Mercurial > repos > bgruening > uniprot_rest_interface

changeset 1:cd2a41c65447 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489
author bgruening
date Fri, 14 Oct 2016 17:59:02 -0400
parents 48522382b6a4
children fe94765e8814
files test-data/test1_map.tab test-data/test1_retrieve.fasta test-data/test2_retrieve.gff tool_dependencies.xml uniprot.py uniprot.xml
diffstat 6 files changed, 175 insertions(+), 164 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/test1_map.tab	Fri Oct 09 16:42:22 2015 -0400
+++ b/test-data/test1_map.tab	Fri Oct 14 17:59:02 2016 -0400
@@ -4,7 +4,7 @@
 A0A077ZFY8	TTRE_0000758701
 M5B8V9	CMN_01519
 M5BAG7	cydC
-S0DS17	FFUJ_00006
+S0DS17	apf8
 A0A077Z587	TTRE_0000309301
 Q13685	AAMP
 O14639	ABLIM1
--- a/test-data/test1_retrieve.fasta	Fri Oct 09 16:42:22 2015 -0400
+++ b/test-data/test1_retrieve.fasta	Fri Oct 14 17:59:02 2016 -0400
@@ -1,4 +1,4 @@
->tr|S0DS17|S0DS17_GIBF5 Related to cytochrom P450 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=FFUJ_00006 PE=3 SV=1
+>sp|S0DS17|APF8_GIBF5 Cytochrome P450 momooxygenase apf8 OS=Gibberella fujikuroi (strain CBS 195.34 / IMI 58289 / NRRL A-6831) GN=apf8 PE=1 SV=1
 MSYQSILLRQVNSLCDNLEEVARDENGGLIDMAMQSDYFTFDVMSEVIFGMAYNALKDTS
 YRFVTGALGSSNIRIGTLVQSPLPAMCRIDKYLFPESIQGRNKFLGFIGSLLRDRSKASF
 AGNGNVFSFLETAKDPDGGNQLSKSEIRAECATLVAAGTDTSSSTLAATLFYLSRNSKCY
@@ -6,7 +6,7 @@
 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 GN=cydC PE=3 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 michiganensis subsp. nebraskensis NCPPB 2581 GN=cydC PE=4 SV=1
 MNRDGVLRLAQPPTRRTLPGLLAGLASAVGAVALLATSAWLITRASEQPPILFLGMAIVG
 VRAFALGRAAFRYLERITSHDAAFRALATLRVGVFERLLPFAPAGLRDTRRGDLLARLVG
 DVDRLQDLPLRVVQPLAVSVVVQAASVAVVGAVLPAAGIALAVVLGVALVVGIGATTALA
@@ -31,7 +31,7 @@
 SASFALILPAGALWALYKSARVTKQKKSGGWTMTHTIAQTCGMVIVAAGAVCSIQAKRDN
 GKHFGSVHGVLGIIVIALLCVQVALGFSKSLIRTEAQRRTINRVHFWLAIVLLPLAFLNI
 ILGLQLIAVPVGLLLGFFVHIFCLLAALGLILPILRFRKANRSVAFPPPNDD
->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=4 SV=1
+>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
 MGGLAMLARQLGHEVTGSDANVYPPMSTLLEKQGIELIQGYDASQLDPQPDLVIIGNAMT
 RGNPCVEAVLEKNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEQCGYKP
 GFVIGGVPGNFEVSARLGESNFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDHAD
@@ -63,7 +63,7 @@
 QLQEEQLMKLNSGLGQLILKEEMEKESRERSSLLASRYDSPINSASHIPSSKTASLPGYG
 RNGLHRPVSTDFAQYNSYGDVSGGVRDYQTLPDGHMPAMRMDRGVSMPNMLEPKIFPYEM
 LMVTNRGRNKILREVDRTRLERHLAPEVFREIFGMSIQEFDRLPLWRRNDMKKKAKLF
->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=3 SV=1
+>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
@@ -86,7 +86,7 @@
 EAARAGEQGRGFAVVASEVRTLASRSAQAAKEIEGLISESVRLIDLGSDEVATAGKTMST
 IVDAVASVTHIMQEIAAASDEQSRGITQVSQAISEMDKVTQQNASLVEEASAAAVSLEEQ
 AARLTEAVDVFRLHKHSVSAEPRGAGEPVSFATV
->tr|Q0P8A9|Q0P8A9_CAMJE Putative formate dehydrogenase, cytochrom B subunit OS=Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) 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) GN=fdhC PE=4 SV=1
 MRKVFVTLLLSVVSLFAYGSERMGQDTQIWDFHRITNIPNYDTFGKLWTTLQGEYIATIA
 LIAVIAVLSAFALHYMVIGPKQFSHDGKKIYAFTLFERLFHFIAAISWVILVPTGFVMMF
 GEVFGGGVFVRVCKNLHAFATILFIISIIPMFLCWIKRMLPASYDIRWMMIVGGYLSKIK
--- a/test-data/test2_retrieve.gff	Fri Oct 09 16:42:22 2015 -0400
+++ b/test-data/test2_retrieve.gff	Fri Oct 14 17:59:02 2016 -0400
@@ -1,45 +1,91 @@
 ##gff-version 3
 ##sequence-region S0DS17 1 369
+S0DS17	UniProtKB	Chain	1	369	.	.	.	ID=PRO_0000437163;Note=Cytochrome P450 momooxygenase apf8	
+S0DS17	UniProtKB	Metal binding	303	303	.	.	.	Note=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798	
 ##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	
+M5BAG7	UniProtKB	Transmembrane	132	153	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	159	181	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	236	259	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+M5BAG7	UniProtKB	Transmembrane	274	296	.	.	.	Note=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius	
+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	
 ##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	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 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;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
-O14639	UniProtKB	Domain	156	216	.	.	.	Note=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
-O14639	UniProtKB	Domain	224	283	.	.	.	Note=LIM zinc-binding 3;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
-O14639	UniProtKB	Domain	283	343	.	.	.	Note=LIM zinc-binding 4;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
-O14639	UniProtKB	Domain	710	778	.	.	.	Note=HP;evidence=ECO:0000255|PROSITE-ProRule:PRU00595	
-O14639	UniProtKB	Coiled coil	590	614	.	.	.	evidence=ECO:0000255	
-O14639	UniProtKB	Modified residue	367	367	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:19690332	
-O14639	UniProtKB	Modified residue	373	373	.	.	.	Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:19690332	
-O14639	UniProtKB	Modified residue	396	396	.	.	.	Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:15592455	
-O14639	UniProtKB	Modified residue	426	426	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:24275569	
-O14639	UniProtKB	Modified residue	431	431	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332	
-O14639	UniProtKB	Modified residue	433	433	.	.	.	Note=Phosphothreonine;evidence=ECO:0000244|PubMed:19690332	
-O14639	UniProtKB	Modified residue	435	435	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:24275569	
-O14639	UniProtKB	Modified residue	439	439	.	.	.	Note=Phosphotyrosine;evidence=ECO:0000244|PubMed:15144186	
-O14639	UniProtKB	Modified residue	455	455	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:24275569	
-O14639	UniProtKB	Modified residue	458	458	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648	
-O14639	UniProtKB	Modified residue	587	587	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648	
-O14639	UniProtKB	Modified residue	640	640	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231	
-O14639	UniProtKB	Modified residue	655	655	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:18669648	
-O14639	UniProtKB	Modified residue	706	706	.	.	.	Note=Phosphoserine;evidence=ECO:0000244|PubMed:24275569	
-O14639	UniProtKB	Alternative sequence	1	316	.	.	.	ID=VSP_012099;Note=In isoform 3%2C isoform 4 and isoform 5.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:17974005	
-O14639	UniProtKB	Alternative sequence	1	81	.	.	.	ID=VSP_012100;Note=In isoform 2 and isoform 6.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:7584044	
-O14639	UniProtKB	Alternative sequence	347	347	.	.	.	ID=VSP_041185;Note=In isoform 5 and isoform 6.;evidence=ECO:0000303|PubMed:14702039	
-O14639	UniProtKB	Alternative sequence	348	373	.	.	.	ID=VSP_012101;Note=In isoform 4.;evidence=ECO:0000303|PubMed:15489334	
-O14639	UniProtKB	Alternative sequence	480	514	.	.	.	ID=VSP_012102;Note=In isoform 3%2C isoform 4 and isoform 5.;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:17974005	
-O14639	UniProtKB	Alternative sequence	531	531	.	.	.	ID=VSP_057209;Note=In isoform 6.;evidence=ECO:0000303|PubMed:14702039	
-O14639	UniProtKB	Natural variant	434	434	.	.	.	ID=VAR_050141;Dbxref=dbSNP:rs11593544	
-O14639	UniProtKB	Natural variant	637	637	.	.	.	ID=VAR_050142;Dbxref=dbSNP:rs7091419	
-O14639	UniProtKB	Sequence conflict	499	499	.	.	.	evidence=ECO:0000305	
-O14639	UniProtKB	Sequence conflict	532	532	.	.	.	evidence=ECO:0000305	
-O14639	UniProtKB	Sequence conflict	563	563	.	.	.	evidence=ECO:0000305	
-O14639	UniProtKB	Sequence conflict	578	578	.	.	.	evidence=ECO:0000305	
+O14639	UniProtKB	Domain	97	156	.	.	.	Note=LIM zinc-binding 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+O14639	UniProtKB	Domain	156	216	.	.	.	Note=LIM zinc-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+O14639	UniProtKB	Domain	224	283	.	.	.	Note=LIM zinc-binding 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+O14639	UniProtKB	Domain	283	343	.	.	.	Note=LIM zinc-binding 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00125	
+O14639	UniProtKB	Domain	710	778	.	.	.	Note=HP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00595	
+O14639	UniProtKB	Coiled coil	590	614	.	.	.	Ontology_term=ECO:0000255;evidence=ECO:0000255	
+O14639	UniProtKB	Modified residue	216	216	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8K4G5	
+O14639	UniProtKB	Modified residue	367	367	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332	
+O14639	UniProtKB	Modified residue	373	373	.	.	.	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332	
+O14639	UniProtKB	Modified residue	396	396	.	.	.	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:15592455;Dbxref=PMID:15592455	
+O14639	UniProtKB	Modified residue	422	422	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163	
+O14639	UniProtKB	Modified residue	426	426	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:24275569;Dbxref=PMID:19690332,PMID:24275569	
+O14639	UniProtKB	Modified residue	431	431	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:19690332,PMID:23186163	
+O14639	UniProtKB	Modified residue	433	433	.	.	.	Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19690332;Dbxref=PMID:19690332	
+O14639	UniProtKB	Modified residue	435	435	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:18669648,PMID:19690332,PMID:20068231,PMID:21406692,PMID:23186163,PMID:24275569	
+O14639	UniProtKB	Modified residue	439	439	.	.	.	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:15144186;Dbxref=PMID:15144186	
+O14639	UniProtKB	Modified residue	452	452	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163	
+O14639	UniProtKB	Modified residue	455	455	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163,ECO:0000244|PubMed:24275569;Dbxref=PMID:18669648,PMID:23186163,PMID:24275569	
+O14639	UniProtKB	Modified residue	458	458	.	.	.	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	498	498	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8K4G5	
+O14639	UniProtKB	Modified residue	587	587	.	.	.	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	640	640	.	.	.	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231	
+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	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	
+O14639	UniProtKB	Alternative sequence	348	373	.	.	.	ID=VSP_012101;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334	
+O14639	UniProtKB	Alternative sequence	480	514	.	.	.	ID=VSP_012102;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	531	531	.	.	.	ID=VSP_057209;Note=In isoform 6. H->HDA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039	
+O14639	UniProtKB	Natural variant	434	434	.	.	.	ID=VAR_050141;Note=P->T;Dbxref=dbSNP:rs11593544	
+O14639	UniProtKB	Natural variant	637	637	.	.	.	ID=VAR_050142;Note=R->G;Dbxref=dbSNP:rs7091419	
+O14639	UniProtKB	Sequence conflict	499	499	.	.	.	Note=R->L;Ontology_term=ECO:0000305;evidence=ECO:0000305	
+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 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	
 ##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 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 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	
@@ -51,5 +97,5 @@
 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;evidence=ECO:0000244|PubMed:24275569	
-Q13685	UniProtKB	Natural variant	250	250	.	.	.	ID=VAR_037061;Dbxref=dbSNP:rs2305835	
+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	
--- a/tool_dependencies.xml	Fri Oct 09 16:42:22 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 14 17:59:02 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="requests" version="2.7">
-        <repository changeset_revision="ad6b0c21d92b" name="package_python_2_7_requests_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7e330b122c8c" name="package_python_2_7_requests_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
--- a/uniprot.py	Fri Oct 09 16:42:22 2015 -0400
+++ b/uniprot.py	Fri Oct 14 17:59:02 2016 -0400
@@ -8,12 +8,14 @@
     map
     retrieve
 """
+import argparse
+import sys
 
 import requests
-import sys, argparse
 
 url = 'http://www.uniprot.org/'
 
+
 def _retrieve(query, format='txt'):
     """_retrieve is not meant for use with the python interface, use `retrieve`
     instead"""
@@ -22,25 +24,12 @@
     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}
 
-    responses = [requests.post(url + tool, data=data, files={'file':' '.join(query)}) for query in queries]
-    page = ''.join([response.text for response in responses])
+    responses = [requests.post(url + tool, data=data, files={'file': ' '.join(_)}) for _ in queries]
+    page = ''.join(response.text for response in responses)
     return page
 
-def retrieve(ids, format='txt'):
-    """ request entries by uniprot acc using batch retrieval
-
-    Args:
-        query: list of ids to retrieve
-        format: txt by default
-
-    Help:
-        possible formats:
-        txt, xml, rdf, fasta, gff"""
-    if type(ids) is not list:
-        ids = [ids]
-    return _retrieve(' '.join(ids), format)
 
 def _map(query, f, t, format='tab'):
     """ _map is not meant for use with the python interface, use `map` instead
@@ -48,44 +37,17 @@
     tool = 'mapping/'
 
     data = {
-            'from':f,
-            'to':t,
-            'format':format,
+            'from': f,
+            'to': t,
+            'format': format,
             'query': query
             }
     response = requests.post(url + tool, data=data)
     page = response.text
     return page
 
-def map(ids, f, t, format='tab'):
-    """ map a list of ids from one format onto another using uniprots mapping api
-    
-    Args:
-        query: id or list of ids to be mapped
-        f: from ACC | P_ENTREZGENEID | ...
-        t: to ...
-        format: tab by default
-
-    Help:
-        for a list of all possible mappings visit
-        'http://www.uniprot.org/faq/28'
-    """
-    if type(ids) is not list:
-        ids = [ids]
-    page = _map(' '.join(ids), f, t, format)
-    result = dict()
-    for row in page.splitlines()[1:]:
-        key, value = row.split('\t')
-        if key in result:
-            result[key].add(value)
-        else:
-            result[key] = set([value])
-    return result
 
 if __name__ == '__main__':
-    import argparse
-    import sys
-
     parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
     subparsers = parser.add_subparsers(dest='tool')
 
@@ -93,16 +55,16 @@
     mapping.add_argument('f', help='from')
     mapping.add_argument('t', help='to')
     mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
-            default=sys.stdin, help='input file (default: stdin)')
+                         default=sys.stdin, help='input file (default: stdin)')
     mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
-            default=sys.stdout, help='output file (default: stdout)')
+                         default=sys.stdout, help='output file (default: stdout)')
     mapping.add_argument('--format', default='tab', help='output format')
 
     retrieve = subparsers.add_parser('retrieve')
-    retrieve.add_argument('inp', metavar = 'in', nargs='?', type=argparse.FileType('r'),
-            default=sys.stdin, help='input file (default: stdin)')
+    retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'),
+                          default=sys.stdin, help='input file (default: stdin)')
     retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
-            default=sys.stdout, help='output file (default: stdout)')
+                          default=sys.stdout, help='output file (default: stdout)')
     retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
 
     args = parser.parse_args()
@@ -113,5 +75,3 @@
 
     elif args.tool == 'retrieve':
         args.out.write(_retrieve(query, format=args.format))
-
-
--- a/uniprot.xml	Fri Oct 09 16:42:22 2015 -0400
+++ b/uniprot.xml	Fri Oct 14 17:59:02 2016 -0400
@@ -24,68 +24,68 @@
         #elif $tool.tool_choice == "map":
             map
 
-            #if $tool.from.category_FROM == "uniprot":
-                $tool.from.db_uniprot_FROM
-            #elif $tool.from.category_FROM == "oseqdb":
-                $tool.from.db_oseqdb
-            #elif $tool.from.category_FROM == "3Dstrdb":
-                $tool.from.db_3Dstrdb
-            #elif $tool.from.category_FROM == "ppidb":
-                $tool.from.db_ppidb
-            #elif $tool.from.category_FROM == "chemistry":
-                $tool.from.db_chemistry
-            #elif $tool.from.category_FROM == "protfgdb":
-                $tool.from.db_protfgdb
-            #elif $tool.from.category_FROM == "polymorphismANDmutation":
-                $tool.from.db_polymorphismANDmutation
-            #elif $tool.from.category_FROM == "db_2DgelDB":
-                $tool.from.db_2DgelDB
-            #elif $tool.from.category_FROM == "ProtocolsMaterialsDB":
-                $tool.from.ProtocolsMaterialsDB
-            #elif $tool.from.category_FROM == "db_GenomeAnnotationDB":
-                $tool.from.db_GenomeAnnotationDB
-            #elif $tool.from.category_FROM == "db_OrganismSpecificGeneDB":
-                $tool.from.db_OrganismSpecificGeneDB
-            #elif $tool.from.category_FROM == "db_phylogenomic":
-                $tool.from.db_phylogenomic
-            #elif $tool.from.category_FROM == "db_EnzymePathwayDB":
-                $tool.from.db_EnzymePathwayDB
-            #elif $tool.from.category_FROM == "db_GeneExpression":
-                $tool.from.db_GeneExpression
-            #elif $tool.from.category_FROM == "db_other":
-                $tool.from.db_other
+            #if $tool.from.category_FROM == "uniprot"
+                '${tool.from.db_uniprot_FROM}'
+            #elif $tool.from.category_FROM == "oseqdb"
+                ${tool.from.db_oseqdb}
+            #elif $tool.from.category_FROM == "3Dstrdb"
+                ${tool.from.db_3Dstrdb}
+            #elif $tool.from.category_FROM == "ppidb"
+                ${tool.from.db_ppidb}
+            #elif $tool.from.category_FROM == "chemistry"
+                ${tool.from.db_chemistry}
+            #elif $tool.from.category_FROM == "protfgdb"
+                ${tool.from.db_protfgdb}
+            #elif $tool.from.category_FROM == "polymorphismANDmutation"
+                ${tool.from.db_polymorphismANDmutation}
+            #elif $tool.from.category_FROM == "2DgelDB"
+                ${tool.from.db_2DgelDB}
+            #elif $tool.from.category_FROM == "ProtocolsMaterialsDB"
+                ${tool.from.db_ProtocolsMaterialsDB}
+            #elif $tool.from.category_FROM == "GenomeAnnotationDB"
+                ${tool.from.db_GenomeAnnotationDB}
+            #elif $tool.from.category_FROM == "OrganismSpecificGeneDB"
+                ${tool.from.db_OrganismSpecificGeneDB}
+            #elif $tool.from.category_FROM == "phylogenomic"
+                ${tool.from.db_phylogenomic}
+            #elif $tool.from.category_FROM == "EnzymePathwayDB"
+                ${tool.from.db_EnzymePathwayDB}
+            #elif $tool.from.category_FROM == "GeneExpression"
+                ${tool.from.db_GeneExpression}
+            #elif $tool.from.category_FROM == "other"
+                ${tool.from.db_other}
             #end if
 
-            #if $tool.to.category_TO == "uniprot":
-                $tool.to.db_uniprot_TO
-            #elif $tool.to.category_TO == "oseqdb":
-                $tool.to.db_oseqdb
-            #elif $tool.to.category_TO == "3Dstrdb":
-                $tool.to.db_3Dstrdb
-            #elif $tool.to.category_TO == "ppidb":
-                $tool.to.db_ppidb
-            #elif $tool.to.category_TO == "chemistry":
-                $tool.to.db_chemistry
-            #elif $tool.to.category_TO == "protfgdb":
-                $tool.to.db_protfgdb
-            #elif $tool.to.category_TO == "polymorphismANDmutation":
-                $tool.to.db_polymorphismANDmutation
-            #elif $tool.to.category_TO == "db_2DgelDB":
-                $tool.to.db_2DgelDB
-            #elif $tool.to.category_TO == "ProtocolsMaterialsDB":
-                $tool.to.ProtocolsMaterialsDB
-            #elif $tool.to.category_TO == "db_GenomeAnnotationDB":
-                $tool.to.db_GenomeAnnotationDB
-            #elif $tool.frtoom.category_TO == "db_OrganismSpecificGeneDB":
-                $tool.to.db_OrganismSpecificGeneDB
-            #elif $tool.to.category_TO == "db_phylogenomic":
-                $tool.to.db_phylogenomic
-            #elif $tool.to.category_TO == "db_EnzymePathwayDB":
-                $tool.to.db_EnzymePathwayDB
-            #elif $tool.to.category_TO == "db_GeneExpression":
-                $tool.to.db_GeneExpression
-            #elif $tool.to.category_TO == "db_other":
-                $tool.to.db_other
+            #if $tool.to.category_TO == "uniprot"
+                ${tool.to.db_uniprot_TO}
+            #elif $tool.to.category_TO == "oseqdb"
+                ${tool.to.db_oseqdb}
+            #elif $tool.to.category_TO == "3Dstrdb"
+                ${tool.to.db_3Dstrdb}
+            #elif $tool.to.category_TO == "ppidb"
+                ${tool.to.db_ppidb}
+            #elif $tool.to.category_TO == "chemistry"
+                ${tool.to.db_chemistry}
+            #elif $tool.to.category_TO == "protfgdb"
+                ${tool.to.db_protfgdb}
+            #elif $tool.to.category_TO == "polymorphismANDmutation"
+                ${tool.to.db_polymorphismANDmutation}
+            #elif $tool.to.category_TO == "2DgelDB"
+                ${tool.to.db_2DgelDB}
+            #elif $tool.to.category_TO == "ProtocolsMaterialsDB"
+                ${tool.to.db_ProtocolsMaterialsDB}
+            #elif $tool.to.category_TO == "GenomeAnnotationDB"
+                ${tool.to.db_GenomeAnnotationDB}
+            #elif $tool.to.category_TO == "OrganismSpecificGeneDB"
+                ${tool.to.db_OrganismSpecificGeneDB}
+            #elif $tool.to.category_TO == "phylogenomic"
+                ${tool.to.db_phylogenomic}
+            #elif $tool.to.category_TO == "EnzymePathwayDB"
+                ${tool.to.db_EnzymePathwayDB}
+            #elif $tool.to.category_TO == "GeneExpression"
+                ${tool.to.db_GeneExpression}
+            #elif $tool.to.category_TO == "other"
+                ${tool.to.db_other}
             #end if
 
             id_file.tabular
@@ -205,10 +205,10 @@
                 <param name="format" type="select" label="Choose format of output file" help="">
                     <option value="fasta">fasta</option>
                     <option value="gff">gff</option>
+                    <option value="txt">Text</option>
                 </param>
             </when>
         </conditional>
-
     </inputs>
     <outputs>
             <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output"
@@ -221,6 +221,11 @@
                 <filter>tool['tool_choice'] == 'retrieve'</filter>
                 <filter>tool['format'] == 'gff'</filter>
             </data>
+            <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output"
+                label="${tool.name} on ${on_string} (retrieve output)">
+               	<filter>tool['tool_choice'] == 'retrieve'</filter>
+                <filter>tool['format'] == 'txt'</filter>
+            </data>
             <data name="outfile_map" format="tabular" from_work_dir="./output"
                 label="${tool.name} on ${on_string} (map output)">
                 <filter>tool['tool_choice'] == 'map'</filter>
@@ -278,15 +283,15 @@
 
 The input is a list of IDs.
 
-*example*:
+*Example*::
 
-Q0P8A9
-A0A077ZHN8
-A0A077ZFY8
-M5B8V9
-M5BAG7
-S0DS17
-....
+    Q0P8A9
+    A0A077ZHN8
+    A0A077ZFY8
+    M5B8V9
+    M5BAG7
+    S0DS17
+    ....
 
 -----