# HG changeset patch # User bgruening # Date 1537021415 14400 # Node ID f7ebd1b4783bd4536065b24df58c522c88187982 # Parent 144e9558d3fd9cfffd677d99f5e8036dbe258faf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit f4fd11072886b30675afb8f8bb459eba9c4671bb 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 @@ -1,4 +1,26 @@ ->sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens GN=AAMP PE=1 SV=2 +>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 +MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS +YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF +AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY +SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP +LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP +RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG +PLLQFSMRR +>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 +MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD +VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP +FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI +TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS +LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA +VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG +RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR +HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS +DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ +RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM +SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN +GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI +ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD +>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens OX=9606 GN=AAMP PE=1 SV=2 MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM @@ -7,7 +29,51 @@ ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG DHKAKVFCVQRPDR ->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 +>sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens OX=9606 GN=ABLIM1 PE=1 SV=3 +MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL +LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI +KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN +CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL +ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG +DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP +GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER +QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP +GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS +SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR +QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG +RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM +LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF +>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 +MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL +ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV +GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA +TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS +FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA +AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA +RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP +GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR +AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE +LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP +>tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) OX=192222 GN=fdhC PE=4 SV=1 +MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA +LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF +GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK +RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI +VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP +SFSYDPNVKI +>tr|A0A077ZHN8|A0A077ZHN8_TRITR HAMP and MCPsignal and TarH and Cytochrom B N dom ain containing protein OS=Trichuris trichiura OX=36087 GN=TTRE_0000819801 PE=4 SV=1 +MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG +HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF +VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM +KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM +FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL +VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG +MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH +HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV +EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST +IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ +AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV +>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 OX=36087 GN=TTRE_0000758701 PE=3 SV=1 MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP GFVIGGVPGNFEVSARLGESNFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDHAD @@ -25,52 +91,7 @@ ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ LKTTRNAYHQKYR ->tr|A0A077ZHN8|A0A077ZHN8_TRITR HAMP and MCPsignal and TarH and Cytochrom B N dom ain containing protein OS=Trichuris trichiura GN=TTRE_0000819801 PE=4 SV=1 -MEFRGFFPRSDRPLINMVHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLG -HLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYF -VIGSALAGYFLWQADRDQRDVTAEIEIRTGLANSSDFLRSARINMIQAGAASRIAEMEAM -KRNIAQAESEIKQSQQGYRAYQNRPVKTPADEALDTELNQRFQAYITGMQPMLKYAKNGM -FEAIINHESEQIRPLDNAYTDILNKAVKIRSTRANQLAELAHQRTRLGGMFMIGAFVLAL -VMTLITFMVLRRIVIRPLQHAAQRIEKIASGDLTMNDEPAGRNEIGRLSRHLQQMQHSLG -MTVGTVRQGAEEIYRGTSEISAGNADLSSRTEEQAAAIEQTAASMEQLTATVKQNADNAH -HASKLAQEASIKASDGGQTVSGVVKTMGAISTSSKKISEITAVINSIAFQTNILALNAAV -EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST -IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ -AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV ->tr|A0A077Z587|A0A077Z587_TRITR Kelch 3 and Kelch 4 and Cytochrom B561 domain con taining protein OS=Trichuris trichiura GN=TTRE_0000309301 PE=4 SV=1 -MGSQQAADETQKVVERIILNINVRKDKRSFGLGIKIKKGNVFVSSIRPGSIAEDHFKLYD -VIKDVNGSRIDSRELCRDLIRTHKVLTVTVERELSKNIEQPGQGDRKSSTECPYLETAQP -FSEMEKNQWSKLPADVREILKKQFATASQYGLQAPARTEQPTQTEHRKVSVLENIVRFEI -TSDVPRDKSLRKPSDGQQLYKIVASYQCISLLADQMIIYLWLRIGWLILTFNLFVTQAVS -LHWKRVAEYGKNPRPQARKHAAFGYDMLRHYVVLFGGQGERDENYNDTWIFDVLAGRWYA -VHRNVAPPAMHGAAFGLNDGKFYLVGGCDQTQCFDDVWVFLTSTFEWHKLAPKGELRPTG -RLGAIGGFYATGSHIIYGLGTTINDQFLEDIFFFDIPMQRWYKIIERLFVYSPFTPHPRR -HMSSLMVSPSEVLLFGGCSKHGQCPTGDAWLFNVQSHVWQSLPFCPSPRMEASAVTLLSS -DDVEPKPAAVLIYGGRRYTSQHLLGSPMLEPDEVVIYDLVGKSWSIRSSKYEDSSGLPEQ -RSAASTASTLTEVYMFGGEAYDGRLLDDFWMLAGDWRESATNQKCQQVNFNLLALHGLLM -SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN -GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI -ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD ->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 -MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS -YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF -AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY -SRVSEEVRNAFSSHQDIKIGPELNSCVYLRACIEETLRMSPPVGAALWREIGPGGMNIGP -LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP -RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG -PLLQFSMRR ->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 -MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL -ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV -GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA -TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS -FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA -AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA -RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP -GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR -AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE -LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP ->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 +>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 MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA @@ -81,24 +102,3 @@ VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT DVPHDLVDRTVELRVAGDRVRTE ->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 -MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA -LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF -GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK -RPVPAGKFNFGQKSWYYIAVFGGFLMIITGGFMYFLDFNSTAIQGLFGLTQIELLRISAI -VHNFLGIVCAVFFGVHIYMAVFAIKGSIHSMISGYKEEEEVYILHSYWYKELSNKKQIEP -SFSYDPNVKI ->sp|O14639|ABLM1_HUMAN Actin-binding LIM protein 1 OS=Homo sapiens GN=ABLIM1 PE=1 SV=3 -MPAFLGLKCLGKLCSSEKSKVTSSERTSARGSNRKRLIVEDRRVSGTSFTAHRRATITHL -LYLCPKDYCPRGRVCNSVDPFVAHPQDPHHPSEKPVIHCHKCGEPCKGEVLRVQTKHFHI -KCFTCKVCGCDLAQGGFFIKNGEYLCTLDYQRMYGTRCHGCGEFVEGEVVTALGKTYHPN -CFACTICKRPFPPGDRVTFNGRDCLCQLCAQPMSSSPKETTFSSNCAGCGRDIKNGQALL -ALDKQWHLGCFKCKSCGKVLTGEYISKDGAPYCEKDYQGLFGVKCEACHQFITGKVLEAG -DKHYHPSCARCSRCNQMFTEGEEMYLQGSTVWHPDCKQSTKTEEKLRPTRTSSESIYSRP -GSSIPGSPGHTIYAKVDNEILDYKDLAAIPKVKAIYDIERPDLITYEPFYTSGYDDKQER -QSLGESPRTLSPTPSAEGYQDVRDRMIHRSTSQGSINSPVYSRHSYTPTTSRSPQHFHRP -GNEPSSGRNSPLPYRPDSRPLTPTYAQAPKHFHVPDQGINIYRKPPIYKQHAALAAQSKS -SEDIIKFSKFPAAQAPDPSETPKIETDHWPGPPSFAVVGPDMKRRSSGREEDDEELLRRR -QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG -RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM -LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF 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 @@ -1,26 +1,12 @@ ##gff-version 3 -##sequence-region S0DS17 1 369 -S0DS17 UniProtKB Chain 1 369 . . . ID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8 -S0DS17 UniProtKB Metal binding 303 303 . . . Note=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798 ##sequence-region A0A077Z587 1 772 A0A077Z587 UniProtKB Transmembrane 593 617 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius A0A077Z587 UniProtKB Transmembrane 637 656 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius A0A077Z587 UniProtKB Transmembrane 668 692 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius A0A077Z587 UniProtKB Transmembrane 704 727 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius A0A077Z587 UniProtKB Transmembrane 733 755 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -A0A077Z587 UniProtKB Domain 20 94 . . . Note=PDZ (DHR);Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50106 +A0A077Z587 UniProtKB Domain 20 94 . . . Note=PDZ;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50106 A0A077Z587 UniProtKB Domain 552 761 . . . Note=Cytochrome b561;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50939 -##sequence-region A0A077ZFY8 1 973 -A0A077ZFY8 UniProtKB Domain 1 89 . . . Note=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225 -A0A077ZFY8 UniProtKB Domain 96 279 . . . Note=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245 -A0A077ZFY8 UniProtKB Domain 300 349 . . . Note=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875 -##sequence-region Q0P8A9 1 310 -Q0P8A9 UniProtKB Transmembrane 55 78 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -Q0P8A9 UniProtKB Transmembrane 99 124 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -Q0P8A9 UniProtKB Transmembrane 136 156 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -Q0P8A9 UniProtKB Transmembrane 195 216 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -Q0P8A9 UniProtKB Transmembrane 244 264 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -Q0P8A9 UniProtKB Domain 93 274 . . . Note=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292 ##sequence-region A0A077ZHN8 1 634 A0A077ZHN8 UniProtKB Transmembrane 14 36 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius A0A077ZHN8 UniProtKB Transmembrane 56 80 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius @@ -30,6 +16,12 @@ A0A077ZHN8 UniProtKB Domain 369 598 . . . Note=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111 A0A077ZHN8 UniProtKB Coiled coil 170 204 . . . Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils A0A077ZHN8 UniProtKB Coiled coil 569 607 . . . Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils +##sequence-region A0A077ZFY8 1 973 +A0A077ZFY8 UniProtKB Domain 1 89 . . . Note=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225 +A0A077ZFY8 UniProtKB Domain 96 279 . . . Note=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245 +A0A077ZFY8 UniProtKB Domain 300 349 . . . Note=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875 +A0A077ZFY8 UniProtKB Coiled coil 867 887 . . . Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils +A0A077ZFY8 UniProtKB Coiled coil 951 971 . . . Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils ##sequence-region M5BAG7 1 563 M5BAG7 UniProtKB Transmembrane 21 43 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius M5BAG7 UniProtKB Transmembrane 49 71 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius @@ -40,28 +32,6 @@ M5BAG7 UniProtKB Domain 20 301 . . . Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929 M5BAG7 UniProtKB Domain 345 559 . . . Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893 M5BAG7 UniProtKB Nucleotide binding 379 386 . . . Note=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434 -##sequence-region Q13685 1 434 -Q13685 UniProtKB Chain 1 434 . . . ID=PRO_0000050832;Note=Angio-associated migratory cell protein -Q13685 UniProtKB Repeat 89 129 . . . Note=WD 1 -Q13685 UniProtKB Repeat 132 171 . . . Note=WD 2 -Q13685 UniProtKB Repeat 173 212 . . . Note=WD 3 -Q13685 UniProtKB Repeat 214 254 . . . Note=WD 4 -Q13685 UniProtKB Repeat 258 299 . . . Note=WD 5 -Q13685 UniProtKB Repeat 315 354 . . . Note=WD 6 -Q13685 UniProtKB Repeat 356 395 . . . Note=WD 7 -Q13685 UniProtKB Repeat 398 433 . . . Note=WD 8 -Q13685 UniProtKB Compositional bias 53 59 . . . Note=Poly-Glu -Q13685 UniProtKB Modified residue 20 20 . . . Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 -Q13685 UniProtKB Natural variant 250 250 . . . ID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835 -##sequence-region M5B8V9 1 582 -M5B8V9 UniProtKB Transmembrane 20 43 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -M5B8V9 UniProtKB Transmembrane 55 77 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -M5B8V9 UniProtKB Transmembrane 134 154 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -M5B8V9 UniProtKB Transmembrane 161 180 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -M5B8V9 UniProtKB Transmembrane 236 260 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -M5B8V9 UniProtKB Domain 20 302 . . . Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929 -M5B8V9 UniProtKB Domain 340 570 . . . Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893 -M5B8V9 UniProtKB Nucleotide binding 372 379 . . . Note=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434 ##sequence-region O14639 1 778 O14639 UniProtKB Chain 1 778 . . . ID=PRO_0000075697;Note=Actin-binding LIM protein 1 O14639 UniProtKB Domain 97 156 . . . Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125 @@ -89,6 +59,7 @@ O14639 UniProtKB Modified residue 655 655 . . . Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 O14639 UniProtKB Modified residue 677 677 . . . Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8K4G5 O14639 UniProtKB Modified residue 706 706 . . . Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 +O14639 UniProtKB Cross-link 620 620 . . . Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:28112733;Dbxref=PMID:28112733 O14639 UniProtKB Alternative sequence 1 316 . . . ID=VSP_012099;Note=In isoform 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 O14639 UniProtKB Alternative sequence 1 81 . . . ID=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 O14639 UniProtKB Alternative sequence 347 347 . . . ID=VSP_041185;Note=In isoform 5 and isoform 6. R->RLPNIRRSSSDFFYSKSLIRRTGRSPSLQ;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 @@ -101,3 +72,35 @@ O14639 UniProtKB Sequence conflict 532 532 . . . Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 O14639 UniProtKB Sequence conflict 563 563 . . . Note=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 O14639 UniProtKB Sequence conflict 578 578 . . . Note=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305 +##sequence-region S0DS17 1 369 +S0DS17 UniProtKB Chain 1 369 . . . ID=PRO_0000437163;Note=Cytochrome P450 monooxygenase apf8 +S0DS17 UniProtKB Metal binding 303 303 . . . Note=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798 +##sequence-region Q0P8A9 1 310 +Q0P8A9 UniProtKB Transmembrane 55 78 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +Q0P8A9 UniProtKB Transmembrane 99 124 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +Q0P8A9 UniProtKB Transmembrane 136 156 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +Q0P8A9 UniProtKB Transmembrane 195 216 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +Q0P8A9 UniProtKB Transmembrane 244 264 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +Q0P8A9 UniProtKB Domain 93 274 . . . Note=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292 +##sequence-region M5B8V9 1 582 +M5B8V9 UniProtKB Transmembrane 20 43 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +M5B8V9 UniProtKB Transmembrane 55 77 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +M5B8V9 UniProtKB Transmembrane 134 154 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +M5B8V9 UniProtKB Transmembrane 161 180 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +M5B8V9 UniProtKB Transmembrane 236 260 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +M5B8V9 UniProtKB Domain 20 302 . . . Note=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929 +M5B8V9 UniProtKB Domain 340 570 . . . Note=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893 +M5B8V9 UniProtKB Nucleotide binding 372 379 . . . Note=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434 +##sequence-region Q13685 1 434 +Q13685 UniProtKB Chain 1 434 . . . ID=PRO_0000050832;Note=Angio-associated migratory cell protein +Q13685 UniProtKB Repeat 89 129 . . . Note=WD 1 +Q13685 UniProtKB Repeat 132 171 . . . Note=WD 2 +Q13685 UniProtKB Repeat 173 212 . . . Note=WD 3 +Q13685 UniProtKB Repeat 214 254 . . . Note=WD 4 +Q13685 UniProtKB Repeat 258 299 . . . Note=WD 5 +Q13685 UniProtKB Repeat 315 354 . . . Note=WD 6 +Q13685 UniProtKB Repeat 356 395 . . . Note=WD 7 +Q13685 UniProtKB Repeat 398 433 . . . Note=WD 8 +Q13685 UniProtKB Compositional bias 53 59 . . . Note=Poly-Glu +Q13685 UniProtKB Modified residue 20 20 . . . Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 +Q13685 UniProtKB Natural variant 250 250 . . . ID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835 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,