Mercurial > repos > bgruening > uniprot_rest_interface

--- 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.tab	Thu Apr 22 17:32:16 2021 +0000
@@ -0,0 +1,2554 @@
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+UniRef50_X2N374	X2N374
+UniRef50_X2N3P8	X2N3P8
+UniRef50_X2N485	X2N485
+UniRef50_X2N4K3	X2N4K3
+UniRef50_X2N4S2	X2N4S2
+UniRef50_X2N530	X2N530
+UniRef50_X2N7H7	X2N7H7
+UniRef50_X2N7K7	X2N7K7
+UniRef50_X2NAE3	X2NAE3
+UniRef50_X2NAF9	X2NAF9
+UniRef50_X2NAM5	X2NAM5
+UniRef50_X2NCR6	X2NCR6
+UniRef50_X2NDM5	X2NDM5
+UniRef50_X2NG16	X2NG16
+UniRef50_X2P110	X2P110
+UniRef50_X3E1V8	X3E1V8
+UniRef50_X3EEJ0	X3EEJ0
+UniRef50_X3EGM7	X3EGM7
+UniRef50_X3EKE6	X3EKE6
+UniRef50_X3ELX1	X3ELX1
+UniRef50_X3EN79	X3EN79
+UniRef50_X3ERM3	X3ERM3
+UniRef50_X3EY15	X3EY15
+UniRef50_X3EYH3	X3EYH3
+UniRef50_X3EZZ6	X3EZZ6
+UniRef50_X3JE73	X3JE73
+UniRef50_X3W1J0	X3W1J0
+UniRef50_X3W353	X3W353
+UniRef50_X3WS87	X3WS87
+UniRef50_X3XQD3	X3XQD3
+UniRef50_X3YW87	X3YW87
+UniRef50_X4FRC6	X4FRC6
+UniRef50_X4RGC4	X4RGC4
+UniRef50_X4WXD8	X4WXD8
+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[