| Previous changeset 4:144e9558d3fd (2018-08-14) Next changeset 6:054483e27a35 (2018-09-16) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit f4fd11072886b30675afb8f8bb459eba9c4671bb |
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modified:
test-data/test1_retrieve.fasta test-data/test2_retrieve.gff uniprot.py |
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| diff -r 144e9558d3fd -r f7ebd1b4783b test-data/test1_retrieve.fasta --- a/test-data/test1_retrieve.fasta Tue Aug 14 16:37:28 2018 -0400 +++ b/test-data/test1_retrieve.fasta Sat Sep 15 10:23:35 2018 -0400 |
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| b'@@ -1,4 +1,26 @@\n->sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2\n+>sp|S0DS17|APF8_GIBF5 Cytochrome P450 monooxygenase apf8 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) OX=1279085 GN=apf8 PE=1 SV=1\n+MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS\n+YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF\n+AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY\n+SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP\n+LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP\n+RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG\n+PLLQFSMRR\n+>tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura OX=36087 GN=TTRE_0000309301 PE=4 SV=1\n+MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD\n+VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP\n+FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI\n+TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS\n+LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA\n+VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG\n+RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR\n+HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS\n+DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ\n+RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM\n+SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN\n+GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI\n+ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD\n+>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens OX=9606 GN=AAMP PE=1 SV=2\n MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG\n NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR\n LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM\n@@ -7,7 +29,51 @@\n ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG\n IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG\n DHKAKVFCVQRPDR\n->tr|A0A077ZFY8|A0A077ZFY8_TRITR PmbA TldD and Mur ligase M and Mur ligase and Mur ligase C and Cytochrom B562 domain containing protein OS=Trichuris trichiura GN=TTRE_0000758701 PE=3 SV=1\n+>sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens OX=9606 GN=ABLIM1 PE=1 SV=3\n+MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL\n+LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI\n+KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN\n+CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL\n+ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG\n+DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP\n+GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER\n+QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP\n+GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS\n+SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR\n+QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG\n+RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM\n+LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF\n+>tr|M5B8V9|M5B8V9_9MICO ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter nebraskensis NCPPB 2581 OX=1097677 GN=CMN_01519 PE=4 SV=1\n+MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL\n+ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV\n+GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA\n+TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS\n+FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA\n+AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA\n+RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP\n+GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR\n+AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE\n+LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP\n+>tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogen'..b'CDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG\n-RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR\n-HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS\n-DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ\n-RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM\n-SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN\n-GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI\n-ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD\n->sp|S0DS17|APF8_GIBF5 Cytochrome P450 monooxygenase apf8 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=apf8 PE=1 SV=1\n-MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS\n-YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF\n-AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY\n-SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP\n-LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP\n-RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG\n-PLLQFSMRR\n->tr|M5B8V9|M5B8V9_9MICO ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=CMN_01519 PE=4 SV=1\n-MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL\n-ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV\n-GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA\n-TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS\n-FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA\n-AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA\n-RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP\n-GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR\n-AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE\n-LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP\n->tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=4 SV=1\n+>tr|M5BAG7|M5BAG7_9MICO ABC transporter, fused permease/ABC transporter involved in the biosynthesis of cytochrom bd, fused permease/ATP-binding protein OS=Clavibacter nebraskensis NCPPB 2581 OX=1097677 GN=cydC PE=4 SV=1\n MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG\n VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG\n DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA\n@@ -81,24 +102,3 @@\n VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL\n VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT\n DVPHDLVDRTVELRVAGDRVRTE\n->tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) GN=fdhC PE=4 SV=1\n-MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA\n-LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF\n-GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK\n-RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI\n-VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP\n-SFSYDPNVKI\n->sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3\n-MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL\n-LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI\n-KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN\n-CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL\n-ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG\n-DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP\n-GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER\n-QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP\n-GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS\n-SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR\n-QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG\n-RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM\n-LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF\n' |
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| diff -r 144e9558d3fd -r f7ebd1b4783b test-data/test2_retrieve.gff --- a/test-data/test2_retrieve.gff Tue Aug 14 16:37:28 2018 -0400 +++ b/test-data/test2_retrieve.gff Sat Sep 15 10:23:35 2018 -0400 |
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| b'@@ -1,26 +1,12 @@\n ##gff-version 3\n-##sequence-region S0DS17 1 369\n-S0DS17\tUniProtKB\tChain\t1\t369\t.\t.\t.\tID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8\t\n-S0DS17\tUniProtKB\tMetal binding\t303\t303\t.\t.\t.\tNote=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798\t\n ##sequence-region A0A077Z587 1 772\n A0A077Z587\tUniProtKB\tTransmembrane\t593\t617\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077Z587\tUniProtKB\tTransmembrane\t637\t656\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077Z587\tUniProtKB\tTransmembrane\t668\t692\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077Z587\tUniProtKB\tTransmembrane\t704\t727\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077Z587\tUniProtKB\tTransmembrane\t733\t755\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077Z587\tUniProtKB\tDomain\t20\t94\t.\t.\t.\tNote=PDZ (DHR);Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50106\t\n+A0A077Z587\tUniProtKB\tDomain\t20\t94\t.\t.\t.\tNote=PDZ;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50106\t\n A0A077Z587\tUniProtKB\tDomain\t552\t761\t.\t.\t.\tNote=Cytochrome b561;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50939\t\n-##sequence-region A0A077ZFY8 1 973\n-A0A077ZFY8\tUniProtKB\tDomain\t1\t89\t.\t.\t.\tNote=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225\t\n-A0A077ZFY8\tUniProtKB\tDomain\t96\t279\t.\t.\t.\tNote=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245\t\n-A0A077ZFY8\tUniProtKB\tDomain\t300\t349\t.\t.\t.\tNote=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875\t\n-##sequence-region Q0P8A9 1 310\n-Q0P8A9\tUniProtKB\tTransmembrane\t55\t78\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t99\t124\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t136\t156\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t195\t216\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tTransmembrane\t244\t264\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-Q0P8A9\tUniProtKB\tDomain\t93\t274\t.\t.\t.\tNote=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292\t\n ##sequence-region A0A077ZHN8 1 634\n A0A077ZHN8\tUniProtKB\tTransmembrane\t14\t36\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n A0A077ZHN8\tUniProtKB\tTransmembrane\t56\t80\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n@@ -30,6 +16,12 @@\n A0A077ZHN8\tUniProtKB\tDomain\t369\t598\t.\t.\t.\tNote=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111\t\n A0A077ZHN8\tUniProtKB\tCoiled coil\t170\t204\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n A0A077ZHN8\tUniProtKB\tCoiled coil\t569\t607\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n+##sequence-region A0A077ZFY8 1 973\n+A0A077ZFY8\tUniProtKB\tDomain\t1\t89\t.\t.\t.\tNote=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225\t\n+A0A077ZFY8\tUniProtKB\tDomain\t96\t279\t.\t.\t.\tNote=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245\t\n+A0A077ZFY8\tUniProtKB\tDomain\t300\t349\t.\t.\t.\tNote=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875\t\n+A0A077ZFY8\tUniProtKB\tCoiled coil\t867\t887\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n+A0A077ZFY8\tUniProtKB\tCoiled coil\t951\t971\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n ##sequence-region M5BAG7 1 563\n M5BAG7\tUniProtKB\tTransmembrane\t21\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n M5BAG7\tUniProtKB\tTransmembrane\t49\t71\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n@@ -40,28 +32,6 @@\n M5B'..b'orm 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:17974005;Dbxref=PMID:14702039,PMID:15489334,PMID:17974005\t\n O14639\tUniProtKB\tAlternative sequence\t1\t81\t.\t.\t.\tID=VSP_012100;Note=In isoform 2 and isoform 6. MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHLLYLCPKDYCPRGRVCNSVDPF->MLMTLEMTELTDPHHTMGDYK;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7584044;Dbxref=PMID:14702039,PMID:7584044\t\n O14639\tUniProtKB\tAlternative sequence\t347\t347\t.\t.\t.\tID=VSP_041185;Note=In isoform 5 and isoform 6. R->RLPNIRRSSSDFFYSKSLIRRTGRSPSLQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039\t\n@@ -101,3 +72,35 @@\n O14639\tUniProtKB\tSequence conflict\t532\t532\t.\t.\t.\tNote=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n O14639\tUniProtKB\tSequence conflict\t563\t563\t.\t.\t.\tNote=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n O14639\tUniProtKB\tSequence conflict\t578\t578\t.\t.\t.\tNote=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n+##sequence-region S0DS17 1 369\n+S0DS17\tUniProtKB\tChain\t1\t369\t.\t.\t.\tID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8\t\n+S0DS17\tUniProtKB\tMetal binding\t303\t303\t.\t.\t.\tNote=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798\t\n+##sequence-region Q0P8A9 1 310\n+Q0P8A9\tUniProtKB\tTransmembrane\t55\t78\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t99\t124\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t136\t156\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t195\t216\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t244\t264\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tDomain\t93\t274\t.\t.\t.\tNote=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292\t\n+##sequence-region M5B8V9 1 582\n+M5B8V9\tUniProtKB\tTransmembrane\t20\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t55\t77\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t134\t154\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t161\t180\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t236\t260\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tDomain\t20\t302\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n+M5B8V9\tUniProtKB\tDomain\t340\t570\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n+M5B8V9\tUniProtKB\tNucleotide binding\t372\t379\t.\t.\t.\tNote=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434\t\n+##sequence-region Q13685 1 434\n+Q13685\tUniProtKB\tChain\t1\t434\t.\t.\t.\tID=PRO_0000050832;Note=Angio-associated migratory cell protein\t\n+Q13685\tUniProtKB\tRepeat\t89\t129\t.\t.\t.\tNote=WD 1\t\n+Q13685\tUniProtKB\tRepeat\t132\t171\t.\t.\t.\tNote=WD 2\t\n+Q13685\tUniProtKB\tRepeat\t173\t212\t.\t.\t.\tNote=WD 3\t\n+Q13685\tUniProtKB\tRepeat\t214\t254\t.\t.\t.\tNote=WD 4\t\n+Q13685\tUniProtKB\tRepeat\t258\t299\t.\t.\t.\tNote=WD 5\t\n+Q13685\tUniProtKB\tRepeat\t315\t354\t.\t.\t.\tNote=WD 6\t\n+Q13685\tUniProtKB\tRepeat\t356\t395\t.\t.\t.\tNote=WD 7\t\n+Q13685\tUniProtKB\tRepeat\t398\t433\t.\t.\t.\tNote=WD 8\t\n+Q13685\tUniProtKB\tCompositional bias\t53\t59\t.\t.\t.\tNote=Poly-Glu\t\n+Q13685\tUniProtKB\tModified residue\t20\t20\t.\t.\t.\tNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569\t\n+Q13685\tUniProtKB\tNatural variant\t250\t250\t.\t.\t.\tID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835\t\n' |
| b |
| diff -r 144e9558d3fd -r f7ebd1b4783b uniprot.py --- a/uniprot.py Tue Aug 14 16:37:28 2018 -0400 +++ b/uniprot.py Sat Sep 15 10:23:35 2018 -0400 |
| [ |
| @@ -19,12 +19,16 @@ def _retrieve(query, format='txt'): """_retrieve is not meant for use with the python interface, use `retrieve` instead""" - tool = 'batch/' + tool = 'uploadlists/' query = list(set(query.split('\n'))) queries = [query[i:i+100] for i in range(0, len(query), 100)] - data = {'format': format} + data = { + 'format': format, + 'from': 'ACC+ID', + 'to': 'ACC' + } responses = [requests.post(url + tool, data=data, files={'file': ' '.join(_)}) for _ in queries] page = ''.join(response.text for response in responses) @@ -34,7 +38,7 @@ def _map(query, f, t, format='tab'): """ _map is not meant for use with the python interface, use `map` instead """ - tool = 'mapping/' + tool = 'uploadlists/' data = { 'from': f, |