# HG changeset patch # User bgruening # Date 1476482342 14400 # Node ID cd2a41c65447f4b8a0b5213c8680c936127a91c8 # Parent 48522382b6a4ea1086a4fd67146b8da2bd0f2b4a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489 diff -r 48522382b6a4 -r cd2a41c65447 test-data/test1_map.tab --- 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 diff -r 48522382b6a4 -r cd2a41c65447 test-data/test1_retrieve.fasta --- 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 diff -r 48522382b6a4 -r cd2a41c65447 test-data/test2_retrieve.gff --- 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 diff -r 48522382b6a4 -r cd2a41c65447 tool_dependencies.xml --- 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 @@ - + diff -r 48522382b6a4 -r cd2a41c65447 uniprot.py --- 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)) - - diff -r 48522382b6a4 -r cd2a41c65447 uniprot.xml --- 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 @@ + - tool['tool_choice'] == 'retrieve' tool['format'] == 'gff' + + tool['tool_choice'] == 'retrieve' + tool['format'] == 'txt' + tool['tool_choice'] == 'map' @@ -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 + .... -----