| Previous changeset 2:aed130b47d36 (2017-05-29) Next changeset 4:d359ec9f0fe1 (2017-05-30) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ca572343d2a24d645dedd6c5d2cb352115ed8bf3 |
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modified:
edgeR_repenrich.R edger-repenrich.xml repenrich.xml test-data/Normalized_counts_file.tab test-data/edgeR_plots.pdf test-data/edgeR_result_file.tab |
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| diff -r aed130b47d36 -r 1805b262c12d edgeR_repenrich.R --- a/edgeR_repenrich.R Mon May 29 17:08:36 2017 -0400 +++ b/edgeR_repenrich.R Tue May 30 10:34:53 2017 -0400 |
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| @@ -147,10 +147,6 @@ write.table(normalizedAbundance, file=opt$countsfile, sep="\t", col.names=TRUE, row.names=FALSE, quote=FALSE) } -# test -print(counts) -print(cpm) - # Conduct fitting of the GLM yfit <- glmFit(y, design) @@ -160,12 +156,12 @@ # Make the comparisons for the GLM my.contrasts <- makeContrasts( - paste0(opt$levelNameB,"_",opt$levelNameA," = ", opt$levelNameB, " - ", opt$levelNameA), + paste0(opt$levelNameA,"_",opt$levelNameB," = ", opt$levelNameA, " - ", opt$levelNameB), levels = design ) # Define the contrasts used in the comparisons -allcontrasts = paste0(opt$levelNameB," vs ",opt$levelNameA) +allcontrasts = paste0(opt$levelNameA," vs ",opt$levelNameB) # Conduct a for loop that will do the fitting of the GLM for each comparison # Put the results into the results objects |
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| diff -r aed130b47d36 -r 1805b262c12d edger-repenrich.xml --- a/edger-repenrich.xml Mon May 29 17:08:36 2017 -0400 +++ b/edger-repenrich.xml Tue May 30 10:34:53 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.0.0"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="1.1.0"> <description>Determines differentially expressed features from RepEnrich counts</description> <requirements> <requirement type="package" version="3.16.5">bioconductor-edger</requirement> @@ -98,25 +98,25 @@ label="Output normalized counts table" /> </inputs> <outputs> - <data format="tabular" name="edger_out" label="edgeR result file on ${on_string}"> + <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}"> <actions> <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" /> </actions> </data> - <data format="pdf" name="plots" label="edgeR plots on ${on_string}" /> - <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> + <data format="pdf" name="plots" label="edgeR plots" /> + <data format="tabular" name="counts_out" label="Normalized counts file"> <filter>normCounts == True</filter> </data> </outputs> <tests> <test> - <param name="factorName" value="genotype"/> - <param name="factorLevel_A" value="wildtype"/> - <param name="countsFiles_A" value="353_fraction_counts.tab,354_fraction_counts.tab"/> - <param name="alignmentFiles_A" value="aligned_353.tab,aligned_354.tab"/> - <param name="factorLevel_B" value="mutant"/> - <param name="countsFiles_B" value="355_fraction_counts.tab,356_fraction_counts.tab"/> - <param name="alignmentFiles_B" value="aligned_355.tab,aligned_356.tab"/> + <param name="factorName" value="Genotype"/> + <param name="factorLevel_A" value="Mutant"/> + <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> + <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/> + <param name="factorLevel_B" value="Wildtype"/> + <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/> + <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/> <param name="normCounts" value="True"/> <output name="counts_out" file="Normalized_counts_file.tab"/> <output name="plots" file="edgeR_plots.pdf"/> |
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| diff -r aed130b47d36 -r 1805b262c12d repenrich.xml --- a/repenrich.xml Mon May 29 17:08:36 2017 -0400 +++ b/repenrich.xml Tue May 30 10:34:53 2017 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.0.0"> +<tool id="repenrich" name="RepEnrich" version="1.1.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -36,7 +36,7 @@ <!-- basic error handling --> <inputs> <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> - <param format="fastq,fastqsanger" label="Single-reads equencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> + <param format="fastq,fastqsanger" label="Single-reads sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> </inputs> |
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| diff -r aed130b47d36 -r 1805b262c12d test-data/Normalized_counts_file.tab --- a/test-data/Normalized_counts_file.tab Mon May 29 17:08:36 2017 -0400 +++ b/test-data/Normalized_counts_file.tab Tue May 30 10:34:53 2017 -0400 |
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| b'@@ -1,211 +1,211 @@\n-Tag\twildtype_1\twildtype_2\tmutant_1\tmutant_2\n-LSU-rRNA_Dme\t157455.221275418\t149201.031867455\t218650.181450173\t354466.098949349\n-FW3_DM\t35.756634311884\t44.2453336153694\t25.3386538652006\t32.2981814492716\n-DMTOM1_LTR\t43.2005545717588\t49.0430203929395\t54.9461072223747\t39.3419337866127\n-R1_DM\t315.957840856997\t262.031236427494\t604.054709763298\t517.028601444589\n-TAHRE\t196.209690086873\t189.678242903128\t149.055512536249\t121.719476366005\n-G4_DM\t157.828320885669\t165.108271224056\t87.0600116574048\t105.226787966377\n-BS\t313.935504138996\t242.355874491196\t203.649150075801\t355.194096523239\n-Stalker2_I-int\t527.184456786045\t604.508533973842\t429.46472687139\t413.519801853174\n-Stalker3_LTR\t25.5158653994552\t21.2745908621546\t21.2656708636846\t20.1863634057947\n-TABOR_I-int\t169.833255871247\t149.309827895896\t215.554792695617\t317.054754599099\n-G7_DM\t6.97060741098101\t4.74922529496845\t76.3292679803337\t35.9059570366902\n-BEL_I-int\t1022.22666828812\t1059.36800967358\t1148.97283940843\t1304.98396962057\n-Gypsy6_I-int\t322.239993215042\t326.921161631196\t445.717495579363\t323.23951274896\n-ACCORD_I-int\t117.166444321613\t104.919109832721\t160.687012069425\t174.461719477315\n-DM412B_LTR\t132.441540808639\t141.022914371002\t219.588612399041\t257.784155662936\n-G2_DM\t57.1417693937208\t54.8583983051458\t48.3666731430026\t65.6271559235199\n-SSU-rRNA_Hsa\t13684.9804569472\t8340.22115575582\t22075.2937251301\t25925.561270609\n-TART_B1\t1086.38207353363\t1042.55187521078\t524.083255060455\t437.142142008891\n-S2_DM\t32.9167572185214\t35.52226674706\t28.0409214335141\t17.6093808433528\n-LOOPER1_DM\t35.3263499037988\t28.5438132524124\t8.61592558013002\t2.66288198118994\n-HOBO\t216.476085707688\t213.42436937797\t171.339429150313\t182.020868327145\n-ARS406_DM\t24.2250121751994\t34.8438059906359\t29.5682900590826\t19.7568663120544\n-G6_DM\t207.698283782749\t168.30672907577\t112.555318714971\t67.5169431359773\n-DOC2_DM\t190.960220308233\t219.9182080466\t176.665637690757\t176.265607271025\n-Baggins1\t220.994071992583\t188.660551768492\t215.398139503251\t157.367735146451\n-NINJA_LTR\t21.1269644369856\t19.6753619362979\t11.6314995331755\t9.79253373727915\n-TRANSIB2\t137.561925264854\t149.067520482887\t131.471191693166\t127.474737422125\n-Gypsy5_LTR\t28.0115149663496\t21.8561286533752\t19.6599756419331\t28.0032105118684\n-MDG3_LTR\t44.6204931184401\t41.0953372462576\t36.2652140327291\t38.9983361116205\n-Gypsy12A_LTR\t131.624000433277\t108.650643993054\t95.4017941508943\t92.5136739916635\n-Gypsy_LTR\t56.1951436959333\t44.4391795457762\t147.684797103047\t149.207290365385\n-TIRANT_LTR\t58.9919923484874\t61.9822362475985\t126.301636345088\t137.095472321908\n-I_DM\t343.668156737687\t339.860377485855\t449.55549879233\t957.692619622151\n-DIVER2_I-int\t287.386956160137\t272.692762599872\t252.44661949781\t229.179649219831\n-P-1_DY\t0.344227526468198\t0.0969229652034378\t0.509122875189502\t0.343597674992251\n-Invader2_I-int\t293.583051636564\t267.022769135471\t233.804889606256\t271.184464987634\n-DOC6_DM\t54.1728069779326\t60.0922384261314\t67.2825461211972\t65.9707535985121\n-BURDOCK_LTR\t12.3491625120466\t17.930748562636\t21.2656708636846\t16.5785878183761\n-SSU-rRNA_Dme\t306.061299471036\t201.260537244939\t389.988122395158\t328.307578455096\n-MAX_LTR\t43.7599243022696\t36.4914963990943\t37.5184395716571\t29.4635006305855\n-STALKER4_LTR\t55.5927455246139\t58.6383939480799\t79.8931281066602\t68.9772332546943\n-XDMR_DM\t142.725338161877\t209.741296700239\t158.572193972484\t136.322377553175\n-BARI_DM\t42.5981564004395\t43.7122573067505\t43.7454039682056\t44.8394965864887\n-Transib-N1_DM\t13.2527597690256\t17.9792100452377\t14.333767101489\t11.1669244372481\n-Gypsy5_I-int\t105.333623099269\t105.936800967358\t110.988786791311\t88.9917978229929\n-XDMR\t53.7425225698474\t69.7845349464752\t69.3582009200467\t77.5671751295006\n-ACCORD2_LTR\t10.1116835900033\t9.30460465953003\t8.34178249348953\t6.52835582485276\n-POGON1\t14.2424139076217\t19.5299774884927\t25.1036740766516\t21.990251199504\n-BS4_DM\t1.46296698748984\t1.0176911346361\t0.313306384732001\t1.97568663120544\n-ALA_DM\t0.215142204042624\t0.290768895610313\t0.352469682823501\t0\n-Gypsy1-I_DM\t351.112076997562\t3'..b'8945524843\t244.924333069087\t296.387839956473\t251.685296931824\n-CIRCE\t162.088136525713\t161.037506685512\t143.964283784354\t134.862087434458\n-DIVER2_LTR\t34.1215535611601\t25.9268931919196\t25.3778171632921\t20.615860499535\n-POGO\t104.43002584229\t120.766014643484\t113.926034148174\t88.6482001480007\n-Gypsy6A_LTR\t26.5485479788598\t27.7684295307849\t31.0564953865596\t18.8119727058257\n-MAX_I-int\t533.337523821664\t445.894101418416\t349.101639187632\t335.437230211185\n-ROOA_LTR\t17.2113763234099\t23.4068960966302\t17.0360346698026\t23.7082395744653\n-DM176_I-int\t156.064154812519\t136.322150558635\t185.08574678043\t197.396864283048\n-Copia2_LTR_DM\t38.3383407603955\t23.5522805444354\t29.2549836743506\t39.5137326241088\n-DM297_I-int\t509.327653850507\t558.760894397819\t3226.54663986442\t3668.33467763602\n-IDEFIX_I-int\t266.475133927194\t268.815843991735\t282.837338816814\t282.265490006134\n-Jockey2\t76.1603402310888\t76.9568343715296\t71.3946924208047\t65.2835582485276\n-TC1-2_DM\t163.809274158054\t191.325933311586\t173.806716930078\t196.451970676819\n-DMRPR\t5.50764042349117\t9.06229724652144\t8.65508887822152\t11.6823209497365\n+Transib5\t38.1058890430296\t28.1750093493646\t48.3209390279733\t46.7653307106587\n+MuDR-1_DEl\t1.253225538928\t0.343597674992251\t0.258170644851148\t0.43615334341547\n+Mariner2_DM\t42.9229747082841\t79.542861760706\t86.5301944659432\t77.1022188193348\n+DOC5_DM\t70.2197934780597\t64.5963628985431\t130.67737473549\t105.791416519552\n+TC1_DM\t102.529514403547\t127.560636840873\t79.1723310876855\t94.9845058993691\n+Gypsy9_LTR\t2.42812448167301\t0.687195349984501\t2.19445048123476\t2.03538226927219\n+DMRP1\t11.5531729369925\t12.369516299721\t11.2734514918335\t11.0007565505902\n+Gypsy10_I-int\t87.5691345325943\t79.6287611794541\t97.1582193456488\t93.5306614213175\n+Gypsy4_LTR\t15.273686255685\t18.7260732870777\t11.7897927815358\t9.40152762473347\n+DM297_LTR\t239.992690704713\t216.122937570126\t64.0693483638933\t71.6260712853405\n+ACCORD2_I-int\t89.5272994371693\t103.079302497675\t126.245445332212\t119.118324235025\n+Invader1_LTR\t98.8873276810378\t163.466593877563\t143.973162945324\t93.5791229039192\n+BEL_LTR\t36.3043773308206\t51.9691483425779\t37.6498857074591\t41.5799520722748\n+IVK_DM\t118.468976726788\t151.956071765323\t144.102248267749\t141.555990679621\n+M4DM\t73.6270004120202\t78.8556664107215\t74.3101172763222\t79.9614462928362\n+FW2_DM\t694.091132075657\t761.412447782827\t612.466826468541\t671.046149586002\n+Copia2_I-int\t141.536159302681\t162.521700271335\t181.493963330357\t167.434422388939\n+MDG1_LTR\t25.4561437594751\t24.1377366682056\t29.6896241578821\t28.2045828742004\n+Gypsy12_LTR\t296.544493148839\t230.210442244808\t270.734949567238\t287.5704377586\n+Gypsy7_I-int\t45.5077523823231\t63.7373687110625\t54.0437216555071\t48.8976359451344\n+FROGGER_I-int\t42.1005454483626\t46.9010826364422\t69.3188181425333\t65.9560778209394\n+Gypsy_I-int\t943.130544639506\t958.723412647127\t293.540023195756\t273.031992978084\n+5S_DM\t247.942840217287\t356.138990129468\t271.810660587451\t503.611727197063\n+GTWIN_I-int\t296.387839956473\t251.685296931824\t234.418945524843\t244.924333069087\n+CIRCE\t143.964283784354\t134.862087434458\t162.088136525713\t161.037506685512\n+DIVER2_LTR\t25.3778171632921\t20.615860499535\t34.1215535611601\t25.9268931919196\n+POGO\t113.926034148174\t88.6482001480007\t104.43002584229\t120.766014643484\n+Gypsy6A_LTR\t31.0564953865596\t18.8119727058257\t26.5485479788598\t27.7684295307849\n+MAX_I-int\t349.101639187632\t335.437230211185\t533.337523821664\t445.894101418416\n+ROOA_LTR\t17.0360346698026\t23.7082395744653\t17.2113763234099\t23.4068960966302\n+DM176_I-int\t185.08574678043\t197.396864283048\t156.064154812519\t136.322150558635\n+Copia2_LTR_DM\t29.2549836743506\t39.5137326241088\t38.3383407603955\t23.5522805444354\n+DM297_I-int\t3226.54663986442\t3668.33467763602\t509.327653850507\t558.760894397819\n+IDEFIX_I-int\t282.837338816814\t282.265490006134\t266.475133927194\t268.815843991735\n+Jockey2\t71.3946924208047\t65.2835582485276\t76.1603402310888\t76.9568343715296\n+TC1-2_DM\t173.806716930078\t196.451970676819\t163.809274158054\t191.325933311586\n+DMRPR\t8.65508887822152\t11.6823209497365\t5.50764042349117\t9.06229724652144\n' 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| diff -r aed130b47d36 -r 1805b262c12d test-data/edgeR_plots.pdf |
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| Binary file test-data/edgeR_plots.pdf has changed |
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| diff -r aed130b47d36 -r 1805b262c12d test-data/edgeR_result_file.tab --- a/test-data/edgeR_result_file.tab Mon May 29 17:08:36 2017 -0400 +++ b/test-data/edgeR_result_file.tab Tue May 30 10:34:53 2017 -0400 |
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| b'@@ -1,209 +1,209 @@\n DM297_I-int\t2.69047105438237\t4.49448726299278e-21\tLTR\tGypsy\n-DM297_LTR\t1.74961921158059\t1.33970311551615e-18\tLTR\tGypsy\n-Gypsy1-I_DM\t2.37388633230267\t4.48026988289666e-16\tLTR\tGypsy\n-NOF_FB\t-2.79644759297337\t4.48026988289666e-16\tDNA\tMULE-NOF\n-G7_DM\t3.25987374806405\t1.55296802933851e-15\tLINE\tJockey\n-Gypsy_I-int\t1.74702179622354\t4.35250852544863e-12\tLTR\tGypsy\n-LINEJ1_DM\t1.94429217926762\t5.18070558191679e-12\tLINE\tJockey\n-TOM_I-int\t1.33935222283437\t6.69227956217608e-12\tLTR\tGypsy\n-GTWIN_LTR\t1.89490932455113\t8.80590960311443e-12\tLTR\tGypsy\n-Gypsy_LTR\t1.56024435809038\t2.99852403113839e-11\tLTR\tGypsy\n+DM297_LTR\t1.74961921158059\t1.33970311552449e-18\tLTR\tGypsy\n+Gypsy1-I_DM\t2.37388633230267\t4.48026988291108e-16\tLTR\tGypsy\n+NOF_FB\t-2.79644759297337\t4.48026988291108e-16\tDNA\tMULE-NOF\n+G7_DM\t3.25987374806405\t1.55296802933692e-15\tLINE\tJockey\n+Gypsy_I-int\t1.74702179622354\t4.35250852545265e-12\tLTR\tGypsy\n+LINEJ1_DM\t1.94429217926762\t5.18070558194078e-12\tLINE\tJockey\n+TOM_I-int\t1.33935222283437\t6.6922795621824e-12\tLTR\tGypsy\n+GTWIN_LTR\t1.89490932455113\t8.80590960313784e-12\tLTR\tGypsy\n+Gypsy_LTR\t1.56024435809038\t2.99852403114994e-11\tLTR\tGypsy\n DM1731_I-int\t1.53134429520835\t6.4920552091728e-10\tLTR\tCopia\n-Gypsy6_LTR\t1.53023046204423\t1.07509345482697e-06\tLTR\tGypsy\n+Gypsy6_LTR\t1.53023046204423\t1.07509345482848e-06\tLTR\tGypsy\n LOOPER1_DM\t-2.46983670012103\t1.61917280285007e-06\tDNA\tPiggyBac\n-TIRANT_LTR\t1.12203469288475\t1.7801266502904e-06\tLTR\tGypsy\n-Gypsy12_I-int\t-1.12204057066646\t2.19485691074398e-06\tLTR\tGypsy\n+TIRANT_LTR\t1.12203469288475\t1.78012665029166e-06\tLTR\tGypsy\n+Gypsy12_I-int\t-1.12204057066646\t2.19485691074579e-06\tLTR\tGypsy\n R2_DM\t1.67889583354494\t2.73035057005978e-06\tLINE\tR2\n-TRANSPAC_LTR\t1.49364968145495\t2.90210475425899e-06\tLTR\tGypsy\n-Copia_LTR\t1.66649088148806\t1.186041112787e-05\tLTR\tCopia\n+TRANSPAC_LTR\t1.49364968145495\t2.9021047542613e-06\tLTR\tGypsy\n+Copia_LTR\t1.66649088148806\t1.18604111278586e-05\tLTR\tCopia\n ACCORD_LTR\t1.3724059468295\t1.75953804703817e-05\tLTR\tGypsy\n TIRANT_I-int\t1.17728139313168\t2.04686461971632e-05\tLTR\tGypsy\n-TART_B1\t-1.14695345949677\t3.0965848472869e-05\tLINE\tJockey\n-TRANSIB1\t-1.3902119423097\t6.16503339250287e-05\tDNA\tCMC-Transib\n-DM412B_LTR\t0.803090050933452\t0.00012443453312394\tLTR\tGypsy\n+TART_B1\t-1.14695345949677\t3.09658484730011e-05\tLINE\tJockey\n+TRANSIB1\t-1.3902119423097\t6.16503339250305e-05\tDNA\tCMC-Transib\n+DM412B_LTR\t0.803090050933452\t0.00012443453312414\tLTR\tGypsy\n MICROPIA_LTR\t-1.29556276189806\t0.000129852108160169\tLTR\tGypsy\n-G6_DM\t-1.05894868960943\t0.000138305097075555\tLINE\tJockey\n-NINJA_I-int\t-0.874264518473233\t0.000155536374045889\tLTR\tPao\n-R1_DM\t0.955905154410719\t0.000189845334696753\tLINE\tR1\n+G6_DM\t-1.05894868960943\t0.000138305097075584\tLINE\tJockey\n+NINJA_I-int\t-0.874264518473233\t0.000155536374046075\tLTR\tPao\n+R1_DM\t0.955905154410719\t0.000189845334697796\tLINE\tR1\n Invader6_LTR\t-1.18865109431199\t0.000212988712815497\tLTR\tGypsy\n Copia_I-int\t1.9331690527025\t0.000223130721644621\tLTR\tCopia\n-BLASTOPIA_LTR\t1.34881958569428\t0.000364879309201074\tLTR\tGypsy\n+BLASTOPIA_LTR\t1.34881958569428\t0.000364879309201161\tLTR\tGypsy\n LSU-rRNA_Hsa\t2.61189118344978\t0.000801598301190925\trRNA\trRNA\n-TRANSPAC_I-int\t1.16122217809542\t0.000845313292127692\tLTR\tGypsy\n-G4_DM\t-0.74970144243323\t0.000914365923267139\tLINE\tJockey\n+TRANSPAC_I-int\t1.16122217809542\t0.000845313292130344\tLTR\tGypsy\n+G4_DM\t-0.74970144243323\t0.000914365923267624\tLINE\tJockey\n SSU-rRNA_Hsa\t1.12389968473263\t0.0010425909765405\trRNA\trRNA\n-DOC5_DM\t-0.809872869194368\t0.00162410751644232\tLINE\tJockey\n-Invader1_I-int\t0.749727833008358\t0.00198920329215514\tLTR\tGypsy\n+DOC5_DM\t-0.809872869194368\t0.00162410751644423\tLINE\tJockey\n+Invader1_I-int\t0.749727833008358\t0.00198920329215702\tLTR\tGypsy\n TRANSIB4\t-1.00230688125284\t0.00206051807311839\tDNA\tCMC-Transib\n MICROPIA_I-int\t-0.751193028928835\t0.00292932704926266\tLTR\tGypsy\n PLACW_DM\t1.16310826488548\t0.00305178248567248\tDNA\tP\n-TABOR_I-int\t0.737702190628259\t0.00354953953974351\tLTR\tGypsy\n+TABOR_I-int\t0.737702190628259\t0.00354953953973759\tLTR\tGypsy'..b'0.228543531933743\t0.760296029745035\tSINE\ttRNA-Deu-L2\n+Gypsy10_LTR\t-0.154651074858764\t0.76240178289376\tLTR\tGypsy\n+QUASIMODO2-LTR_DM\t-0.155430480903998\t0.76240178289376\tLTR\tGypsy\n+Copia2_LTR_DM\t0.147979193864449\t0.76240178289376\tLTR\tCopia\n BS4_DM\t-0.253251631796478\t0.81092436860891\tLINE\tJockey\n G_DM\t0.0902785903431559\t0.81092436860891\tLINE\tJockey\n-IVK_DM\t-0.0807211765160779\t0.81870908545043\tLINE\tI\n-Gypsy5_I-int\t-0.0774807293903186\t0.835273508730751\tLTR\tGypsy\n-Gypsy12_LTR\t-0.0832045482918072\t0.835273508730751\tLTR\tGypsy\n-Gypsy6A_LTR\t-0.116239966704279\t0.835273508730751\tLTR\tGypsy\n-IDEFIX_I-int\t0.0781972363147815\t0.835273508730751\tLTR\tGypsy\n+IVK_DM\t-0.0807211765160779\t0.818709085450591\tLINE\tI\n+Gypsy5_I-int\t-0.0774807293903186\t0.835273508731359\tLTR\tGypsy\n+Gypsy12_LTR\t-0.0832045482918072\t0.835273508731359\tLTR\tGypsy\n+Gypsy6A_LTR\t-0.116239966704279\t0.835273508731359\tLTR\tGypsy\n+IDEFIX_I-int\t0.0781972363147815\t0.835273508731359\tLTR\tGypsy\n PROTOP_B\t-0.0745501769371703\t0.846311908195535\tDNA\tP\n DMRP1\t0.100504519100353\t0.846311908195535\tUnknown\tUnknown\n-Copia1-LTR_DM\t-0.0961752276665428\t0.850550157756422\tLTR\tCopia\n-TC1-2_DM\t0.0595720035046981\t0.853067020850901\tDNA\tTcMar-Tc1\n-LSU-rRNA_Cel\t-0.0920825033469626\t0.861339242540399\trRNA\trRNA\n-Gypsy7_I-int\t0.0826410967604942\t0.861339242540399\tLTR\tGypsy\n-Gypsy5_LTR\t-0.0710979993807782\t0.905487490634908\tLTR\tGypsy\n-Gypsy4_I-int\t-0.0516274039610208\t0.905487490634908\tLTR\tGypsy\n-QUASIMODO_LTR\t-0.0643467685962964\t0.905487490634908\tLTR\tGypsy\n-Gypsy2-LTR_DM\t0.0652192786223383\t0.905487490634908\tLTR\tGypsy\n-DMLTR5\t0.0726894766496021\t0.905487490634908\tLTR\tGypsy\n-Stalker2_LTR\t-0.0523210063310555\t0.917308330496028\tLTR\tGypsy\n-ROVER-I_DM\t-0.0408110836395496\t0.922716163337709\tLTR\tGypsy\n+Copia1-LTR_DM\t-0.0961752276665428\t0.850550157756311\tLTR\tCopia\n+TC1-2_DM\t0.0595720035046981\t0.853067020850826\tDNA\tTcMar-Tc1\n+LSU-rRNA_Cel\t-0.0920825033469626\t0.861339242519926\trRNA\trRNA\n+Gypsy7_I-int\t0.0826410967604942\t0.861339242519926\tLTR\tGypsy\n+Gypsy5_LTR\t-0.0710979993807782\t0.905487490633946\tLTR\tGypsy\n+Gypsy4_I-int\t-0.0516274039610208\t0.905487490633946\tLTR\tGypsy\n+QUASIMODO_LTR\t-0.0643467685962964\t0.905487490633946\tLTR\tGypsy\n+Gypsy2-LTR_DM\t0.0652192786223383\t0.905487490633946\tLTR\tGypsy\n+DMLTR5\t0.0726894766496021\t0.905487490633946\tLTR\tGypsy\n+Stalker2_LTR\t-0.0523210063310555\t0.917308330496379\tLTR\tGypsy\n+ROVER-I_DM\t-0.0408110836395496\t0.922716163337686\tLTR\tGypsy\n MDG1_I-int\t-0.0411424164719924\t0.937452811422426\tLTR\tGypsy\n ALA_DM\t-0.11425480149938\t0.942917068804402\tUnknown\tUnknown\n DNAREP1_DM\t0.039354033592028\t0.942917068804402\tRC\tHelitron\n-BARI_DM\t0.0372716083617889\t0.94985097135805\tDNA\tTcMar-Tc1\n-Gypsy2_I-int\t-0.0261599267227275\t0.95196577198178\tLTR\tGypsy\n-DMTOM1_LTR\t0.0349640382618226\t0.953829042791583\tLTR\tGypsy\n-IDEFIX_LTR\t0.0219961145617681\t0.957715681080671\tLTR\tGypsy\n-STALKER4_I-int\t0.0241275307638275\t0.957715681080671\tLTR\tGypsy\n-Gypsy3_LTR\t-0.0298883238815861\t0.957715681080671\tLTR\tGypsy\n-MINOS\t0.0330479824589295\t0.957715681080671\tDNA\tTcMar-Tc1\n-G2_DM\t0.0226097987515835\t0.962242582650612\tLINE\tJockey\n-Copia1-I_DM\t0.0124236833262227\t0.963045943681216\tLTR\tCopia\n-Invader4_LTR\t0.016495431966038\t0.963045943681216\tLTR\tGypsy\n-M4DM\t-0.0173659751457427\t0.963045943681216\tDNA\tCMC-Transib\n+BARI_DM\t0.0372716083617889\t0.949850971355763\tDNA\tTcMar-Tc1\n+Gypsy2_I-int\t-0.0261599267227275\t0.951965771983562\tLTR\tGypsy\n+DMTOM1_LTR\t0.0349640382618226\t0.953829042793374\tLTR\tGypsy\n+IDEFIX_LTR\t0.0219961145617681\t0.957715681080923\tLTR\tGypsy\n+STALKER4_I-int\t0.0241275307638275\t0.957715681080923\tLTR\tGypsy\n+Gypsy3_LTR\t-0.0298883238815861\t0.957715681080923\tLTR\tGypsy\n+MINOS\t0.0330479824589295\t0.957715681080923\tDNA\tTcMar-Tc1\n+G2_DM\t0.0226097987515835\t0.962242582647045\tLINE\tJockey\n+Copia1-I_DM\t0.0124236833262227\t0.963045943681341\tLTR\tCopia\n+Invader4_LTR\t0.016495431966038\t0.963045943681341\tLTR\tGypsy\n+M4DM\t-0.0173659751457427\t0.963045943681341\tDNA\tCMC-Transib\n BS\t0.00565217021634194\t0.997858051773989\tLINE\tJockey\n FTZ_DM\t0\t1\tUnknown\tUnknown\n FUSHI_DM\t0\t1\tUnknown\tUnknown\n' |