| Previous changeset 0:48522382b6a4 (2015-10-09) Next changeset 2:fe94765e8814 (2017-04-10) |
|
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit fb201f32a92466c2bd8086e91bbf777401f1b489 |
|
modified:
test-data/test1_map.tab test-data/test1_retrieve.fasta test-data/test2_retrieve.gff tool_dependencies.xml uniprot.py uniprot.xml |
| b |
| 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 |
| b |
| @@ -4,7 +4,7 @@ A0A077ZFY8 TTRE_0000758701 M5B8V9 CMN_01519 M5BAG7 cydC -S0DS17 FFUJ_00006 +S0DS17 apf8 A0A077Z587 TTRE_0000309301 Q13685 AAMP O14639 ABLIM1 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -1,45 +1,91 @@\n ##gff-version 3\n ##sequence-region S0DS17 1 369\n+S0DS17\tUniProtKB\tChain\t1\t369\t.\t.\t.\tID=PRO_0000437163;Note=Cytochrome P450 momooxygenase apf8\t\n+S0DS17\tUniProtKB\tMetal binding\t303\t303\t.\t.\t.\tNote=Iron (heme axial ligand);Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P04798\t\n ##sequence-region M5BAG7 1 563\n+M5BAG7\tUniProtKB\tTransmembrane\t21\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t49\t71\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t132\t153\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t159\t181\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t236\t259\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tTransmembrane\t274\t296\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5BAG7\tUniProtKB\tDomain\t20\t301\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n+M5BAG7\tUniProtKB\tDomain\t345\t559\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n ##sequence-region A0A077Z587 1 772\n+A0A077Z587\tUniProtKB\tTransmembrane\t593\t617\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077Z587\tUniProtKB\tTransmembrane\t637\t656\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077Z587\tUniProtKB\tTransmembrane\t668\t692\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077Z587\tUniProtKB\tTransmembrane\t704\t727\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077Z587\tUniProtKB\tTransmembrane\t733\t755\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077Z587\tUniProtKB\tDomain\t20\t94\t.\t.\t.\tNote=PDZ (DHR);Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50106\t\n+A0A077Z587\tUniProtKB\tDomain\t552\t761\t.\t.\t.\tNote=Cytochrome b561;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50939\t\n ##sequence-region A0A077ZFY8 1 973\n+A0A077ZFY8\tUniProtKB\tDomain\t1\t89\t.\t.\t.\tNote=Mur_ligase;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01225\t\n+A0A077ZFY8\tUniProtKB\tDomain\t96\t279\t.\t.\t.\tNote=Mur_ligase_M;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF08245\t\n+A0A077ZFY8\tUniProtKB\tDomain\t300\t349\t.\t.\t.\tNote=Mur_ligase_C;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF02875\t\n ##sequence-region O14639 1 778\n O14639\tUniProtKB\tChain\t1\t778\t.\t.\t.\tID=PRO_0000075697;Note=Actin-binding LIM protein 1\t\n-O14639\tUniProtKB\tDomain\t97\t156\t.\t.\t.\tNote=LIM zinc-binding 1;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n-O14639\tUniProtKB\tDomain\t156\t216\t.\t.\t.\tNote=LIM zinc-binding 2;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n-O14639\tUniProtKB\tDomain\t224\t283\t.\t.\t.\tNote=LIM zinc-binding 3;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n-O14639\tUniProtKB\tDomain\t283\t343\t.\t.\t.\tNote=LIM zinc-binding 4;evidence=ECO:0000255|PROSITE-ProRule:PRU00125\t\n-O14639\tUniProtKB\tDomain\t710\t778\t.\t.\t.\tNote=HP;evidence=ECO:0000255|PROSITE-ProRule:PRU00595\t\n-O14639\tUniProtKB\tCoiled coil\t590\t614\t.\t.\t.\tevidence=ECO:0000255\t\n-O14639\tUniProtKB\tModified residue\t367\t367\t.\t.\t.\tNote=Phosphoserine;evidence=ECO:0000244|PubMed:19690332\t\n-O14639\tUniProtKB\tModified residue\t373\t373\t.\t.\t.\tNote=Phosphotyrosine;evidence=ECO:0000244|PubMed:19690332\t\n-O14639\tUniProtKB\tModified residue\t396\t396\t.\t.\t.\tNote=Phosphotyrosine;evidence=ECO:0000244|PubMed:15592455\t\n-O14639\tUniProtKB\tModified residue\t426\t426\t.\t.\t.\tNote=Phosphoserine;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:24275569\t\n-O14639\tUniProtKB\tModified residue\t431\t431\t.\t.\t.\tNote=Phosphoserine;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332\t\n-O14639\tUniProtKB\tModified residue\t433\t433\t.\t.\t.\tNote=Phosphothreonine;evidence=ECO:0000244|Pu'..b'34\t.\t.\t.\tID=VAR_050141;Note=P->T;Dbxref=dbSNP:rs11593544\t\n+O14639\tUniProtKB\tNatural variant\t637\t637\t.\t.\t.\tID=VAR_050142;Note=R->G;Dbxref=dbSNP:rs7091419\t\n+O14639\tUniProtKB\tSequence conflict\t499\t499\t.\t.\t.\tNote=R->L;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n+O14639\tUniProtKB\tSequence conflict\t532\t532\t.\t.\t.\tNote=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n+O14639\tUniProtKB\tSequence conflict\t563\t563\t.\t.\t.\tNote=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n+O14639\tUniProtKB\tSequence conflict\t578\t578\t.\t.\t.\tNote=V->I;Ontology_term=ECO:0000305;evidence=ECO:0000305\t\n ##sequence-region M5B8V9 1 582\n+M5B8V9\tUniProtKB\tTransmembrane\t20\t43\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t55\t77\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t134\t154\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t161\t180\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tTransmembrane\t236\t260\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+M5B8V9\tUniProtKB\tDomain\t20\t302\t.\t.\t.\tNote=ABC transmembrane type-1;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50929\t\n+M5B8V9\tUniProtKB\tDomain\t340\t570\t.\t.\t.\tNote=ABC transporter;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50893\t\n ##sequence-region A0A077ZHN8 1 634\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t14\t36\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t56\t80\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t113\t132\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tTransmembrane\t290\t310\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+A0A077ZHN8\tUniProtKB\tDomain\t312\t364\t.\t.\t.\tNote=HAMP;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50885\t\n+A0A077ZHN8\tUniProtKB\tDomain\t369\t598\t.\t.\t.\tNote=Methyl-accepting transducer;Ontology_term=ECO:0000259;evidence=ECO:0000259|PROSITE:PS50111\t\n+A0A077ZHN8\tUniProtKB\tCoiled coil\t170\t204\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n+A0A077ZHN8\tUniProtKB\tCoiled coil\t569\t607\t.\t.\t.\tOntology_term=ECO:0000256;evidence=ECO:0000256|SAM:Coils\t\n ##sequence-region Q0P8A9 1 310\n+Q0P8A9\tUniProtKB\tTransmembrane\t55\t78\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t99\t124\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t136\t156\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t195\t216\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tTransmembrane\t244\t264\t.\t.\t.\tNote=Helical;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:Phobius\t\n+Q0P8A9\tUniProtKB\tDomain\t93\t274\t.\t.\t.\tNote=Ni_hydr_CYTB;Ontology_term=ECO:0000259;evidence=ECO:0000259|Pfam:PF01292\t\n ##sequence-region Q13685 1 434\n Q13685\tUniProtKB\tChain\t1\t434\t.\t.\t.\tID=PRO_0000050832;Note=Angio-associated migratory cell protein\t\n Q13685\tUniProtKB\tRepeat\t89\t129\t.\t.\t.\tNote=WD 1\t\n@@ -51,5 +97,5 @@\n Q13685\tUniProtKB\tRepeat\t356\t395\t.\t.\t.\tNote=WD 7\t\n Q13685\tUniProtKB\tRepeat\t398\t433\t.\t.\t.\tNote=WD 8\t\n Q13685\tUniProtKB\tCompositional bias\t53\t59\t.\t.\t.\tNote=Poly-Glu\t\n-Q13685\tUniProtKB\tModified residue\t20\t20\t.\t.\t.\tNote=Phosphoserine;evidence=ECO:0000244|PubMed:24275569\t\n-Q13685\tUniProtKB\tNatural variant\t250\t250\t.\t.\t.\tID=VAR_037061;Dbxref=dbSNP:rs2305835\t\n+Q13685\tUniProtKB\tModified residue\t20\t20\t.\t.\t.\tNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569\t\n+Q13685\tUniProtKB\tNatural variant\t250\t250\t.\t.\t.\tID=VAR_037061;Note=I->V;Dbxref=dbSNP:rs2305835\t\n' |
| b |
| 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 |
| b |
| @@ -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> |
| b |
| 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)) - - |
| b |
| 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" + ${tool.to.db_other} #end if id_file.tabular @@ -205,10 +205,10 @@ <param name="format" type="select" label="Choose format of output file" help=""> <option value="fasta">fasta</option> <option value="gff">gff</option> + <option value="txt">Text</option> </param> </when> </conditional> - </inputs> <outputs> <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" @@ -221,6 +221,11 @@ <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'gff'</filter> </data> + <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output" + label="${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 + .... ----- |