Mercurial > repos > bgruening > uniprot_rest_interface
changeset 7:bfdc6a7ffd3a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit ddbed5f0b0879b4a001d2da6a521b0c9a39c1e7b"
| author | bgruening |
|---|---|
| date | Thu, 22 Apr 2021 17:32:16 +0000 |
| parents | 054483e27a35 |
| children | af5eccf83605 |
| files | macros.xml test-data/id_uniprot.tab test-data/test.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 |
| diffstat | 9 files changed, 2708 insertions(+), 128 deletions(-) [+] |
line wrap: on
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--- a/macros.xml Sun Sep 16 13:41:08 2018 -0400 +++ b/macros.xml Thu Apr 22 17:32:16 2021 +0000 @@ -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>
--- 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 @@ -7,3 +7,4 @@ A0A077Z587 Q13685 O14639 +WRONGIDWHICHDOESNOTEXIST \ No newline at end of file
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+UniRef50_X4X4C7 X4X4C7 +UniRef50_X4XFI8 X4XFI8 +UniRef50_X4XHM9 X4XHM9 +UniRef50_X4ZJB4 X4ZJB4 +UniRef50_X4ZSZ9 X4ZSZ9 +UniRef50_X5AT19 X5AT19 +UniRef50_X5DW04 X5DW04 +UniRef50_X5G1M7 X5G1M7 +UniRef50_X5K4I4 X5K4I4 +UniRef50_X7LA43 X7LA43 +UniRef50_X7QK55 X7QK55 +UniRef50_X8K474 X8K474 +UniRef50_X8L2K3 X8L2K3 +UniRef50_Y1IXG9 Y1IXG9 +UniRef50_Y1MEW7 Y1MEW7 +UniRef50_Z2DBM9 Z2DBM9
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -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
--- 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 @@ -1,27 +1,4 @@ ##gff-version 3 -##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;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 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 -A0A077ZHN8 UniProtKB Transmembrane 113 132 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -A0A077ZHN8 UniProtKB Transmembrane 290 310 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius -A0A077ZHN8 UniProtKB Domain 312 364 . . . Note=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885 -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 @@ -32,6 +9,43 @@ 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 +M5BAG7 UniProtKB Region 317 337 . . . Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-lite +##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 +A0A077ZHN8 UniProtKB Transmembrane 113 132 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +A0A077ZHN8 UniProtKB Transmembrane 290 310 . . . Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius +A0A077ZHN8 UniProtKB Domain 312 364 . . . Note=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885 +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 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 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;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 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 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 @@ -72,25 +86,12 @@ 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 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 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
--- 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()
--- 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[