| Previous changeset 6:054483e27a35 (2018-09-16) Next changeset 8:af5eccf83605 (2022-11-21) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b" |
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modified:
macros.xml test-data/id_uniprot.tab test-data/test1_map.tab test-data/test1_retrieve.fasta test-data/test2_map.tab test-data/test2_retrieve.gff uniprot.py uniprot.xml |
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added:
test-data/test.tab |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a macros.xml --- a/macros.xml Sun Sep 16 13:41:08 2018 -0400 +++ b/macros.xml Thu Apr 22 17:32:16 2021 +0000 |
| b |
| @@ -46,7 +46,6 @@ <option value="ACC+ID">UniProtKB AC/ID</option> <option value="ACC">UniProtKB AC</option> <option value="ID">UniProtKB ID</option> - <option value="ACC">UniProtKB AC</option> <option value="UPARC">UniParc</option> <option value="NF50">UniRef50</option> <option value="NF90">UniRef90</option> @@ -59,7 +58,6 @@ help=""> <option value="ACC">UniProtKB AC</option> <option value="ID">UniProtKB ID</option> - <option value="ACC">UniProtKB AC</option> <option value="UPARC">UniParc</option> <option value="NF50">UniRef50</option> <option value="NF90">UniRef90</option> |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/id_uniprot.tab --- a/test-data/id_uniprot.tab Sun Sep 16 13:41:08 2018 -0400 +++ b/test-data/id_uniprot.tab Thu Apr 22 17:32:16 2021 +0000 |
| b |
| @@ -7,3 +7,4 @@ A0A077Z587 Q13685 O14639 +WRONGIDWHICHDOESNOTEXIST \ No newline at end of file |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/test.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.tab Thu Apr 22 17:32:16 2021 +0000 |
| b |
| b'@@ -0,0 +1,2554 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|
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/test1_map.tab --- a/test-data/test1_map.tab Sun Sep 16 13:41:08 2018 -0400 +++ b/test-data/test1_map.tab Thu Apr 22 17:32:16 2021 +0000 |
| b |
| @@ -1,10 +1,10 @@ From To -Q0P8A9 fdhC +A0A077Z587 TTRE_0000309301 +A0A077ZFY8 TTRE_0000758701 A0A077ZHN8 TTRE_0000819801 -A0A077ZFY8 TTRE_0000758701 M5B8V9 CMN_01519 M5BAG7 cydC +O14639 ABLIM1 +Q0P8A9 fdhC +Q13685 AAMP S0DS17 apf8 -A0A077Z587 TTRE_0000309301 -Q13685 AAMP -O14639 ABLIM1 |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/test1_retrieve.fasta --- a/test-data/test1_retrieve.fasta Sun Sep 16 13:41:08 2018 -0400 +++ b/test-data/test1_retrieve.fasta Thu Apr 22 17:32:16 2021 +0000 |
| b |
| @@ -1,3 +1,23 @@ +>sp|Q13685|AAMP_HUMAN Angio-associated migratory cell protein OS=Homo sapiens OX=9606 GN=AAMP PE=1 SV=2 +MESESESGAAADTPPLETLSFHGDEEIIEVVELDPGPPDPDDLAQEMEDVDFEEEEEEEG +NEEGWVLEPQEGVVGSMEGPDDSEVTFALHSASVFCVSLDPKTNTLAVTGGEDDKAFVWR +LSDGELLFECAGHKDSVTCAGFSHDSTLVATGDMSGLLKVWQVDTKEEVWSFEAGDLEWM +EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR +IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP +ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG +IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG +DHKAKVFCVQRPDR +>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 OX=1097677 GN=CMN_01519 PE=4 SV=1 +MKPLDPRLLRHSASARTMLAVGAVVSVVQTAALVAFCWSLTQLVVRAIGGADQAALAPVL +ALAVGSAVVRGAAAWLLDVTGARGAARVTAELRRRALRAIADLGPAWTAARSRGRLATIV +GPGLDALDPYFARYVPQLILTALATPIVVAVLLLSDPLTGVTVLVTLPVIPVFMVLVGWA +TQEVQRRQWSRLTELASSFLEVVDGLSTLLVFRRARRQTARIRRVTEEYRVETMRVLRIS +FLSGFVLELAASLSVALVAVSVGVRLIGGQLDLEVGLFVLLLAPEAFLPIRQVGVQFHAA +AEGVAAADDVLGILEEERAARATRPVPGPATATPPAGDALVIRDLAVARGDRAVLSGVSA +RFPRGRVTAVTGPSGVGKSSLLGAMLGHLPAGGAAGWIDDDASSLRPPVPTEIAWAGQRP +GLVAGTVRENVALGVADPDDALVRRALALAAADGIDPDLVLGVGGQGLSGGQAQRVAVAR +AVHRALALDCPLVLLDEPSSALDAATEERLAAGIRALADQGRAVVVVTHRGALVRAADAE +LRLGGASGEDDAPAAVGSSVGAGRVAPARIAPEPAWRAQVAP >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 @@ -6,6 +26,17 @@ LTLPAGVDVGTGIYSLHHNAAYHPEPFKYLPERWLVGEGSSTSESVELARSAFAPFSRGP RSCVGKGFAYHELTLTIAHILHRFDFSATEEDFALRHGSEGPGGINEFLLHDHVTGARSG PLLQFSMRR +>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 OX=1097677 GN=cydC PE=4 SV=1 +MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG +VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG +DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA +GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG +VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR +RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED +ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI +VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL +VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT +DVPHDLVDRTVELRVAGDRVRTE >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 @@ -20,41 +51,7 @@ 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 -EWHPRAPVLLAGTADGNTWMWKVPNGDCKTFQGPNCPATCGRVLPDGKRAVVGYEDGTIR -IWDLKQGSPIHVLKGTEGHQGPLTCVAANQDGSLILTGSVDCQAKLVSATTGKVVGVFRP -ETVASQPSLGEGEESESNSVESLGFCSVMPLAAVGYLDGTLAIYDLATQTLRHQCQHQSG -IVQLLWEAGTAVVYTCSLDGIVRLWDARTGRLLTDYRGHTAEILDFALSKDASLVVTTSG -DHKAKVFCVQRPDR ->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 +>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=3 SV=1 MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK @@ -91,14 +88,17 @@ ENGEIQYPVSEITIAVSSLVFSSASFAADLEDNMETLNDNLKVVEKADNAAQVKDALTKM RAAALDAQKATPPKLEGKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQ LKTTRNAYHQKYR ->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 -GRAETRIAPLRARLQDLVLDFVGGLDVLTSFGAVDDRLAAIDRAATELRRAELRSAAAAG -VTTGVVLAGTGAVAGWTVLQGVPGLASGTLDPAWLALAALVPLALVEQATAVPLAVQAWR -RVRTSAERVAGVVPETVPDEIPREPDDAADAQPVTADASPAGTTLEVRDLVTRWPGADED -ALAPVSLVVRPGETVVVRGPSGSGKSSLAAALARFLESRGAYELDGRDARSMPPSAVRRI -VGLCEQAPHLFDASIRQNLLFARDDATDDELVAVLARVGLADWTAGRGGLDARVGDRGGL -VSGGQAQRIALARALLADFPVLVLDEPTADVDAERARAVLRDVLTAARDRGPGVLLLTHT -DVPHDLVDRTVELRVAGDRVRTE +>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 |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/test2_map.tab --- a/test-data/test2_map.tab Sun Sep 16 13:41:08 2018 -0400 +++ b/test-data/test2_map.tab Thu Apr 22 17:32:16 2021 +0000 |
| b |
| @@ -1,5 +1,4 @@ From To +NM_001087 AAMP_HUMAN NM_130786 A1BG_HUMAN NM_130786 V9HWD8_HUMAN -NM_001087 A0A024R410_HUMAN -NM_001087 AAMP_HUMAN |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a test-data/test2_retrieve.gff --- a/test-data/test2_retrieve.gff Sun Sep 16 13:41:08 2018 -0400 +++ b/test-data/test2_retrieve.gff Thu Apr 22 17:32:16 2021 +0000 |
| b |
| b'@@ -1,27 +1,4 @@\n ##gff-version 3\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;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 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-A0A077ZHN8\tUniProtKB\tTransmembrane\t113\t132\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tTransmembrane\t290\t310\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n-A0A077ZHN8\tUniProtKB\tDomain\t312\t364\t.\t.\t.\tNote=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885\t\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@@ -32,6 +9,43 @@\n M5BAG7\tUniProtKB\tDomain\t20\t301\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n M5BAG7\tUniProtKB\tDomain\t345\t559\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n M5BAG7\tUniProtKB\tNucleotide binding\t379\t386\t.\t.\t.\tNote=ATP;Ontology_term=ECO:0000256;evidence=ECO:0000256|PROSITE-ProRule:PRU00434\t\n+M5BAG7\tUniProtKB\tRegion\t317\t337\t.\t.\t.\tNote=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite\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+A0A077ZHN8\tUniProtKB\tTransmembrane\t113\t132\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t290\t310\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tDomain\t312\t364\t.\t.\t.\tNote=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885\t\n+A0A077ZHN8\tUniProtKB\tDomain\t369\t598\t.'..b'0P8A9\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 O14639 1 778\n O14639\tUniProtKB\tChain\t1\t778\t.\t.\t.\tID=PRO_0000075697;Note=Actin-binding LIM protein 1\t\n O14639\tUniProtKB\tDomain\t97\t156\t.\t.\t.\tNote=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n@@ -72,25 +86,12 @@\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 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 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' |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a uniprot.py --- a/uniprot.py Sun Sep 16 13:41:08 2018 -0400 +++ b/uniprot.py Thu Apr 22 17:32:16 2021 +0000 |
| [ |
| @@ -7,47 +7,61 @@ available services: map retrieve + +rewitten using inspiration form: https://findwork.dev/blog/advanced-usage-python-requests-timeouts-retries-hooks/ """ import argparse import sys import requests +from requests.adapters import HTTPAdapter +from requests.packages.urllib3.util.retry import Retry -url = 'https://www.uniprot.org/' + +DEFAULT_TIMEOUT = 5 # seconds +URL = 'https://www.uniprot.org/' + +retry_strategy = Retry( + total=5, + backoff_factor=2, + status_forcelist=[429, 500, 502, 503, 504], + allowed_methods=["HEAD", "GET", "OPTIONS", "POST"] +) -def _retrieve(query, format='txt'): - """_retrieve is not meant for use with the python interface, use `retrieve` - instead""" - tool = 'uploadlists/' - - query = list(set(query.split('\n'))) - queries = [query[i:i+100] for i in range(0, len(query), 100)] +class TimeoutHTTPAdapter(HTTPAdapter): + def __init__(self, *args, **kwargs): + self.timeout = DEFAULT_TIMEOUT + if "timeout" in kwargs: + self.timeout = kwargs["timeout"] + del kwargs["timeout"] + super().__init__(*args, **kwargs) - 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) - return page + def send(self, request, **kwargs): + timeout = kwargs.get("timeout") + if timeout is None: + kwargs["timeout"] = self.timeout + return super().send(request, **kwargs) -def _map(query, f, t, format='tab'): +def _map(query, f, t, format='tab', chunk_size=100): """ _map is not meant for use with the python interface, use `map` instead """ tool = 'uploadlists/' + data = {'format': format, 'from': f, 'to': t} - data = { - 'from': f, - 'to': t, - 'format': format, - 'query': query - } - response = requests.post(url + tool, data=data) + req = [] + for i in range(0, len(query), chunk_size): + q = query[i:i + chunk_size] + req.append(dict([("url", URL + tool), + ('data', data), + ("files", {'file': ' '.join(q)})])) + return req + response = requests.post(URL + tool, data=data) + response.raise_for_status() page = response.text + if "The service is temporarily unavailable" in page: + exit("The UNIPROT service is temporarily unavailable. Please try again later.") return page @@ -72,10 +86,23 @@ retrieve.add_argument('-f', '--format', help='specify output format', default='txt') args = parser.parse_args() - query = args.inp.read() + + # get the IDs from the file as sorted list + # (sorted is convenient for testing) + query = set() + for line in args.inp: + query.add(line.strip()) + query = sorted(query) if args.tool == 'map': - args.out.write(_map(query, args.f, args.t, args.format)) + pload = _map(query, args.f, args.t, chunk_size=100) + elif args.tool == 'retrieve': + pload = _map(query, 'ACC+ID', 'ACC', args.format, chunk_size=100) - elif args.tool == 'retrieve': - args.out.write(_retrieve(query, format=args.format)) + adapter = TimeoutHTTPAdapter(max_retries=retry_strategy) + http = requests.Session() + http.mount("https://", adapter) + for i, p in enumerate(pload): + response = http.post(**p) + args.out.write(response.text) + http.close() |
| b |
| diff -r 054483e27a35 -r bfdc6a7ffd3a uniprot.xml --- a/uniprot.xml Sun Sep 16 13:41:08 2018 -0400 +++ b/uniprot.xml Thu Apr 22 17:32:16 2021 +0000 |
| [ |
| @@ -1,10 +1,10 @@ -<tool id="uniprot" name="UniProt" version="0.2"> +<tool id="uniprot" name="UniProt" version="0.3"> <description>ID mapping and retrieval</description> <macros> <import>macros.xml</import> </macros> <requirements> - <requirement type="package" version="2.19.1">requests</requirement> + <requirement type="package" version="2.25.1">requests</requirement> </requirements> <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> <command detect_errors="aggressive"><![CDATA[ |