| Previous changeset 12:6753a9261390 (2013-04-03) Next changeset 14:6365217cd3de (2013-04-25) |
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Commit message:
Uploaded v0.2.2, adds missing test files |
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modified:
tools/protein_analysis/README tools/protein_analysis/tmhmm2.xml |
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added:
test-data/empty_psortb_terse.tabular test-data/rxlr_win_et_al_2007.fasta test-data/rxlr_win_et_al_2007.tabular test-data/rxlr_win_et_al_2007_sp3.tabular |
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| diff -r 6753a9261390 -r dc958c2a963a test-data/empty_psortb_terse.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/empty_psortb_terse.tabular Tue Apr 23 12:47:49 2013 -0400 |
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| @@ -0,0 +1,1 @@ +#SeqID Localization Score |
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| diff -r 6753a9261390 -r dc958c2a963a test-data/rxlr_win_et_al_2007.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rxlr_win_et_al_2007.fasta Tue Apr 23 12:47:49 2013 -0400 |
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| b'@@ -0,0 +1,2702 @@\n+>Ps_scaffold_13_F542 \n+MEGVRLVLLLALHYGLDCRHVDFVTAFLNGPIDVEIYMKQPEFFDDGSGRVCRLLRSLYGLKKAPRIWYKTLDKYLRQCGFQRMEEFTFVGZ\n+>Pr_scaffold_91_R259 \n+MVRPMFFFLFCFVPMAVAILLLEFLRHFNVRRISSSFVLNLARFLRLKPRILGRVINRSLGDLLFLAFLIGGNIYVFQYYYRARVERMKTRSPNLDFSMYLEMIALTFGFVCVFNMAFLFLPATRNCVWMEFLNISYANGIKYHRWVGVVTVVTAFLHCLGYYWSWIREGTWVKEALPCFNCEVGGEGKDPWMNFFGLIALLSFLSIGFTSISWVRRKMYNTFYSVHHLFILGTIFAVLHWNPILAWIFPSVMLYVICRAISSSNGFTPVTVREFTTISHDVVKVVLSRSTAPAGNYKVGQFVYLNVPAISKLQWHAFTIASSPRTSPDTLTILLKSLGDWTDDLVRYSEDCKKNNVLPTMYMDGYYGGSLEMYDEYSTVCLVGGGIGVTPLFAILEDIVAKLQHGGSLRQKVFFIFTFRELSLLEEIHPLLMQIKELDPQQHYFSLHFSLTRAPTNEQLDQTIDHDRLTGNPHVSATRYDTAVTSKAPRPFAEPLRSRTSRVVMYTVVFFLTFLIWIIVKYGSKVQADNDNLWPLQNFVEITLVIVVAMLGVYAFTFVDDKRNKGSTGFSGSLLTPGGVQPYASDAHTLRDLVTDYRVAVGQRPNMAQLMQKVHNSHKQFSSTHPDAGSNGNSTVGVFISGPGALKNATENAISAIGVRHFDVHEEEFELZ\n+>Ps_scaffold_118_R275 \n+MILPTFFFLLCFLPMAVAILLFELLRHFNVRRIASSHVLKLTRILRLKPRIMGRVLHKSFGEFLFLGFVIGGNVYVFQYFYRDNIAPYEDFSSSVDTTTYLQTIALTFGYVCIYNMAFLFLPATRNCVWMEFLNISYANGVRYHRWFGILTILTALLHCTGFYWSWIREGTWVEDALPCFRNCKVGEDGKYRWTNTFGTIALLCFLAIGVTSVGRIRRKMYEAFYYVHHLFIIATIFVVLHWNSTLAWLFPSVMVYAASRALSVSNALTPVSVREFTTLSNDVIKIVLERSSTRAGEFKVGNFVYLNVPATSKLQWHPFTISSSPKASPETLTILLKSLGDWTQELVKYSDECKKNNVLPTIYMDGYYGASLELYVEYATVCLVGGGIGVTPLLAILEDLVAKLRQSKAPKQKVFFIFTFRELSLLEEIHPLLMQIKELDPQQQYFSLHFSLTRPPTDDQLDYQIDHSRLSGKPHVSAASYDTSSTKKTPVPFAEPLRSPISRVVVYTASFFLTLLLWIVVKFGNKIQVDDGNLWPLQNFVEIILVILVALLGFLVFSFIEDKKKQKSAGTTSRQTVTPGGVGNPYTSDVHTLRDLLAEHHVEVGHRPNMDELVRKALDEHKLFTSTHPETETKGNSTIGVFISGPKALKDSTATAIADIGALNFDIHEEEFKLZ\n+>Ps_scaffold_36_R1276 \n+MFFFLFCFIPMAVSIVLLEFLRHFNVRRISSAYVLNLARFLRLKPRIMGRVVNKSVGELLFLGFLVGGNIYVFQYFYRARVERMKTRMPDLDFTAYLQMVALTFGFVCVFNMAFLFLPATRNCVWMEFLNISYANGIKYHRWVGVITVVTAFLHCLGYYWAWIKEGTWVKEALPCFNCEVGTEGKDPWMNFFGLIALLAFLAIGFTSISWVRRKMYNTFYSVHHLFILGTVFAVLHWNPILAWIFPSVMLYVICRALSSSNGFTPVAVREFTIISHDVVKVVVARSTSRTGNYKVGQFVYLNAPAISKLQWHAFTISSSPRTSPDTLTILLKSLGDWTEELVKYSEDCKHNNVLPTIYVDGYYGASLEMYDEYSTVCLVGGGIGVTPLFSILEDVVAKLQQGSSIRQKVYFIFTFRELSLLEEIHPLLMQIKELDPQEQYFSLHFSLTRAPTNDQLDQELDHGRLAGKPHVSAVRYDTSVSSKVPHPFAEPLRSRTSKLTMYTVVFFLTFLIWIVVKYGNKVQADDANLWPLQNFVEITLVIVVAMLGVYAFAFVESKRHKESTAASSHLMTPGGIQPYASDAHTFRDLVTDYRVAVGQRPNMAELMRKVHNGHKQFAASHPGVGAPGNSTVGVFFSGPGALKHAMESAISDIGVRHFDVHEEEFELZ\n+>Pr_scaffold_100_R514 \n+MRFCNAFLATLLILLATTVNAEKSIRSSIITNVAYGRASRGRLLRKADADEANAIDTEERGVLSSIKNWGNMQYWLAVGKSDDQVKKALKMEGLTDAALKAHPNYKQLEKFWYKREGREMDDWLEEGMSTKDVWDDLGLAGMSKAQRKNSDELRQYVRYATKYDDEIWLRKNSIFQPKVYYEGSPAEMKVKVQIWAKAKRKSWYVKEMLDLDGLSKAMRETNPNNKYYLEFLKLTGRSERZ\n+>Hp_Contig1209.2_R7 \n+MWRILCSVCVTCLWIQWNQATCEQEEVTIAGSIQEFWDSGIRQLRAVAKREFRRSETKIHGARLLLSLRHLDRTPREPSPQMTSPVQPPDSQEEPALLTRLRIYQKPCTHZ\n+>Pr_scaffold_92_R336 \n+MKVSKLIMALAALCVALCAPVTGAEGVDNTRTRLLRQESAAFANKPAETGGTRKDSTNPLRRRDQALVSAHRVYDPVSGLACSLVGECVACPDSESDESCRETGFRQELDCPRAKDPTAENLLTKPEDERETRFKACSPADTARPGVAVVKFEVGDCRYAVLETYZ\n+>Ps_scaffold_34_R1273 \n+MRSFMKAPMGGSFLLPPASASTDVPSSSSPAPSATTTTPWPCSSTTRSRWSRQLRGPSSSIGISGIRHRLTSPLESDAWAAMKPALRPISLTTPIPLGTQRASVLAERMARWASSTAVLKPKLRSRRSTSLSMVLGTPATATASLRRRHSSEILLAARWVPSPPITYTCETPFVVRKLIILSTSKPPRFEPRMVPPZ\n+>Ps_scaffold_13_R408 \n+MQLCSPLKCTVALFLVFCLVQLVESCIHDSLDHKFVTAAQNYDDNHPFQVSERKRRLRSEDIVQGSTRQLDDAIYQPIRMTPYYDNSSLNNLTDAARARIFEVVDEAIQRVSRALRVVPVSGNLFAERFCTSRYSTTPPVCHSISDKEYCLEMPIPDDHFAPVRYCDKCTSNGCTNDECTISPAGTGVPNSDFMIYVRAESTANCESGSTLAYASTCQQDQYDRPTFGTVNFCPLQISTAASAFERQVSTALHEFTHALGFSARFFPLMRDEDGNPRTPRDEQGNPPTFSVGTCPNGKEIDYYVEPADTTITYSTERGHVVAKMVTPRVRAFVQDHFNCSRLDGAEVESQDGGCLGSHWEERLFEPEYMTPVDSYRNVFSALTLAFFADSGWYRVNASMSEIMHFGRKKGCGFATKKCVNPSTQVPIAADHFCSSSDFRGCSVDAMSRSICSLSTKEQTIPEEYQYFPNDPKKGGVNMFADFCPLNVGYANGDCTISTNLLKLGDTSINAFGETYCPTCRCTATSLRSVDSTSWGISPARQSGCYAMRCVGDSTSTVVELTFPRSNSSDTVSVNCTKKEETLSVPGFTGTITCPDPLVVCEVDDPSRILLTEELVNSDSSTDTGDGSVSVGSDDYPDDSGDTSTTNSSGKSASASYSSSSNSSSSGLSTGGIATINTGTTTSGADGERLASLWIVLSAAWLVLANVEZ\n+>Ps_scaffold_104_R912 \n+MWSLGVLLAIMLAGAPLVEKPTSEDRQFRVLSHGGGVRKLRRVFPRKLSEVTWDLLEKLLSMDPRKRPTLEQVVEHPFLTSDLHHHTPNYSNCFSRZ\n+>Hp_Contig1403.2_F21 \n+MLFSIVMVAPLYSALGQSRPVFMLTVSLDRELRLWNENACLESLVAATCVERMTGLGGHAYSVSYNAATGIIAAG'..b'MAKFELWFKQNKSPDEVKAMLKVGAGPIVNTKDYDLWNQYSVFYKISQREKETKANIPZ\n+>Ps_scaffold_23_F1315 \n+MLAVSPPSALVLGVGLRVVLGTEEWERMFSLRRNLRQFSKIIVLSGVMYAGYPVYQLLFTKVNHTPYELPVLLVLPIPSARYHSEMEGLTADNVGRAVSGILAYALLELTSFVALAIITKRSCGIRTLYQLAFVLETQWSLIVSKVILWMLFTLTFRVVHFGKFLLTLGZ\n+>Pr_scaffold_328_F13 \n+MRFCNAFLASLLILLAITVAAEKSTRSSSIPDVGYNRGRLLRKTDTAKANAIDTEERGIWSSIKNWGKMQYWLAVDKSDEQVIKALKMDGLTGAALKAHPNYKKLEKFWYKREGRDMDGWFEDGMSPKDVWNDLGLAGMSKAQRKNSDELRAYVRYATKYDNAIWNHKNSIFQPPVEYGGSPAEMHVNVQIWAKANRKKWYVKEMLGLDGMSKAERKADPDYEYYLEFLKLTKRSERZ\n+>Pr_scaffold_2147_R3 \n+MYLGLRFLLGRCAALCSLRLGCLAGHISAGWGRLLRLHRVVGLRRFVARLHCRWLFLYRLWLGLLGHRRLDSLHLLFCHDLAAINALGLLLCSLDGLLLLVNLVHFVSFRQREPRLEPVVQVVKHRVTLRVVEQRVEVAVKDLKLLVLGRQTLVEDLRQLETRDLVVRPHHHEHRQLAQRAVLVLHPGVRFQSLHRLERLRAHPGRHGLRHRQRVGLEVVHVVLISAQEVPVNSGHDASLGDELAQRSGEHRLHSQRGGHFDQQGRSHQHHGTEGVLAAZ\n+>Pr_scaffold_39_F355 \n+MHWCACAYFSLASVTSSAEIDHGWDYWSPPRSAVRIESTDLSLDFLVHRFLRGIFFASTAFTKKGKVFEPTEHDEYMFTFFVDFVGLVTMAFMIGEMANLYVSYISNEVEFRKNHIAVDLYLERWHITGKLRARSHAFLSSLWSSHRGVNYQAIFDEIPQVIRTESISHIANLPLRVFVNNVFRPFATAHPHDRDLEALTRGIAQHLKYEGYPRDECVLVEGSVSKEMYFVVKGHLISTTDDDQQQDSSTQQTGKHYKKGDFFGEHGLLGYSVGVSTVKTVSACDLLSLSSEALLQVILSRPLFQTALSIAVEGYRELCHRTRFSRKPLEKDDWGLVLFRILDTRRKQWIEEAYAFSATNDDDPFNEPWTVSCLRPGHEAGLVTISSPPTCVKVFEMLLRLIATRGLLATRHLHDSVVQYQKSLPIMTADLSSPRGNSMPVTERSDSSKISGNKLSYLQZ\n+>Ps_scaffold_118_F134 \n+MLYLLVIYWSACAYLAVATRVGFASDWEDWLPSQELQLEDPLNPSSKQLALRLLRGLSFAVTTIVKKTYIPTPTTALVFVFHIVMSFIGLLVMSYVIGELASLFISYIDLEVGFRKNCIAVELYLRRLRLSEQLKARTTAFMTSLWSSHAGVNYEELLAEMPCDIRVACVLHVSNKPLDWFIMKVATPLCWEGDESTDALTLSLAKRLRFESYPRDENVVAEGSVVRAMYFVIKGHLKMESRFLIHRALGLRDGSYFGERGLLACNISAYNVRTVRACDLLSLSSEAFAQVLNKYPFSRLALKLCYAASKLLKVQNIASCSKPNMEEHWGAALLSLLHTIRDQRLATLAANDRAGVYTDADASFTASAVVLNGDLTALSTLKGPLPSMRRGPQLESRRRRGKGCSRTMTHQQRGQNSRHHRQSPLNGESYLLTSMKCLTRWIQLNAALRRLHRCSTSYWRPTRLIGKQALIHQLALRZ\n+>Ps_scaffold_5_R3563 \n+MLYLLVIYWAACAYLVVAMQAGFGTEWEGWLPSQELEISDPDDPSPTQLARRFLRGLFFATTAFVKKARNLAPETASLYAFQIAASFTGLITMSFVLGELASLFISYIGLEVNFRKNHIAVELYLTRLRVSDRLKLRTYAFMTSLWSSHAGVNYEELLTEMPHSIRTACVLHTAKEPLDWFIMKVISPICWDGGESVRAFTLSLAERLQFECCPRNENVVTEGSIVRAMYFVIKGHLQMQSRSLLARPVGLRDGSYFGERGLLGCTISSYTVRSVRACDLLSLSSEAFAQVLQQHAFSRLALQICTSAHKHLKAQYHAPCSRVDMEDRWGEALLHCVKEFQSVHEAAVANTSAVVSADRANVAATPDASFSDIEAPRLSSFFRRGGTESELNLGEGGSVVACEARADDSAELPTRLREMFNALDTTTTCYEAFAALLHCMLPTDPLDWDATFATATNTDLTATLATLSASGSISYRYRSVLPTIDTSFNAKEEPVDGRPHAHHEEQERDQVDETGEIEAREEEQQADGEAVAGPTIGDAMAAMVTEVPAPATSVDQRQPTRFRPTVVHLQPQLLPHRLAGPHVRDLZ\n+>Ps_scaffold_53_R22 \n+MQQIYVVVVITSIVGIAFAAVRTLSPWAKLMQWNPVHCITTVVTSQSQKARRLRAMSTKASSDGDNDIDEVEVVLELDSTSRNYTPDNLRACDFVAEDAVTHQDRAARLYLRGFKISVVIVILIVLPAIIVAVSSASPALIAYAALNATLNEMFAHVLGDTSQSYVHRDGDASWVETFIHSATENYTLFADDSLYRRTTGFHGDLAFNINVSDDDPPNVLLIVVEFSDSTIPITLSERKIRPTYSTVRTLPSRQVGQARRRLHELLVKLENESLSREPPVRTAAVRZ\n+>Pr_scaffold_14_R620 \n+MRTTFLWVLVLLTLVAYAHADDNEPKTPAPTSSASSRDNDPTIQEIRGLRNAGMKLNDARDFKGSIEKLRGAITLLHGRVFGEARRTVTEPADISQDAALYAQILNDYGSVLIRAKQYDEAIEVLEDSVAMVEKIYGDSHPSLGLSLRSLADAYMAKEQYKKAISKYKTLRKHVKQGLGTTHEAYIEASMRIAEGYKKLGNKEKNLKVLKQAVTAQGGEINGLTTGVAELYMELSTAHLAVNEVDEALRAAEVASAVFLQRDGEDTLSYAFSLNALAGVKMRQKKVDESIKLLEHAHRIAVKIYGENDAITEASAKTLKEVREYQLDIQAEKDELZ\n+>Hp_Contig1340.1_F7 \n+MRVRRVTWLCVTLAFVSSSSAVYIAKDPHPKPSEATSPANARDQDPVIQEVRGLRNAGMKLNDTKDFRGATGKLRKAITLLHHRVFGEGRHDVTDPQDTSQDAALYSQLLNDYGSVLIRGEEYDEAIEVLEDSVAMVQKIYGDSHPSLGLSLRSLADAYMAKKQYQKAIGKYKTLRKHVKRGLGVTHEAYIEASLRIAEGYKKLGKKEKNLKVLREAVEAQGGQINGLTRGIAELYMELSTAHVAMNEIDEAQKAAEMASAVFLERDGEDTLSFAFSLNALAGVKMRQQKVDEAIELLEHAHKIAVDLYGEHDAITKGSATTLMEVKKHKLDLEAEKEELZ\n+>Ps_scaffold_37_R313 \n+MRALRLLFLCALLLAATLLCCTHASDADADADAPNTPEPTSSASARDNDPTIQQVRGLRNAGMKLNDAKDFTGAIEKLRGAITLLHERVFGEGRHAVSDPAEISQDAALYAQILNDYGSVLIRAKQYDEAIEVLEDSVAMVDKIYGDSHPSLGLSLRSLADAYMAKEKYQKAINKYKTLRKHVKKGLGVTHEAYIEASLRIAEGYKKLGKKKKNLKVLKDAVKAQGGEINGLTTGIAELYMELSTAHVAVNEIDDALRAAETASAVFLQRDGEDTLTYAFSLNALAGVKMRQKKVDDAIELLERAHKIAVKIYGDNDPITQASAKTLREVKEYKLDLHAQKDELZ\n+>Pr_scaffold_30_R354 \n+MLCGLVASSLSVAISAIAKWLHSRVSQPSLQRPSNLHLRGAATQQKEPRSLRANLPRGVLRTYTHTCATPTPSRAWRAPIQPTQFAKGRRRNRQLQTKSSAKTPQFPVRHPSYZ\n\\ No newline at end of file\n' |
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| diff -r 6753a9261390 -r dc958c2a963a test-data/rxlr_win_et_al_2007.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rxlr_win_et_al_2007.tabular Tue Apr 23 12:47:49 2013 -0400 |
| b |
| b'@@ -0,0 +1,1352 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|
| b |
| diff -r 6753a9261390 -r dc958c2a963a test-data/rxlr_win_et_al_2007_sp3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rxlr_win_et_al_2007_sp3.tabular Tue Apr 23 12:47:49 2013 -0400 |
| b |
| b'@@ -0,0 +1,1352 @@\n+#ID\tNN_Cmax_score\tNN_Cmax_pos\tNN_Cmax_pred\tNN_Ymax_score\tNN_Ymax_pos\tNN_Ymax_pred\tNN_Smax_score\tNN_Smax_pos\tNN_Smax_pred\tNN_Smean_score\tNN_Smean_pred\tNN_D_score\tNN_D_pred\tHMM_type\tHMM_Cmax_score\tHMM_Cmax_pos\tHMM_Cmax_pred\tHMM_Sprob_score\tHMM_Sprob_pred\n+Ps_scaffold_13_F542\t0.265\t19\tN\t0.415\t19\tY\t0.928\t13\tY\t0.766\tY\t0.590\tY\tS\t0.855\t19\tY\t0.934\tY\n+Pr_scaffold_91_R259\t0.916\t19\tY\t0.701\t19\tY\t0.995\t12\tY\t0.952\tY\t0.826\tY\tS\t0.696\t19\tY\t0.937\tY\n+Ps_scaffold_118_R275\t0.946\t19\tY\t0.675\t19\tY\t0.996\t12\tY\t0.972\tY\t0.824\tY\tS\t0.896\t19\tY\t0.981\tY\n+Ps_scaffold_36_R1276\t0.518\t15\tY\t0.543\t15\tY\t0.993\t8\tY\t0.965\tY\t0.754\tY\tS\t0.924\t19\tY\t0.973\tY\n+Pr_scaffold_100_R514\t0.937\t22\tY\t0.894\t22\tY\t0.992\t6\tY\t0.944\tY\t0.919\tY\tS\t0.990\t22\tY\t0.999\tY\n+Hp_Contig1209.2_R7\t0.657\t21\tY\t0.661\t21\tY\t0.969\t4\tY\t0.771\tY\t0.716\tY\tS\t0.493\t21\tN\t0.999\tY\n+Pr_scaffold_92_R336\t0.789\t27\tY\t0.780\t25\tY\t0.995\t14\tY\t0.888\tY\t0.834\tY\tS\t0.378\t25\tN\t1.000\tY\n+Ps_scaffold_34_R1273\t0.779\t21\tY\t0.462\t21\tY\t0.781\t2\tN\t0.425\tN\t0.444\tY\tS\t0.624\t21\tY\t0.963\tY\n+Ps_scaffold_13_R408\t0.936\t26\tY\t0.894\t26\tY\t0.980\t7\tY\t0.916\tY\t0.905\tY\tS\t0.948\t26\tY\t0.975\tY\n+Ps_scaffold_104_R912\t0.135\t24\tN\t0.318\t18\tN\t0.982\t5\tY\t0.892\tY\t0.605\tY\tS\t0.528\t18\tY\t0.993\tY\n+Hp_Contig1403.2_F21\t0.505\t19\tY\t0.471\t19\tY\t0.965\t13\tY\t0.711\tY\t0.591\tY\tS\t0.485\t17\tN\t0.936\tY\n+Ps_scaffold_1196_R6\t0.792\t21\tY\t0.775\t21\tY\t0.962\t3\tY\t0.837\tY\t0.806\tY\tS\t0.797\t21\tY\t0.999\tY\n+Ps_scaffold_1_F1329\t0.471\t20\tY\t0.618\t20\tY\t0.985\t13\tY\t0.901\tY\t0.760\tY\tS\t0.382\t22\tN\t1.000\tY\n+Ps_scaffold_44_F1120\t0.866\t19\tY\t0.752\t19\tY\t0.998\t13\tY\t0.971\tY\t0.862\tY\tS\t0.723\t19\tY\t0.999\tY\n+Ps_scaffold_31_R804\t0.952\t18\tY\t0.861\t18\tY\t0.937\t13\tY\t0.838\tY\t0.850\tY\tS\t0.989\t18\tY\t0.991\tY\n+Hp_Contig247.1_F26\t0.829\t25\tY\t0.556\t25\tY\t0.924\t4\tY\t0.580\tY\t0.568\tY\tS\t0.936\t25\tY\t0.993\tY\n+Hp_Contig470.2_F39\t0.298\t27\tN\t0.417\t27\tY\t0.962\t5\tY\t0.760\tY\t0.588\tY\tS\t0.763\t27\tY\t0.994\tY\n+Ps_scaffold_170_R30\t0.931\t22\tY\t0.889\t22\tY\t0.994\t13\tY\t0.958\tY\t0.923\tY\tS\t0.932\t22\tY\t1.000\tY\n+Pr_scaffold_6_F1061\t0.533\t23\tY\t0.493\t23\tY\t0.937\t13\tY\t0.710\tY\t0.602\tY\tS\t0.867\t23\tY\t0.945\tY\n+Ps_scaffold_21_F1644\t0.104\t22\tN\t0.251\t22\tN\t0.915\t12\tY\t0.767\tY\t0.509\tY\tS\t0.489\t19\tN\t0.765\tY\n+Ps_scaffold_151_R307\t0.761\t19\tY\t0.554\t19\tY\t0.947\t12\tY\t0.730\tY\t0.642\tY\tS\t0.571\t19\tY\t1.000\tY\n+Ps_scaffold_35_R465\t0.864\t19\tY\t0.553\t19\tY\t0.935\t12\tY\t0.629\tY\t0.591\tY\tS\t0.754\t19\tY\t0.999\tY\n+Pr_scaffold_45_R508\t0.848\t19\tY\t0.473\t19\tY\t0.913\t12\tY\t0.593\tY\t0.533\tY\tS\t0.736\t19\tY\t0.998\tY\n+Ps_scaffold_80_F1085\t0.402\t21\tY\t0.576\t21\tY\t0.984\t7\tY\t0.918\tY\t0.747\tY\tS\t0.667\t21\tY\t1.000\tY\n+Ps_scaffold_55_F1302\t0.891\t29\tY\t0.848\t29\tY\t0.993\t22\tY\t0.720\tY\t0.784\tY\tS\t0.938\t29\tY\t0.996\tY\n+Pr_scaffold_138_F106\t0.276\t21\tN\t0.453\t21\tY\t0.962\t7\tY\t0.892\tY\t0.672\tY\tS\t0.297\t21\tN\t0.998\tY\n+Pr_scaffold_344_R1\t0.635\t25\tY\t0.706\t25\tY\t0.966\t14\tY\t0.868\tY\t0.787\tY\tS\t0.692\t25\tY\t1.000\tY\n+Pr_scaffold_383_F12\t0.581\t25\tY\t0.661\t25\tY\t0.961\t11\tY\t0.839\tY\t0.750\tY\tS\t0.672\t25\tY\t0.999\tY\n+Pr_scaffold_71_R550\t0.718\t24\tY\t0.739\t24\tY\t0.972\t5\tY\t0.869\tY\t0.804\tY\tS\t0.806\t24\tY\t0.996\tY\n+Ps_scaffold_71_R524\t0.528\t20\tY\t0.597\t20\tY\t0.887\t2\tY\t0.733\tY\t0.665\tY\tS\t0.539\t20\tY\t0.996\tY\n+Ps_scaffold_28_F319\t0.681\t21\tY\t0.725\t21\tY\t0.980\t13\tY\t0.951\tY\t0.838\tY\tS\t0.612\t21\tY\t1.000\tY\n+Ps_scaffold_1171_F2\t0.938\t24\tY\t0.845\t24\tY\t0.948\t10\tY\t0.842\tY\t0.843\tY\tS\t0.845\t24\tY\t1.000\tY\n+Pr_scaffold_91_R59\t0.653\t26\tY\t0.716\t26\tY\t0.995\t4\tY\t0.882\tY\t0.799\tY\tS\t0.608\t26\tY\t1.000\tY\n+Ps_scaffold_28_R952\t0.601\t24\tY\t0.613\t24\tY\t0.987\t1\tY\t0.771\tY\t0.692\tY\tS\t0.334\t18\tN\t1.000\tY\n+Pr_scaffold_135_R105\t0.887\t19\tY\t0.840\t19\tY\t0.991\t13\tY\t0.961\tY\t0.900\tY\tS\t0.572\t19\tY\t1.000\tY\n+Ps_scaffold_14_R1497\t0.595\t18\tY\t0.622\t24\tY\t0.963\t11\tY\t0.853\tY\t0.738\tY\tS\t0.539\t24\tY\t1.000\tY\n+Ps_scaffold_126_F506\t0.736\t25\tY\t0.736\t25\tY\t0.985\t13\tY\t0.851\tY\t0.793\tY\tS\t0.396\t25\tN\t0.957\tY\n+Pr_scaffold_37_R1053\t0.325\t19\tY\t0.519\t19\tY\t0.975\t4\tY\t0.894\tY\t0.707\tY\tS\t0.465\t19\tN\t0.999\tY\n+Pr_scaffold_1392_F8\t0.457\t21\tY\t0.592\t21\tY\t0.997\t13\tY\t0.965\tY\t0.778\tY\tS\t0.490\t21\tN\t1.000\tY\n+Pr_scaffold_71_R484\t0.436\t21\tY\t0.578\t21\tY\t0.995\t13\tY\t0.966\tY\t0.772\tY\tS\t0.483\t23\tN\t1.000\tY\n+Pr_scaffold_7_F2227\t0.267\t24\tN\t0.473\t24\tY\t0.997\t13\tY\t0.956\tY\t0.715\tY\tS\t0.315\t26\tN\t0.998\tY\n+'..b'939\t21\tY\t1.000\tY\n+Pr_scaffold_39_F377\t0.645\t29\tY\t0.396\t29\tY\t0.925\t12\tY\t0.453\tN\t0.425\tN\tS\t0.492\t29\tN\t0.993\tY\n+Ps_scaffold_2_F3681\t0.309\t16\tN\t0.345\t16\tY\t0.746\t4\tN\t0.500\tY\t0.422\tN\tS\t0.747\t40\tY\t0.980\tY\n+Ps_scaffold_256_R67\t0.309\t16\tN\t0.345\t16\tY\t0.746\t4\tN\t0.500\tY\t0.422\tN\tS\t0.747\t40\tY\t0.980\tY\n+Pr_scaffold_5_R1766\t0.257\t29\tN\t0.264\t21\tN\t0.900\t12\tY\t0.587\tY\t0.426\tN\tS\t0.781\t29\tY\t0.983\tY\n+Pr_scaffold_396_F3\t0.666\t20\tY\t0.666\t20\tY\t0.984\t13\tY\t0.850\tY\t0.758\tY\tS\t0.494\t20\tN\t1.000\tY\n+Pr_scaffold_562_R9\t0.666\t20\tY\t0.666\t20\tY\t0.984\t13\tY\t0.850\tY\t0.758\tY\tS\t0.494\t20\tN\t1.000\tY\n+Ps_scaffold_44_R66\t0.511\t21\tY\t0.619\t21\tY\t0.995\t13\tY\t0.956\tY\t0.787\tY\tS\t0.785\t21\tY\t1.000\tY\n+Pr_scaffold_1361_R8\t0.895\t26\tY\t0.804\t26\tY\t0.981\t12\tY\t0.814\tY\t0.809\tY\tS\t0.654\t26\tY\t0.999\tY\n+Ps_scaffold_19_F620\t0.552\t17\tY\t0.547\t17\tY\t0.842\t8\tN\t0.645\tY\t0.596\tY\tS\t0.796\t17\tY\t0.991\tY\n+Ps_scaffold_11_R1749\t0.628\t23\tY\t0.591\t28\tY\t0.987\t19\tY\t0.938\tY\t0.765\tY\tS\t0.332\t27\tN\t0.999\tY\n+Ps_scaffold_1_R4238\t0.342\t21\tY\t0.525\t21\tY\t0.985\t13\tY\t0.900\tY\t0.712\tY\tS\t0.815\t21\tY\t1.000\tY\n+Ps_scaffold_103_F23\t0.286\t20\tN\t0.331\t20\tY\t0.979\t12\tY\t0.809\tY\t0.570\tY\tS\t0.572\t29\tY\t0.991\tY\n+Hp_Contig1138.2_F22\t0.856\t25\tY\t0.609\t25\tY\t0.959\t2\tY\t0.636\tY\t0.623\tY\tS\t0.585\t25\tY\t0.997\tY\n+Hp_Contig1106.7_F4\t0.280\t19\tN\t0.328\t16\tN\t0.942\t3\tY\t0.688\tY\t0.508\tY\tS\t0.481\t19\tN\t0.905\tY\n+Pr_scaffold_47_F441\t0.942\t26\tY\t0.567\t26\tY\t0.872\t10\tY\t0.485\tY\t0.526\tY\tS\t0.952\t26\tY\t0.963\tY\n+Ps_scaffold_133_F273\t0.777\t25\tY\t0.802\t25\tY\t0.998\t13\tY\t0.912\tY\t0.857\tY\tS\t0.724\t22\tY\t1.000\tY\n+Hp_Contig315.7_R3\t0.448\t20\tY\t0.604\t20\tY\t0.972\t2\tY\t0.904\tY\t0.754\tY\tS\t0.755\t25\tY\t0.999\tY\n+Ps_scaffold_54_R1198\t0.571\t19\tY\t0.551\t19\tY\t0.822\t12\tN\t0.614\tY\t0.582\tY\tS\t0.271\t21\tN\t0.910\tY\n+Ps_scaffold_108_R86\t0.842\t21\tY\t0.810\t21\tY\t0.982\t13\tY\t0.870\tY\t0.840\tY\tS\t0.958\t21\tY\t1.000\tY\n+Ps_scaffold_92_F150\t0.554\t20\tY\t0.611\t20\tY\t0.990\t13\tY\t0.946\tY\t0.778\tY\tS\t0.403\t22\tN\t0.996\tY\n+Ps_scaffold_25_R1748\t0.844\t25\tY\t0.832\t25\tY\t0.969\t5\tY\t0.887\tY\t0.860\tY\tS\t0.692\t25\tY\t0.989\tY\n+Hp_Contig954.2_R1\t0.390\t19\tY\t0.557\t19\tY\t0.973\t13\tY\t0.874\tY\t0.715\tY\tS\t0.485\t19\tN\t1.000\tY\n+Hp_Contig166.8_F9\t0.831\t25\tY\t0.673\t25\tY\t0.975\t14\tY\t0.722\tY\t0.697\tY\tS\t0.553\t25\tY\t0.978\tY\n+Ps_scaffold_39_F1803\t0.733\t21\tY\t0.749\t21\tY\t0.972\t3\tY\t0.860\tY\t0.805\tY\tS\t0.878\t21\tY\t1.000\tY\n+Ps_scaffold_53_R735\t0.476\t20\tY\t0.628\t20\tY\t0.969\t3\tY\t0.901\tY\t0.764\tY\tS\t0.646\t20\tY\t1.000\tY\n+Ps_scaffold_4_F3257\t0.441\t22\tY\t0.576\t26\tY\t0.990\t13\tY\t0.902\tY\t0.739\tY\tS\t0.479\t26\tN\t0.999\tY\n+Ps_scaffold_23_F812\t0.761\t21\tY\t0.812\t21\tY\t0.991\t13\tY\t0.949\tY\t0.881\tY\tS\t0.905\t21\tY\t1.000\tY\n+Pr_scaffold_27_R109\t0.785\t24\tY\t0.798\t24\tY\t0.986\t14\tY\t0.887\tY\t0.842\tY\tS\t0.536\t24\tY\t0.996\tY\n+Hp_Contig646.6_F13\t0.658\t19\tY\t0.729\t19\tY\t0.987\t13\tY\t0.940\tY\t0.835\tY\tS\t0.590\t19\tY\t1.000\tY\n+Ps_scaffold_72_R321\t0.570\t24\tY\t0.490\t19\tY\t0.931\t4\tY\t0.686\tY\t0.588\tY\tS\t0.688\t19\tY\t0.983\tY\n+Pr_scaffold_50_R933\t0.767\t24\tY\t0.707\t24\tY\t0.984\t3\tY\t0.787\tY\t0.747\tY\tS\t0.655\t24\tY\t1.000\tY\n+Ps_scaffold_37_R1245\t0.440\t24\tY\t0.602\t24\tY\t0.995\t13\tY\t0.913\tY\t0.757\tY\tS\t0.259\t24\tN\t1.000\tY\n+Pr_scaffold_50_F261\t0.602\t21\tY\t0.677\t21\tY\t0.970\t3\tY\t0.871\tY\t0.774\tY\tS\t0.822\t21\tY\t1.000\tY\n+Ps_scaffold_23_F1315\t0.391\t22\tY\t0.431\t22\tY\t0.896\t12\tY\t0.651\tY\t0.541\tY\tS\t0.953\t22\tY\t0.972\tY\n+Pr_scaffold_328_F13\t0.640\t22\tY\t0.720\t22\tY\t0.995\t14\tY\t0.966\tY\t0.843\tY\tS\t0.548\t22\tY\t0.997\tY\n+Pr_scaffold_2147_R3\t0.561\t25\tY\t0.429\t25\tY\t0.979\t12\tY\t0.742\tY\t0.586\tY\tS\t0.511\t25\tY\t0.991\tY\n+Pr_scaffold_39_F355\t0.409\t18\tY\t0.455\t18\tY\t0.895\t2\tY\t0.605\tY\t0.530\tY\tS\t0.548\t18\tY\t0.991\tY\n+Ps_scaffold_118_F134\t0.482\t19\tY\t0.597\t19\tY\t0.981\t6\tY\t0.888\tY\t0.743\tY\tS\t0.528\t19\tY\t0.981\tY\n+Ps_scaffold_5_R3563\t0.424\t19\tY\t0.566\t19\tY\t0.987\t6\tY\t0.932\tY\t0.749\tY\tS\t0.302\t19\tN\t0.985\tY\n+Ps_scaffold_53_R22\t0.937\t20\tY\t0.766\t20\tY\t0.979\t14\tY\t0.880\tY\t0.823\tY\tS\t0.803\t20\tY\t0.935\tY\n+Pr_scaffold_14_R620\t1.000\t21\tY\t0.955\t21\tY\t0.992\t3\tY\t0.949\tY\t0.952\tY\tS\t0.967\t21\tY\t1.000\tY\n+Hp_Contig1340.1_F7\t0.909\t22\tY\t0.886\t22\tY\t0.985\t13\tY\t0.921\tY\t0.903\tY\tS\t0.808\t22\tY\t0.998\tY\n+Ps_scaffold_37_R313\t0.563\t25\tY\t0.680\t25\tY\t0.998\t14\tY\t0.965\tY\t0.823\tY\tS\t0.805\t25\tY\t1.000\tY\n+Pr_scaffold_30_R354\t0.230\t19\tN\t0.332\t19\tY\t0.910\t5\tY\t0.701\tY\t0.517\tY\tS\t0.617\t19\tY\t0.963\tY\n' |
| b |
| diff -r 6753a9261390 -r dc958c2a963a tools/protein_analysis/README --- a/tools/protein_analysis/README Wed Apr 03 11:12:31 2013 -0400 +++ b/tools/protein_analysis/README Tue Apr 23 12:47:49 2013 -0400 |
| b |
| @@ -19,6 +19,7 @@ Contributions/revisions copyright 2011 Konrad Paszkiewicz. All rights reserved. See the included LICENCE file for details (an MIT style open source licence). + Requirements ============ @@ -45,6 +46,7 @@ Verify each of the tools is installed and working from the command line (when logged in as the Galaxy user if appropriate). + Manual Installation =================== @@ -93,17 +95,8 @@ Leave out the lines for any tools you do not wish to use in Galaxy. -4. Copy/move the following test files (from these archive) to Galaxy - subfolder test-data: - -four_human_proteins.fasta -four_human_proteins_signalp3.tabular -four_human_proteins_tmhmm2.tabular -empty.fasta -empty_tmhmm2.tabular -empty_signalp3.tabular -k12_ten_proteins.fasta -k12_ten_proteins_psortb_p_terse.tabular +4. Copy/move the test-data files (from this archive) to Galaxy's + subfolder test-data. 5. Run the Galaxy functional tests for these new wrappers with: @@ -145,6 +138,9 @@ v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed v0.2.0 - Added PSORTb wrapper to the suite, based on earlier work contributed by Konrad Paszkiewicz. +v0.2.1 - Use a script to create the Tool Shed tar-ball (removed some stray + files accidentally included previously via a wildcard). +v0.2.2 - Include missing test files. Developers @@ -159,33 +155,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/psortb.xml tools/protein_analysis/psortb.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular test-data/k12_ten_proteins.fasta test-data/k12_ten_proteins_psortb_p_terse.tabular - -Check this worked: +$ ./tools/protein_analysis/make_tmhmm_and_signalp.sh -$ tar -tzf ~/tmhmm_signalp_etc.tar.gz -tools/protein_analysis/LICENSE -tools/protein_analysis/README -tools/protein_analysis/suite_config.xml -tools/protein_analysis/seq_analysis_utils.py -tools/protein_analysis/signalp3.xml -tools/protein_analysis/signalp3.py -tools/protein_analysis/tmhmm2.xml -tools/protein_analysis/tmhmm2.py -tools/protein_analysis/promoter2.xml -tools/protein_analysis/promoter2.py -tools/protein_analysis/psortb.xml -tools/protein_analysis/psortb.py -tools/protein_analysis/wolf_psort.xml -tools/protein_analysis/wolf_psort.py -tools/protein_analysis/rxlr_motifs.xml -tools/protein_analysis/rxrl_motifs.py -tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm -test-data/four_human_proteins.fasta -test-data/four_human_proteins.signalp3.tabular -test-data/four_human_proteins.tmhmm2.tabular -test-data/empty.fasta -test-data/empty_tmhmm2.tabular -test-data/empty_signalp3.tabular -test-data/k12_ten_proteins.fasta -test-data/k12_ten_proteins_psortb_p_terse.tabular +This simplifies ensuring a consistent set of files is bundled each time, +including all the relevant test files. |
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| diff -r 6753a9261390 -r dc958c2a963a tools/protein_analysis/tmhmm2.xml --- a/tools/protein_analysis/tmhmm2.xml Wed Apr 03 11:12:31 2013 -0400 +++ b/tools/protein_analysis/tmhmm2.xml Tue Apr 23 12:47:49 2013 -0400 |
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| @@ -90,6 +90,8 @@ =================================== === ===== ======= ======= ==================== +----- + **References** Krogh, Larsson, von Heijne, and Sonnhammer. |