICRLFSFFSKFYDSNFIGNDPFVRNLVDRYSQPFEFPDVYWPEDGVSRVLACYTIEEIYPNWVDGDTDYVIESYNLD |
|>sp|Q6GZW4 |011R_FRG3G|Uncharacterizedprotein011R |Frogvirus3(isolateGoorha)OX=654924 |FV3-011R |4 |1 |MTSVKTIAMLAMLVIVAALIYMGYRTFTSMQSKLNELESRVNAPQLRPPVMSPIVPLNFIESEDLDKELD |
|>sp|Q6GZW3 |012L_FRG3G|Uncharacterizedprotein012L |Frogvirus3(isolateGoorha)OX=654924 |FV3-012L |4 |1 |MCAKLVEMAFGPVNADSPPLTAEEKESAVEKLVGSKPFPALKKKYHDKVPAQDPKYCLFSFVEVLPSCDIKAAGAEEMCSCCIKRRRGQVFGVACVRGTAHTLAKAKQKADKLVGDYDSVHVVQTCHVGRPFPLVSSGMAQETVAPSAMEAAEAAMDAKSAEKRKERMRQKLEMRKREQEIKARNRKLLEDPSCDPDAEEETDLERYATLRVKTTCLLENAKNASAQIKEYLASMRKSAEAVVAMEAADPTLVENYPGLIRDSRAKMGVSKQDTEAFLKMSSFDCLTAASELETMGF |
|>sp|Q197E7 |013L_IIV3 |UncharacterizedproteinIIV3-013L |Invertebrateiridescentvirus3OX=345201|IIV3-013L|4 |1 |MYYRDQYGNVKYAPEGMGPHHAASSSHHSAQHHHMTKENFSMDDVHSWFEKYKMWFLYALILALIFGVFMWWSKYNHDKKRSLNTASIFY |
+---+----------------+----------+------------------------------------------+-------------------------------------+---------+----------------+---------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
only showing top 20 rows
In [5]:
sc.stop()