| Next changeset 1:6bbc90a11c3f (2018-04-18) |
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Commit message:
planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/askor commit 08a187f91ba050d584e586d2fcc99d984dac607c |
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added:
AskoR.R AskoR_DE.R askor_de.xml test-data/AskoAvsK.txt test-data/AskoT1AvsT1K.txt test-data/AskoT1vsT0.txt test-data/AskoT1vsT2.txt test-data/Contrasts.txt test-data/Samples.txt test-data/condition.asko.txt test-data/context.asko.txt test-data/contrast.asko.txt test-data/counts.csv test-data/out.pdf |
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| diff -r 000000000000 -r ceef9bc6bbc7 AskoR.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AskoR.R Thu Apr 12 05:23:45 2018 -0400 |
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| b'@@ -0,0 +1,651 @@\n+asko3c <- function(data_list){\n+ asko<-list()\n+\n+ ######### Condition ############\n+\n+ condition<-unique(data_list$samples$condition) # retrieval of different condition\'s names\n+ col1<-which(colnames(data_list$samples)=="condition") # determination of number of the column "condition"\n+ colcol<-which(colnames(data_list$samples)=="color")\n+ if(is.null(parameters$fileofcount)){\n+ col2<-which(colnames(data_list$samples)=="file") # determination of number of the column "replicate"\n+ column_name<-colnames(data_list$samples[,c(-col1,-col2,-colcol)]) # retrieval of column names needful to create the file condition\n+ }else{column_name<-colnames(data_list$samples[,c(-col1,-colcol)])}\n+ condition_asko<-data.frame(row.names=condition) # initialization of the condition\'s data frame\n+ #level<-list() # initialization of the list will contain the level\n+ # of each experimental factor\n+ for (name in column_name){ # for each experimental factor :\n+ # if(str_detect(name, "condition")){ # for the column of conditions, the level is fixed to 0 because\n+ # level<-append(level, 0) # "condition" must be the first column of the data frame\n+ # }else{ #\n+ # level<-append(level, length(levels(data_list$samples[,name]))) # adding to the list the level of other experimental factors\n+ # }\n+ #\n+ condition_asko$n<-NA # initialization of new column in the condition\'s data frame\n+ colnames(condition_asko)[colnames(condition_asko)=="n"]<-name # to rename the new column with with the name of experimental factor\n+ for(condition_name in condition){ # for each condition\'s names\n+ condition_asko[condition_name,name]<-as.character(unique(data_list$samples[data_list$samples$condition==condition_name, name]))\n+ } # filling the condition\'s data frame\n+ }\n+ # order_level<-order(unlist(level)) # list to vector\n+ # condition_asko<-condition_asko[,order_level] # order columns according to their level\n+ #asko$condition<-condition_asko # adding data frame of conditions to asko object\n+\n+ #print(condition_asko)\n+\n+\n+ #############contrast + context##################\n+ i=0\n+\n+ contrast_asko<-data.frame(row.names = colnames(data_list$contrast)) # initialization of the contrast\'s data frame\n+ contrast_asko$Contrast<-NA # all columns are created et initialized with\n+ contrast_asko$context1<-NA # NA values\n+ contrast_asko$context2<-NA #\n+\n+ list_context<-list() # initialization of context and condition lists\n+ list_condition<-list() # will be used to create the context data frame\n+ if(parameters$mk_context==TRUE){\n+ for (contrast in colnames(data_list$contrast)){ # for each contrast :\n+ i='..b'="character", default="Set2", dest="palette",\n+ help="Color palette (ggplot)[default= %default]", metavar="character"),\n+ make_option(c("-R", "--regex"), type="logical", default=FALSE, dest="regex",\n+ help="use regex when selecting/removing samples [default= %default]", metavar="logical"),\n+ make_option(c("-S", "--select"), type="character", default=NULL, dest="select_sample",\n+ help="selected samples [default= %default]", metavar="character"),\n+ make_option(c("-r", "--remove"), type="character", default=NULL, dest="rm_sample",\n+ help="removed samples [default= %default]", metavar="character"),\n+ make_option(c("--th_cpm"), type="double", default=0.5, dest="threshold_cpm",\n+ help="CPM\'s threshold [default= %default]", metavar="double"),\n+ make_option(c("--rep"), type="integer", default=3, dest="replicate_cpm",\n+ help="Minimum number of replicates [default= %default]", metavar="integer"),\n+ make_option(c("--th_FDR"), type="double", default=0.05, dest="threshold_FDR",\n+ help="FDR threshold [default= %default]", metavar="double"),\n+ make_option(c("-n", "--normalization"), type="character", default="TMM", dest="normal_method",\n+ help="normalization method (TMM/RLE/upperquartile/none) [default= %default]", metavar="character"),\n+ make_option(c("--adj"), type="character", default="fdr", dest="p_adj_method",\n+ help="p-value adjust method (holm/hochberg/hommel/bonferroni/BH/BY/fdr/none) [default= %default]", metavar="character"),\n+ make_option("--glm", type="character", default="qlf", dest="glm",\n+ help=" GLM method (lrt/qlf) [default= %default]", metavar="character"),\n+ make_option(c("--lfc"), type="logical", default="TRUE", dest="logFC",\n+ help="logFC in the summary table [default= %default]", metavar="logical"),\n+ make_option("--fc", type="logical", default="TRUE", dest="FC",\n+ help="FC in the summary table [default= %default]", metavar="logical"),\n+ make_option(c("--lcpm"), type="logical", default="FALSE", dest="logCPM",\n+ help="logCPm in the summary table [default= %default]", metavar="logical"),\n+ make_option("--fdr", type="logical", default="TRUE", dest="FDR",\n+ help="FDR in the summary table [default= %default]", metavar="logical"),\n+ make_option("--lr", type="logical", default="FALSE", dest="LR",\n+ help="LR in the summary table [default= %default]", metavar="logical"),\n+ make_option(c("--sign"), type="logical", default="TRUE", dest="Sign",\n+ help="Significance (1/0/-1) in the summary table [default= %default]", metavar="logical"),\n+ make_option(c("--expr"), type="logical", default="TRUE", dest="Expression",\n+ help="Significance expression in the summary table [default= %default]", metavar="logical"),\n+ make_option(c("--mc"), type="logical", default="TRUE", dest="mean_counts",\n+ help="Mean counts in the summary table [default= %default]", metavar="logical"),\n+ make_option(c("--hm"), type="logical", default="TRUE", dest="heatmap",\n+ help="generation of the expression heatmap [default= %default]", metavar="logical"),\n+ make_option(c("--nh"), type="integer", default="50", dest="numhigh",\n+ help="number of genes in the heatmap [default= %default]", metavar="integer")\n+ )\n+ opt_parser = OptionParser(option_list=option_list)\n+ parameters = parse_args(opt_parser)\n+\n+ if(is.null(parameters$rm_sample) == FALSE ) {\n+ str_replace_all(parameters$rm_sample, " ", "")\n+ parameters$rm_sample<-strsplit2(parameters$rm_sample, ",")\n+ }\n+\n+ if(is.null(parameters$select_sample) == FALSE ) {\n+ str_replace_all(parameters$select_sample, " ", "")\n+ parameters$select_sample<-strsplit2(parameters$select_sample, ",")\n+ }\n+\n+ dir.create(parameters$out_dir)\n+ return(parameters)\n+}\n' |
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| diff -r 000000000000 -r ceef9bc6bbc7 AskoR_DE.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/AskoR_DE.R Thu Apr 12 05:23:45 2018 -0400 |
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| @@ -0,0 +1,44 @@ +askor_path<-Sys.getenv("ASKOR_PATH") +source(paste0(askor_path,"/AskoR.R")) + +############################################## +## Parameters ## +############################################## + +parameters<-Asko_start() +setwd(parameters$dir_path) +# source("/home/flegeai/local/askoR/askoStart.R") +#parameters$col_genes=1 +#parameters$col_counts=7 +# parameters$regex=FALSE +#parameters$rm_sample=list("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4") +# #parameters$select_sample=c("T0_4", "T1K_4", "T1A_4", "T2A_4", "T2K_4", "T3K_4", "T3A_4") +# #parameters$rm_sample=list("_4") +# parameters$organism = "Ap" +# parameters$fileofcount = NULL +# parameters$annotation_file = "annotation.txt" +# parameters$sample_file = "Samples.txt" +# parameters$contrast_file = "Contrasts.txt" +# parameters$mk_context="manual" +# parameters$glm="qlf" + + +######################################## +## Loading the data from the samples ##+ +######################################## + +data<-loadData(parameters) +cat("Total number of genes : ", dim(data$dge$counts)[1], "\n") +cat("Total number of samples : ", dim(data$dge$counts)[2], "\n") +cat("summary of CPM by samples\n") +summary(cpm(data$dge)) +pdf(parameters$output_pdf) +asko_data<-asko3c(data) +cat("Filtering genes with more than ", parameters$threshold_cpm, " CPM in ",parameters$replicate_cpm,"samples\n") +asko_filt<-GEfilt(data$dge, parameters) +cat("Total number of filtered genes : ", dim(asko_filt$counts)[1], "\n") +asko_norm<-GEnorm(asko_filt,parameters) +GEcorr(asko_norm,parameters) +cat("Statistical analysis\n") +DEanalysis(asko_norm,data, asko_data,parameters) +dev.off() |
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| diff -r 000000000000 -r ceef9bc6bbc7 askor_de.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/askor_de.xml Thu Apr 12 05:23:45 2018 -0400 |
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| b'@@ -0,0 +1,165 @@\n+<tool id="askor_de" name="AskoR DE" version="0.1">\n+ <description>EdgeR for AskOmics</description>\n+ <requirements>\n+ <requirement type="package" version="3.34.6">bioconductor-limma</requirement>\n+ <requirement type="package" version="1.4.30">r-statmod</requirement>\n+ <requirement type="package" version="3.20.7">bioconductor-edger</requirement>\n+ <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\n+ <requirement type="package" version="0.7.0">r-ggrepel</requirement>\n+ <requirement type="package" version="3.0.1">r-gplots</requirement>\n+ <requirement type="package" version="1.4.4">r-optparse</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ export ASKOR_PATH=\'$__tool_directory__\'\n+\n+ &&\n+\n+ Rscript \'$__tool_directory__/AskoR_DE.R\'\n+ --out \'${out_pdf}\'\n+ --outdir askor_output\n+ --fileofcount \'${fileofcounts}\'\n+ --sample \'${samples}\'\n+ --contrasts \'${contrasts}\'\n+ #if $adv.organism\n+ --org \'${adv.organism}\'\n+ #end if\n+ #if $adv.colgenes\n+ --col_genes ${adv.colgenes}\n+ #end if\n+ #if $adv.palette\n+ --palette \'${adv.palette}\'\n+ #end if\n+ #if $selection.sel\n+ --select \'${selection.sel}\'\n+ #end if\n+ #if $selection.remove\n+ --remove \'${selection.remove}\'\n+ #end if\n+ #if $thresholds.th_cpm\n+ --th_cpm ${thresholds.th_cpm}\n+ #end if\n+ #if $thresholds.rep\n+ --rep ${thresholds.rep}\n+ #end if\n+ #if $thresholds.th_FDR\n+ --th_FDR ${thresholds.th_FDR}\n+ #end if\n+ #if $stats.norm\n+ --normalization \'${stats.norm}\'\n+ #end if\n+ #if $stats.adj\n+ --adj \'${stats.adj}\'\n+ #end if\n+ #if $stats.glm\n+ --glm \'${stats.glm}\'\n+ #end if\n+ #if $adv.nh\n+ --nh ${adv.nh}\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param format="csv" name="fileofcounts" type="data" label="File of counts" />\n+ <param format="tsv" name="samples" type="data" label="Descriptions of the samples" />\n+ <param format="tsv" name="contrasts" type="data" label="Descriptions of the contrasts" />\n+ <section name="adv" title="Format options" expanded="false">\n+ <param name="colgenes" type="integer" label="Column of the genes" value="1" optional="true" />\n+ <!--param name="sep" type="text" label="Field separator" value="\\t" optional="true" /-->\n+ <param name="palette" type="text" label="Color palette (Rcolorbrewer)" value="Set2" optional="true" />\n+ <param name="organism" type="text" label="Organism" value="Asko" optional="true" />\n+ <param name="nh" type="integer" label="Number of genes in the heatmap" value="50" optional="true" />\n+ </section>\n+ <section name="selection" title="Samples selection options" expanded="false">\n+ <param name="sel" type="text" label="List of selected samples (separated by comma)" optional="true" />\n+ <param name="remove" type="text" label="List of removed samples (separated by comma)" optional="true" />\n+ </section>\n+ <section name="thresholds" title="Threshold options" expanded="false">\n+ <param name="th_cpm" type="float" label="Minimum CPM value for selecting a gene" value="0.5" optional="true" />\n+ <param name="rep" type="integer" label="Number of samples with CPM > th_comp for selecting a gene" value="3" optional="true" />\n+ <param name="th_FDR" type="float" label="FDR threshold for reporting a differential gene" value="0.05" optional="true" />\n+ </section>\n+ <section name="stats" '..b'am>\n+ <param name="glm" type="select" label="GLM method">\n+ <option value="qlf">qlf</option>\n+ <option value="lrt">lrt</option>\n+ </param>\n+ <param name="adj" type="select" label="Multitest correction method">\n+ <option value="fdr">fdr</option>\n+ <option value="holm">holm</option>\n+ <option value="hochberg">hochberg</option>\n+ <option value="hommel">hommel</option>\n+ <option value="bonferroni">bonferroni</option>\n+ <option value="BH">BH</option>\n+ <option value="BY">BY</option>\n+ <option value="none">none</option>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="pdf" name="out_pdf" label="${tool.name} on ${on_string}: Graphics" />\n+ <data name="output" format="tsv" label="${tool.name} on ${on_string}">\n+ <discover_datasets pattern="(?P<designation>.+)\\.txt" ext="tsv" visible="true" directory="askor_output" />\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="fileofcounts" ftype="csv" value="counts.csv" />\n+ <param name="samples" ftype="tsv" value="Samples.txt" />\n+ <param name="contrasts" ftype="tsv" value="Contrasts.txt" />\n+ <section name="adv">\n+ <param name="colgenes" value="3" />\n+ </section>\n+ <section name="thresholds">\n+ <param name="th_cpm" value="10" />\n+ </section>\n+ <output name="out_pdf" file="out.pdf" compare="sim_size"/>\n+ <output name="output">\n+ <discovered_dataset designation="AskoAvsK" ftype="tsv" file="AskoAvsK.txt" compare="sim_size" />\n+ <discovered_dataset designation="AskoT1AvsT1K" ftype="tsv" file="AskoT1AvsT1K.txt" compare="sim_size" />\n+ <discovered_dataset designation="AskoT1vsT0" ftype="tsv" file="AskoT1vsT0.txt" compare="sim_size" />\n+ <discovered_dataset designation="AskoT1vsT2" ftype="tsv" file="AskoT1vsT2.txt" compare="sim_size" />\n+ <discovered_dataset designation="condition.asko" ftype="tsv" file="condition.asko.txt" compare="sim_size" />\n+ <discovered_dataset designation="context.asko" ftype="tsv" file="context.asko.txt" compare="sim_size" />\n+ <discovered_dataset designation="contrast.asko" ftype="tsv" file="contrast.asko.txt" compare="sim_size" />\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+This tools generates a list of differential genes from various contrasts in an AskOmics format (https://askomics.github.io/).\n+\n+Example tabular input file of counts:\n+\n+============ ========== =============== =========== =========== ======\n+miRNA\t read_count\tprecursor\t total\t A32\t A34\n+------------ ---------- --------------- ----------- ----------- ------\n+GL349623_679 346.00 GL349623_679 146.00 16.00 130.0\n+GL349624_956 13.00 GL349624_956 13.00 0 13.0\n+============ ========== =============== =========== =========== ======\n+\n+Example tabular sample description file:\n+\n+============ ========== =============== ===========\n+ID condition stage treatment\n+------------ ---------- --------------- -----------\n+A32 T3A T3 Acetone\n+A34 T3A T3 Acetone\n+============ ========== =============== ===========\n+\n+Example tabular contrast description file:\n+\n+============ ========================= =======================\n+Contrast context1_of@Context context2_of@Context\n+------------ ------------------------- -----------------------\n+T1vsT0 T1 T0\n+T1vsT2 T1 T2\n+============ ========================= =======================\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r ceef9bc6bbc7 test-data/AskoAvsK.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoAvsK.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| b'@@ -0,0 +1,176 @@\n+Test_id\tmeasured_in@Contrast\tis@gene\tlogFC\tFC\tPValue\tExpression\tSignificance\tFDR\tA/T0A\tA/T1A\tA/T2A\tA/T3A\tK/T1K\tK/T2K\tK/T3K\n+AvsK_GL350151_32884\tAvsK\tGL350151_32884\t-1.4658015841445\t2.76216898522126\t0.00264391592225013\tA=K\t0\t0.115671321598443\t21.9770142082978\t4.60243759106838\t7.06858703220598\t6.83597436231163\t24.7243951164809\t18.050368601277\t19.5984932428693\n+AvsK_GL350151_32898\tAvsK\tGL350151_32898\t-1.47172576071689\t2.77353467197652\t0.00240957402121667\tA=K\t0\t0.115671321598443\t22.8405187946568\t4.60243759106838\t7.06858703220598\t7.18922297617649\t25.6087427706126\t18.2429383304036\t20.3505714255447\n+AvsK_GL350151_32906\tAvsK\tGL350151_32906\t-1.47172576071689\t2.77353467197652\t0.00240957402121667\tA=K\t0\t0.115671321598443\t22.8405187946568\t4.60243759106838\t7.06858703220598\t7.18922297617649\t25.6087427706126\t18.2429383304036\t20.3505714255447\n+AvsK_GL351656_44862\tAvsK\tGL351656_44862\t-1.47172576071689\t2.77353467197652\t0.00240957402121667\tA=K\t0\t0.115671321598443\t22.8405187946568\t4.60243759106838\t7.06858703220598\t7.18922297617649\t25.6087427706126\t18.2429383304036\t20.3505714255447\n+AvsK_GL349642_4945\tAvsK\tGL349642_4945\t-0.869495926967361\t1.82702443243324\t0.0200438004479275\tA=K\t0\t0.157995720064168\t417.507843046818\t116.896489669693\t101.61231882496\t75.4079099203981\t328.413968129475\t202.836868768343\t186.903274026939\n+AvsK_GL349642_4959\tAvsK\tGL349642_4959\t-0.869495926967361\t1.82702443243324\t0.0200438004479275\tA=K\t0\t0.157995720064168\t417.507843046818\t116.896489669693\t101.61231882496\t75.4079099203981\t328.413968129475\t202.836868768343\t186.903274026939\n+AvsK_GL349642_4961\tAvsK\tGL349642_4961\t-0.855495896450042\t1.80938058523392\t0.0222654184608194\tA=K\t0\t0.157995720064168\t82.6553684877643\t26.2552964125283\t20.5220334361146\t16.7156895246482\t69.0764764157016\t45.5079252688433\t35.4402876558247\n+AvsK_GL349642_4963\tAvsK\tGL349642_4963\t-0.869495926967361\t1.82702443243324\t0.0200438004479275\tA=K\t0\t0.157995720064168\t417.507843046818\t116.896489669693\t101.61231882496\t75.4079099203981\t328.413968129475\t202.836868768343\t186.903274026939\n+AvsK_GL349643_5190\tAvsK\tGL349643_5190\t-1.16487635288432\t2.24213998375816\t0.0150785191695021\tA=K\t0\t0.157995720064168\t14.4449688927881\t2.73632941954876\t4.84406512480566\t2.93603778210461\t11.030329473906\t7.56335986023563\t10.5777541213807\n+AvsK_GL349773_18697\tAvsK\tGL349773_18697\t-0.91546742240643\t1.8861800810935\t0.00725049539559815\tA=K\t0\t0.157995720064168\t24.1677107608458\t13.3933664191246\t17.0744059570634\t13.8406685924913\t23.7616433874445\t27.0937814638994\t32.1556867228994\n+AvsK_GL349919_26520\tAvsK\tGL349919_26520\t-0.566471255216122\t1.48089695284404\t0.0184409026827921\tA=K\t0\t0.157995720064168\t124.499541153818\t72.073883410293\t70.3745660356144\t56.6307559204322\t116.176752645774\t101.682183109349\t94.7831139445446\n+AvsK_GL349919_26570\tAvsK\tGL349919_26570\t-0.978323108293458\t1.97017407972835\t0.0148075561063123\tA=K\t0\t0.157995720064168\t103.917583708274\t25.4501089849405\t33.7588466169947\t25.8020894426586\t87.6001270254807\t60.8751850112748\t61.0103250089133\n+AvsK_GL349919_26592\tAvsK\tGL349919_26592\t-1.19391878774136\t2.28773316159769\t0.017590782384399\tA=K\t0\t0.157995720064168\t29.3005113304337\t6.67628355694396\t7.31005430057552\t8.81996932074199\t25.3243219280574\t21.114150881836\t17.8078415758978\n+AvsK_GL350151_32862\tAvsK\tGL350151_32862\t-0.95030830628354\t1.93228554630381\t0.00918521700631609\tA=K\t0\t0.157995720064168\t86.6918238501263\t29.3696377720969\t38.7976244676746\t37.8104530962714\t86.6672382227376\t68.4955728606815\t74.3338430597042\n+AvsK_GL350151_32866\tAvsK\tGL350151_32866\t-0.972137634108357\t1.96174515089933\t0.00840324818023401\tA=K\t0\t0.157995720064168\t88.4737434506241\t29.8894059094906\t39.1623257237904\t36.5707413609292\t88.817436670779\t69.6964707324995\t75.846823875837\n+AvsK_GL350151_32870\tAvsK\tGL350151_32870\t-1.23554484577466\t2.35470257954074\t0.0166687645011988\tA=K\t0\t0.157995720064168\t16.8331341845551\t6.52577459753034\t5.93033577721228\t5.24487769901275\t20.259888596177\t15.0244479823509\t14.3399933936587\n+AvsK_GL350151_32910\tAvsK\tGL350151_32910\t-0.76110888328131'..b'5514703\t379.069596290388\n+AvsK_api-mir-9b\tAvsK\tapi-mir-9b\t0.0385033971553266\t1.02704784928473\t0.783762109394139\tA=K\t0\t0.862631252477826\t376.361439667079\t436.573003510837\t398.350992944513\t415.493971885812\t335.799016629453\t364.731785016796\t391.941058078227\n+AvsK_api-mir-34\tAvsK\tapi-mir-34\t-0.047003921762674\t1.03311719606348\t0.799312897918059\tA=K\t0\t0.874248482097877\t33.78320785053\t33.6733146899426\t36.5841102943991\t75.4315901355026\t26.767434430309\t37.427678364582\t62.5278754461016\n+AvsK_api-mir-3016\tAvsK\tapi-mir-3016\t0.0708655877421499\t1.05034668130115\t0.826909647602724\tA=K\t0\t0.898814834350787\t31.184883216559\t10.4497505123629\t5.33918096274054\t5.83303583149121\t21.1433464017102\t5.2451550522054\t5.31862877995631\n+AvsK_GL349801_20413\tAvsK\tGL349801_20413\t0.0435856177678198\t1.03067223847775\t0.862187240266329\tA=K\t0\t0.912423580011872\t18.9258171290887\t19.7476856197604\t15.6293738213989\t18.2029055558623\t14.9856656593161\t15.2885918081573\t16.7328814031433\n+AvsK_api-mir-252b\tAvsK\tapi-mir-252b\t-0.0432783324776981\t1.03045273492187\t0.872564637171943\tA=K\t0\t0.912423580011872\t70.3219832837863\t80.5998452829956\t87.3965220353206\t133.122575098307\t66.0945308776993\t89.0590652091734\t105.469416792266\n+AvsK_api-mir-277\tAvsK\tapi-mir-277\t0.0214744928271797\t1.014996317245\t0.886881773510312\tA=K\t0\t0.912423580011872\t74.0187227137694\t95.8454418109413\t101.094878069469\t138.38081811116\t59.950707904155\t93.4734733070941\t124.973319561987\n+AvsK_api-mir-29\tAvsK\tapi-mir-29\t0.0273401385118148\t1.01913144489008\t0.890832263031452\tA=K\t0\t0.912423580011872\t107.910313729097\t105.245364266731\t98.7017420713852\t79.8792663335928\t94.6171458451392\t94.9590209808936\t72.2709794245771\n+AvsK_api-mir-3036-1\tAvsK\tapi-mir-3036-1\t-0.0233521058686877\t1.01631815654608\t0.890603796414289\tA=K\t0\t0.912423580011872\t468.48378934247\t355.864419414785\t375.340801378356\t389.66489521967\t378.098568231729\t371.431717521057\t358.320995881957\n+AvsK_api-mir-3036-2\tAvsK\tapi-mir-3036-2\t-0.0233521058686877\t1.01631815654608\t0.890603796414289\tA=K\t0\t0.912423580011872\t468.48378934247\t355.864419414785\t375.340801378356\t389.66489521967\t378.098568231729\t371.431717521057\t358.320995881957\n+AvsK_api-mir-3036-3\tAvsK\tapi-mir-3036-3\t-0.0231499688035336\t1.01617576943556\t0.891568183897315\tA=K\t0\t0.912423580011872\t468.48378934247\t356.02291302258\t375.157547119293\t389.66489521967\t377.932084361907\t371.431717521057\t358.320995881957\n+AvsK_api-mir-3036-4\tAvsK\tapi-mir-3036-4\t-0.0231499688035336\t1.01617576943556\t0.891568183897315\tA=K\t0\t0.912423580011872\t468.48378934247\t356.02291302258\t375.157547119293\t389.66489521967\t377.932084361907\t371.431717521057\t358.320995881957\n+AvsK_api-mir-3036-5\tAvsK\tapi-mir-3036-5\t-0.0231499688035336\t1.01617576943556\t0.891568183897315\tA=K\t0\t0.912423580011872\t468.48378934247\t356.02291302258\t375.157547119293\t389.66489521967\t377.932084361907\t371.431717521057\t358.320995881957\n+AvsK_api-mir-9a\tAvsK\tapi-mir-9a\t-0.0283397691516339\t1.01983783675679\t0.848692896454689\tA=K\t0\t0.912423580011872\t841.300362032995\t812.438450656032\t879.112275743298\t1109.15485486028\t786.952021519981\t819.629737700813\t961.930573546304\n+AvsK_api-mir-7\tAvsK\tapi-mir-7\t-0.028830626121343\t1.02018488146532\t0.901282950260523\tA=K\t0\t0.917003001718556\t192.866444597218\t181.345502480794\t207.034028814017\t198.912796525837\t189.343819213867\t173.186336148056\t186.872702427546\n+AvsK_api-mir-3043-1\tAvsK\tapi-mir-3043-1\t-0.047426737362225\t1.03342001964741\t0.925825733899933\tA=K\t0\t0.925825733899933\t50.1296395288814\t57.6997552376986\t48.3999867820141\t44.4558265605947\t40.4424775820102\t51.5082654013472\t48.4219380775634\n+AvsK_api-mir-3043-2\tAvsK\tapi-mir-3043-2\t-0.047426737362225\t1.03342001964741\t0.925825733899933\tA=K\t0\t0.925825733899933\t50.1296395288814\t57.6997552376986\t48.3999867820141\t44.4558265605947\t40.4424775820102\t51.5082654013472\t48.4219380775634\n+AvsK_api-mir-3043-3\tAvsK\tapi-mir-3043-3\t-0.047426737362225\t1.03342001964741\t0.925825733899933\tA=K\t0\t0.925825733899933\t50.1296395288814\t57.6997552376986\t48.3999867820141\t44.4558265605947\t40.4424775820102\t51.5082654013472\t48.4219380775634\n' |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/AskoT1AvsT1K.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1AvsT1K.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| b'@@ -0,0 +1,176 @@\n+Test_id\tmeasured_in@Contrast\tis@gene\tlogFC\tFC\tPValue\tExpression\tSignificance\tFDR\tT1A/T1A\tT1K/T1K\n+T1AvsT1K_GL349642_4945\tT1AvsT1K\tGL349642_4945\t-1.51050082924554\t2.84908927626456\t0.0325406523649849\tT1A=T1K\t0\t0.226146729807717\t116.896489669693\t328.413968129475\n+T1AvsT1K_GL349642_4959\tT1AvsT1K\tGL349642_4959\t-1.51050082924554\t2.84908927626456\t0.0325406523649849\tT1A=T1K\t0\t0.226146729807717\t116.896489669693\t328.413968129475\n+T1AvsT1K_GL349642_4963\tT1AvsT1K\tGL349642_4963\t-1.51050082924554\t2.84908927626456\t0.0325406523649849\tT1A=T1K\t0\t0.226146729807717\t116.896489669693\t328.413968129475\n+T1AvsT1K_GL349642_4967\tT1AvsT1K\tGL349642_4967\t-1.97373986469\t3.92785007847171\t0.0258331015676455\tT1A=T1K\t0\t0.226146729807717\t6.64462795004153\t25.6873101470662\n+T1AvsT1K_GL349643_5180\tT1AvsT1K\tGL349643_5180\t-2.03033393204775\t4.08499392267698\t0.0235010575102647\tT1A=T1K\t0\t0.226146729807717\t4.54212254256334\t17.4668387068677\n+T1AvsT1K_GL349643_5182\tT1AvsT1K\tGL349643_5182\t-2.05332502278382\t4.15061472722808\t0.025644995276629\tT1A=T1K\t0\t0.226146729807717\t4.31590876285712\t16.8703162971331\n+T1AvsT1K_GL349643_5190\tT1AvsT1K\tGL349643_5190\t-2.10030669556043\t4.28800531956913\t0.0200142821918946\tT1A=T1K\t0\t0.226146729807717\t2.73632941954876\t11.030329473906\n+T1AvsT1K_GL349645_5442\tT1AvsT1K\tGL349645_5442\t-1.86137255910447\t3.6335318668081\t0.0328569344298816\tT1A=T1K\t0\t0.226146729807717\t14.8582519250457\t52.996163581116\n+T1AvsT1K_GL349919_26570\tT1AvsT1K\tGL349919_26570\t-1.82005151771302\t3.53093807044136\t0.0177844713678188\tT1A=T1K\t0\t0.226146729807717\t25.4501089849405\t87.6001270254807\n+T1AvsT1K_GL349919_26592\tT1AvsT1K\tGL349919_26592\t-2.04867364035024\t4.1372543101038\t0.0335989427142894\tT1A=T1K\t0\t0.226146729807717\t6.67628355694396\t25.3243219280574\n+T1AvsT1K_GL350151_32862\tT1AvsT1K\tGL350151_32862\t-1.60518545010683\t3.0423485576661\t0.0196696225009638\tT1A=T1K\t0\t0.226146729807717\t29.3696377720969\t86.6672382227376\n+T1AvsT1K_GL350151_32866\tT1AvsT1K\tGL350151_32866\t-1.61402230907525\t3.06104087360107\t0.02011994144567\tT1A=T1K\t0\t0.226146729807717\t29.8894059094906\t88.817436670779\n+T1AvsT1K_GL350151_32884\tT1AvsT1K\tGL350151_32884\t-2.49624962959045\t5.64216802207781\t0.00756439706040851\tT1A=T1K\t0\t0.226146729807717\t4.60243759106838\t24.7243951164809\n+T1AvsT1K_GL350151_32890\tT1AvsT1K\tGL350151_32890\t-1.35097712821537\t2.55084834312908\t0.0300022327131185\tT1A=T1K\t0\t0.226146729807717\t17.5104113748143\t42.2838873109649\n+T1AvsT1K_GL350151_32898\tT1AvsT1K\tGL350151_32898\t-2.54430493829757\t5.83327034653207\t0.00640778257543885\tT1A=T1K\t0\t0.226146729807717\t4.60243759106838\t25.6087427706126\n+T1AvsT1K_GL350151_32906\tT1AvsT1K\tGL350151_32906\t-2.54430493829757\t5.83327034653207\t0.00640778257543885\tT1A=T1K\t0\t0.226146729807717\t4.60243759106838\t25.6087427706126\n+T1AvsT1K_GL350151_32910\tT1AvsT1K\tGL350151_32910\t-1.35369228094108\t2.55565356116857\t0.0275501325768629\tT1A=T1K\t0\t0.226146729807717\t17.7366251545205\t42.92724866839\n+T1AvsT1K_GL350737_41242\tT1AvsT1K\tGL350737_41242\t-1.35369228094108\t2.55565356116857\t0.0275501325768629\tT1A=T1K\t0\t0.226146729807717\t17.7366251545205\t42.92724866839\n+T1AvsT1K_GL351656_44862\tT1AvsT1K\tGL351656_44862\t-2.54430493829757\t5.83327034653207\t0.00640778257543885\tT1A=T1K\t0\t0.226146729807717\t4.60243759106838\t25.6087427706126\n+T1AvsT1K_GL366836_47437\tT1AvsT1K\tGL366836_47437\t-1.97373986469\t3.92785007847171\t0.0258331015676455\tT1A=T1K\t0\t0.226146729807717\t6.64462795004153\t25.6873101470662\n+T1AvsT1K_GL366836_47447\tT1AvsT1K\tGL366836_47447\t-1.97373986469\t3.92785007847171\t0.0258331015676455\tT1A=T1K\t0\t0.226146729807717\t6.64462795004153\t25.6873101470662\n+T1AvsT1K_api-mir-210\tT1AvsT1K\tapi-mir-210\t1.07892833969205\t2.11246631948654\t0.0166401855616645\tT1A=T1K\t0\t0.226146729807717\t45.7488925668745\t20.0195697686999\n+T1AvsT1K_api-mir-252a\tT1AvsT1K\tapi-mir-252a\t0.771658396805771\t1.70723114052703\t0.0131086796680285\tT1A=T1K\t0\t0.226146729807717\t489.114196700038\t289.171809924299\n+T1AvsT1K_api-mir-277\tT1AvsT1K\tapi-mir-277\t0.66530286763414\t1.58590116943775\t0.0271266048425514\tT1A=T1K\t0\t0.226146729807717\t95.845441'..b'vsT1K\tGL350223_34252\t-0.390391727934582\t1.31074925688528\t0.706305457833014\tT1A=T1K\t0\t0.808240019658039\t21.0291469282923\t33.5756424868145\n+T1AvsT1K_api-mir-137\tT1AvsT1K\tapi-mir-137\t0.186715835542089\t1.13816982419691\t0.706632702901028\tT1A=T1K\t0\t0.808240019658039\t31.1024416700597\t30.2080451857782\n+T1AvsT1K_api-mir-317\tT1AvsT1K\tapi-mir-317\t0.154683152724126\t1.11317711342353\t0.70119192803689\tT1A=T1K\t0\t0.808240019658039\t41.9865638867419\t39.973195910454\n+T1AvsT1K_api-mir-1\tT1AvsT1K\tapi-mir-1\t0.206633192721761\t1.15399197610351\t0.715386664916463\tT1A=T1K\t0\t0.812939391950526\t180.619849632683\t163.746504291107\n+T1AvsT1K_GL350343_36481\tT1AvsT1K\tGL350343_36481\t0.135258154903011\t1.09828932337501\t0.753231343222206\tT1A=T1K\t0\t0.844971058101834\t21.1875817224896\t18.2147172220669\n+T1AvsT1K_api-mir-190\tT1AvsT1K\tapi-mir-190\t0.107095457169907\t1.07705763828919\t0.750699383766064\tT1A=T1K\t0\t0.844971058101834\t234.550188295047\t221.766347279128\n+T1AvsT1K_api-mir-3031\tT1AvsT1K\tapi-mir-3031\t-0.127017586898592\t1.09203385789487\t0.759337885524585\tT1A=T1K\t0\t0.846395732272626\t167.696215387838\t188.245374819867\n+T1AvsT1K_api-let-7\tT1AvsT1K\tapi-let-7\t-0.154131118343296\t1.11275124761865\t0.777366978733461\tT1A=T1K\t0\t0.861007729609846\t17.1052875628726\t20.3697975474495\n+T1AvsT1K_api-mir-3036-1\tT1AvsT1K\tapi-mir-3036-1\t-0.0717554902779335\t1.05099477011198\t0.820621713010342\tT1A=T1K\t0\t0.884509709914779\t355.864419414785\t378.098568231729\n+T1AvsT1K_api-mir-3036-2\tT1AvsT1K\tapi-mir-3036-2\t-0.0717554902779335\t1.05099477011198\t0.820621713010342\tT1A=T1K\t0\t0.884509709914779\t355.864419414785\t378.098568231729\n+T1AvsT1K_api-mir-3036-3\tT1AvsT1K\tapi-mir-3036-3\t-0.0704524082070421\t1.05004591114379\t0.823857615520622\tT1A=T1K\t0\t0.884509709914779\t356.02291302258\t377.932084361907\n+T1AvsT1K_api-mir-3036-4\tT1AvsT1K\tapi-mir-3036-4\t-0.0704524082070421\t1.05004591114379\t0.823857615520622\tT1A=T1K\t0\t0.884509709914779\t356.02291302258\t377.932084361907\n+T1AvsT1K_api-mir-3036-5\tT1AvsT1K\tapi-mir-3036-5\t-0.0704524082070421\t1.05004591114379\t0.823857615520622\tT1A=T1K\t0\t0.884509709914779\t356.02291302258\t377.932084361907\n+T1AvsT1K_GL350343_36473\tT1AvsT1K\tGL350343_36473\t-0.0803215727804929\t1.05725367325285\t0.843102219890161\tT1A=T1K\t0\t0.894199324125928\t162.229342389252\t175.96217279623\n+T1AvsT1K_api-mir-9a\tT1AvsT1K\tapi-mir-9a\t0.0552772681366053\t1.03905877835059\t0.841852631382137\tT1A=T1K\t0\t0.894199324125928\t812.438450656032\t786.952021519981\n+T1AvsT1K_GL350222_34242\tT1AvsT1K\tGL350222_34242\t0.0435103136018807\t1.0306184420166\t0.865141422507651\tT1A=T1K\t0\t0.912046680354452\t207.385266113065\t204.094293618538\n+T1AvsT1K_api-mir-278\tT1AvsT1K\tapi-mir-278\t0.0916778374889447\t1.06560875263065\t0.871969642453005\tT1A=T1K\t0\t0.913740643289077\t41.6572236507995\t44.3288514195503\n+T1AvsT1K_api-mir-13a\tT1AvsT1K\tapi-mir-13a\t-0.0577710158969872\t1.04085638017562\t0.880278617656449\tT1A=T1K\t0\t0.916956893392134\t2096.25066535355\t2190.65508578226\n+T1AvsT1K_api-mir-100\tT1AvsT1K\tapi-mir-100\t0.0779682997371763\t1.05553052426604\t0.909634934101297\tT1A=T1K\t0\t0.941929665489509\t36.6867961405426\t37.0363811562773\n+T1AvsT1K_api-mir-1000\tT1AvsT1K\tapi-mir-1000\t0.0256716372214375\t1.01795348338184\t0.941634856429541\tT1A=T1K\t0\t0.952967111416255\t53.3343119331074\t54.472321032134\n+T1AvsT1K_api-mir-2765\tT1AvsT1K\tapi-mir-2765\t0.017272797414015\t1.0120445491827\t0.945284347259186\tT1A=T1K\t0\t0.952967111416255\t504.166562590324\t501.98589724328\n+T1AvsT1K_api-mir-3024\tT1AvsT1K\tapi-mir-3024\t0.0424576452626954\t1.02986672133513\t0.927125295801725\tT1A=T1K\t0\t0.952967111416255\t32.9381588675413\t31.2093737502546\n+T1AvsT1K_api-mir-3047-1\tT1AvsT1K\tapi-mir-3047-1\t0.0434904464155084\t1.03060424958709\t0.947521585065305\tT1A=T1K\t0\t0.952967111416255\t203.230252972802\t205.085416847614\n+T1AvsT1K_api-mir-3047-2\tT1AvsT1K\tapi-mir-3047-2\t0.0434904464155084\t1.03060424958709\t0.947521585065305\tT1A=T1K\t0\t0.952967111416255\t203.230252972802\t205.085416847614\n+T1AvsT1K_api-mir-7\tT1AvsT1K\tapi-mir-7\t-0.0166613391579242\t1.01161570465349\t0.969415185409705\tT1A=T1K\t0\t0.969415185409705\t181.345502480794\t189.343819213867\n' |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/AskoT1vsT0.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1vsT0.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| b'@@ -0,0 +1,176 @@\n+Test_id\tmeasured_in@Contrast\tis@gene\tlogFC\tFC\tPValue\tExpression\tSignificance\tFDR\tT1/T1A\tT1/T1K\tT0/T0A\n+T1vsT0_api-mir-929\tT1vsT0\tapi-mir-929\t1.52200528879093\t2.87189954935435\t0.000170167334348828\tT1>T0\t1\t0.0297792835110449\t45.7383427423633\t30.9159434838904\t13.4370060260247\n+T1vsT0_api-mir-92b-1\tT1vsT0\tapi-mir-92b-1\t-0.80417146137229\t1.74614269544508\t0.00072380827948343\tT1<T0\t-1\t0.0422221496365334\t387.715661705752\t354.519703647672\t646.587652568849\n+T1vsT0_api-mir-92b-2\tT1vsT0\tapi-mir-92b-2\t-0.80417146137229\t1.74614269544508\t0.00072380827948343\tT1<T0\t-1\t0.0422221496365334\t387.715661705752\t354.519703647672\t646.587652568849\n+T1vsT0_api-let-7\tT1vsT0\tapi-let-7\t-1.53453421279761\t2.89694885184873\t0.00146821012161706\tT1=T0\t0\t0.0642341928207463\t17.1052875628726\t20.3697975474495\t51.7676372940973\n+T1vsT0_api-mir-927\tT1vsT0\tapi-mir-927\t1.15503837103483\t2.22690246409265\t0.00200001763952061\tT1=T0\t0\t0.0700006173832214\t1222.6871883341\t742.960038441659\t427.238639370503\n+T1vsT0_api-mir-3049\tT1vsT0\tapi-mir-3049\t1.17606609803573\t2.2595979517563\t0.00334451529015501\tT1=T0\t0\t0.0975483626295212\t94.7105661640103\t53.1156765046011\t30.8771272639274\n+T1vsT0_api-mir-1000\tT1vsT0\tapi-mir-1000\t0.928576960535918\t1.90339760451986\t0.00667764422859585\tT1=T0\t0\t0.129843082222697\t53.3343119331074\t54.472321032134\t28.0436223189252\n+T1vsT0_api-mir-2c\tT1vsT0\tapi-mir-2c\t-0.678556842418134\t1.60053790308009\t0.00563721477548487\tT1=T0\t0\t0.129843082222697\t49.1092218181985\t66.1195303451075\t90.5431058071145\n+T1vsT0_api-mir-3032\tT1vsT0\tapi-mir-3032\t-1.17166162670415\t2.25271003879347\t0.00666595628195355\tT1=T0\t0\t0.129843082222697\t31.6881532348652\t36.4674445149938\t77.401034703635\n+T1vsT0_api-mir-92a-1\tT1vsT0\tapi-mir-92a-1\t-0.788487446647344\t1.72726261270839\t0.00912051552886509\tT1=T0\t0\t0.14509911068649\t72.386227867033\t54.1490720179198\t108.083086611924\n+T1vsT0_api-mir-92a-2\tT1vsT0\tapi-mir-92a-2\t-0.788487446647344\t1.72726261270839\t0.00912051552886509\tT1=T0\t0\t0.14509911068649\t72.386227867033\t54.1490720179198\t108.083086611924\n+T1vsT0_GL350757_41318\tT1vsT0\tGL350757_41318\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_GL350757_41320\tT1vsT0\tGL350757_41320\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_GL350757_41322\tT1vsT0\tGL350757_41322\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_GL350757_41324\tT1vsT0\tGL350757_41324\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_GL350757_41326\tT1vsT0\tGL350757_41326\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_GL350757_41328\tT1vsT0\tGL350757_41328\t0.667804971676578\t1.58865402613014\t0.0177413336544925\tT1=T0\t0\t0.163407020501905\t154.093033384431\t133.130797853428\t88.834921709588\n+T1vsT0_api-mir-3024\tT1vsT0\tapi-mir-3024\t-1.02252339864184\t2.03146906938746\t0.0118617416669047\tT1=T0\t0\t0.163407020501905\t32.9381588675413\t31.2093737502546\t64.7212050546698\n+T1vsT0_api-mir-87a\tT1vsT0\tapi-mir-87a\t0.670153407973832\t1.59124216214274\t0.0147127885334211\tT1=T0\t0\t0.163407020501905\t359.274465229513\t241.568668415364\t183.898246585246\n+T1vsT0_GL349826_21746\tT1vsT0\tGL349826_21746\t0.855235891010956\t1.80905452436164\t0.019806064601511\tT1=T0\t0\t0.170889771265973\t36.9544600878111\t24.0458636715105\t16.4951684939482\n+T1vsT0_api-mir-315\tT1vsT0\tapi-mir-315\t-0.500904121575693\t1.41510011267714\t0.0205067725519167\tT1=T0\t0\t0.170889771265973\t20928.2550507448\t16149.5398678988\t26012.4718189252\n+T1vsT0_api-mir-279a\tT1vsT0\tapi-mir-279a\t-0.391706524343188\t1.31194434933307\t0.025491145454786\tT1=T0\t0\t0.202770475208525\t1807.69888237487\t1417.07904547563\t2099.23183214755\n+T1vsT0_GL350468_38246\tT1vsT0\tGL350468_38246\t0.72138272754746\t1.648761'..b'\t1008034.59361181\n+T1vsT0_api-mir-3033\tT1vsT0\tapi-mir-3033\t0.0508557287878096\t1.03587916923696\t0.789146678837066\tT1=T0\t0\t0.902618750303833\t502.552807518651\t332.193472624891\t394.957854143393\n+T1vsT0_api-mir-7\tT1vsT0\tapi-mir-7\t-0.0839548640418031\t1.05991962237934\t0.821089236842164\tT1=T0\t0\t0.933055950957005\t181.345502480794\t189.343819213867\t192.866444597218\n+T1vsT0_api-mir-3043-1\tT1vsT0\tapi-mir-3043-1\t-0.0606704498728051\t1.04295032857273\t0.840298758796115\tT1=T0\t0\t0.93663874388102\t57.6997552376986\t40.4424775820102\t50.1296395288814\n+T1vsT0_api-mir-3043-2\tT1vsT0\tapi-mir-3043-2\t-0.0606704498728051\t1.04295032857273\t0.840298758796115\tT1=T0\t0\t0.93663874388102\t57.6997552376986\t40.4424775820102\t50.1296395288814\n+T1vsT0_api-mir-3043-3\tT1vsT0\tapi-mir-3043-3\t-0.0606704498728051\t1.04295032857273\t0.840298758796115\tT1=T0\t0\t0.93663874388102\t57.6997552376986\t40.4424775820102\t50.1296395288814\n+T1vsT0_api-mir-317\tT1vsT0\tapi-mir-317\t0.0627695821790897\t1.04446893379184\t0.855892214174629\tT1=T0\t0\t0.947981882788355\t41.9865638867419\t39.973195910454\t38.1499577028816\n+T1vsT0_api-mir-277\tT1vsT0\tapi-mir-277\t0.037580817237381\t1.02639127891326\t0.878902194393551\tT1=T0\t0\t0.967345182508625\t95.8454418109413\t59.950707904155\t74.0187227137694\n+T1vsT0_GL349650_6636\tT1vsT0\tGL349650_6636\t0.0164233199330276\t1.01144881967945\t0.950944499891273\tT1=T0\t0\t0.967532037824197\t687.359529366427\t484.997109051297\t571.761575450836\n+T1vsT0_GL349650_6638\tT1vsT0\tGL349650_6638\t0.0164233199330276\t1.01144881967945\t0.950944499891273\tT1=T0\t0\t0.967532037824197\t687.359529366427\t484.997109051297\t571.761575450836\n+T1vsT0_GL349650_6640\tT1vsT0\tGL349650_6640\t0.0164233199330276\t1.01144881967945\t0.950944499891273\tT1=T0\t0\t0.967532037824197\t687.359529366427\t484.997109051297\t571.761575450836\n+T1vsT0_GL349650_6646\tT1vsT0\tGL349650_6646\t0.0164233199330276\t1.01144881967945\t0.950944499891273\tT1=T0\t0\t0.967532037824197\t687.359529366427\t484.997109051297\t571.761575450836\n+T1vsT0_GL349742_15837\tT1vsT0\tGL349742_15837\t-0.0271288863461452\t1.01898222557699\t0.886388345249162\tT1=T0\t0\t0.967532037824197\t16838.4837907878\t12660.4383260529\t14878.3230778168\n+T1vsT0_GL350137_32551\tT1vsT0\tGL350137_32551\t-0.0750197975296233\t1.05337549090811\t0.933710532905093\tT1=T0\t0\t0.967532037824197\t204.143997030395\t578.995678143302\t358.835578453794\n+T1vsT0_GL350137_32552\tT1vsT0\tGL350137_32552\t-0.0737373050949295\t1.05243950251709\t0.935206728203719\tT1=T0\t0\t0.967532037824197\t116.544493511701\t279.125976791414\t186.851752515656\n+T1vsT0_GL355572_46131\tT1vsT0\tGL355572_46131\t0.0164233356871345\t1.01144883072439\t0.950945774318639\tT1=T0\t0\t0.967532037824197\t687.359529366427\t484.997109051297\t571.761575450836\n+T1vsT0_api-mir-10\tT1vsT0\tapi-mir-10\t0.0311495747947241\t1.02182601743353\t0.937687018813089\tT1=T0\t0\t0.967532037824197\t1609762.52422668\t1080955.87403039\t1290939.44087786\n+T1vsT0_api-mir-190\tT1vsT0\tapi-mir-190\t-0.0356914356001437\t1.02504797662293\t0.901881664477287\tT1=T0\t0\t0.967532037824197\t234.550188295047\t221.766347279128\t231.485466971721\n+T1vsT0_api-mir-278\tT1vsT0\tapi-mir-278\t-0.0362475819316304\t1.02544319983334\t0.939540537737326\tT1=T0\t0\t0.967532037824197\t41.6572236507995\t44.3288514195503\t41.1737470124825\n+T1vsT0_api-mir-3041\tT1vsT0\tapi-mir-3041\t0.0411648933341176\t1.02894430472213\t0.89846959252644\tT1=T0\t0\t0.967532037824197\t83.1697934295355\t68.7196716946604\t73.6148441337726\n+T1vsT0_api-mir-9b\tT1vsT0\tapi-mir-9b\t0.0164413646692999\t1.01146147061456\t0.942020116365711\tT1=T0\t0\t0.967532037824197\t436.573003510837\t335.799016629453\t376.361439667079\n+T1vsT0_api-mir-252b\tT1vsT0\tapi-mir-252b\t0.0211214044961437\t1.01474793522848\t0.961180689316308\tT1=T0\t0\t0.972292604799733\t80.5998452829956\t66.0945308776993\t70.3219832837863\n+T1vsT0_GL350223_34252\tT1vsT0\tGL350223_34252\t-0.0338080435006178\t1.02371068245646\t0.967881073478121\tT1=T0\t0\t0.973443608383168\t21.0291469282923\t33.5756424868145\t24.5027562953933\n+T1vsT0_GL350370_36909\tT1vsT0\tGL350370_36909\t0.00621519395425303\t1.00431733712833\t0.981568484688693\tT1=T0\t0\t0.981568484688693\t656.82657433825\t458.154802585589\t547.199142865752\n' |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/AskoT1vsT2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AskoT1vsT2.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| b'@@ -0,0 +1,176 @@\n+Test_id\tmeasured_in@Contrast\tis@gene\tlogFC\tFC\tPValue\tExpression\tSignificance\tFDR\tT1/T1A\tT1/T1K\tT2/T2A\tT2/T2K\n+T1vsT2_api-mir-3024\tT1vsT2\tapi-mir-3024\t3.12174170464632\t8.70438099023781\t9.00393166340146e-05\tT1>T2\t1\t0.0157568804109526\t32.9381588675413\t31.2093737502546\t9.39844720626758\t12.6426867572395\n+T1vsT2_api-mir-316\tT1vsT2\tapi-mir-316\t-2.56031506201473\t5.89836483907807\t0.000564267422216593\tT1<T2\t-1\t0.0493733994439519\t29.2940452013454\t14.9534399843751\t47.3316760732136\t57.1450820793195\n+T1vsT2_GL350757_41318\tT1vsT2\tGL350757_41318\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_GL350757_41320\tT1vsT2\tGL350757_41320\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_GL350757_41322\tT1vsT2\tGL350757_41322\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_GL350757_41324\tT1vsT2\tGL350757_41324\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_GL350757_41326\tT1vsT2\tGL350757_41326\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_GL350757_41328\tT1vsT2\tGL350757_41328\t-1.2236513594056\t2.33537035719147\t0.0070903245043704\tT1=T2\t0\t0.0689337104591566\t154.093033384431\t133.130797853428\t222.856316018568\t210.398577789772\n+T1vsT2_api-mir-1\tT1vsT2\tapi-mir-1\t-2.32668513849045\t5.01651386769124\t0.00690315235901703\tT1=T2\t0\t0.0689337104591566\t180.619849632683\t163.746504291107\t381.774966277306\t371.099133673289\n+T1vsT2_api-mir-14\tT1vsT2\tapi-mir-14\t-1.75201918397251\t3.36829660344174\t0.00135175295890012\tT1=T2\t0\t0.0689337104591566\t5174.26337501864\t4324.71028742041\t9057.45291271703\t8316.36967033474\n+T1vsT2_api-mir-210\tT1vsT2\tapi-mir-210\t-1.99423211838173\t3.98403996177628\t0.00219873520800795\tT1=T2\t0\t0.0689337104591566\t45.7488925668745\t20.0195697686999\t66.6050846850626\t60.1807998129075\n+T1vsT2_api-mir-3016\tT1vsT2\tapi-mir-3016\t2.8083270926824\t7.00471859094321\t0.0027257406187562\tT1=T2\t0\t0.0689337104591566\t10.4497505123629\t21.1433464017102\t5.33918096274054\t5.2451550522054\n+T1vsT2_api-mir-3018\tT1vsT2\tapi-mir-3018\t-2.08253865932694\t4.23551870074831\t0.00531939401449926\tT1=T2\t0\t0.0689337104591566\t25.0073508370315\t8.62911781908716\t30.3840920325039\t31.7226039874993\n+T1vsT2_api-mir-929\tT1vsT2\tapi-mir-929\t-1.64972083151462\t3.13772916703121\t0.00343047066299578\tT1=T2\t0\t0.0689337104591566\t45.7383427423633\t30.9159434838904\t73.3466164710049\t60.643677777599\n+T1vsT2_api-mir-92a-1\tT1vsT2\tapi-mir-92a-1\t1.52984952229575\t2.88755719389213\t0.0035885903084464\tT1=T2\t0\t0.0689337104591566\t72.386227867033\t54.1490720179198\t35.5759781605864\t38.8155292844677\n+T1vsT2_api-mir-92a-2\tT1vsT2\tapi-mir-92a-2\t1.52984952229575\t2.88755719389213\t0.0035885903084464\tT1=T2\t0\t0.0689337104591566\t72.386227867033\t54.1490720179198\t35.5759781605864\t38.8155292844677\n+T1vsT2_api-mir-92b-1\tT1vsT2\tapi-mir-92b-1\t1.05599824524424\t2.07915634146282\t0.00607088774431841\tT1=T2\t0\t0.0689337104591566\t387.715661705752\t354.519703647672\t262.91725714257\t251.764612041121\n+T1vsT2_api-mir-92b-2\tT1vsT2\tapi-mir-92b-2\t1.05599824524424\t2.07915634146282\t0.00607088774431841\tT1=T2\t0\t0.0689337104591566\t387.715661705752\t354.519703647672\t262.91725714257\t251.764612041121\n+T1vsT2_api-mir-927\tT1vsT2\tapi-mir-927\t-1.40356536452645\t2.64554574582873\t0.0123315109227036\tT1=T2\t0\t0.113579705867007\t1222.6871883341\t742.960038441659\t1720.16476297276\t1394.20082468705\n+T1vsT2_GL349826_21746\tT1vsT2\tGL349826_21746\t-1.19291272037751\t2.28613836070488\t0.0341430337873126\tT1=T2\t0\t0.288955230397108\t36.9544600878111\t24.0458636715105\t51.7665621942847\t39.7552622980635\n+T1vsT2_GL350222_34242\tT1vsT2\tGL350222_34242\t-0.79707086088568\t'..b'-3\tT1vsT2\tapi-mir-3036-3\t-0.0616916243095803\t1.04368881536419\t0.890051535678869\tT1=T2\t0\t0.973221981180124\t356.02291302258\t377.932084361907\t375.157547119293\t371.431717521057\n+T1vsT2_api-mir-3036-4\tT1vsT2\tapi-mir-3036-4\t-0.0616916243095803\t1.04368881536419\t0.890051535678869\tT1=T2\t0\t0.973221981180124\t356.02291302258\t377.932084361907\t375.157547119293\t371.431717521057\n+T1vsT2_api-mir-3036-5\tT1vsT2\tapi-mir-3036-5\t-0.0616916243095803\t1.04368881536419\t0.890051535678869\tT1=T2\t0\t0.973221981180124\t356.02291302258\t377.932084361907\t375.157547119293\t371.431717521057\n+T1vsT2_api-mir-3043-1\tT1vsT2\tapi-mir-3043-1\t-0.0973262703093035\t1.06978899689003\t0.843794553084964\tT1=T2\t0\t0.973221981180124\t57.6997552376986\t40.4424775820102\t48.3999867820141\t51.5082654013472\n+T1vsT2_api-mir-3043-2\tT1vsT2\tapi-mir-3043-2\t-0.0973262703093035\t1.06978899689003\t0.843794553084964\tT1=T2\t0\t0.973221981180124\t57.6997552376986\t40.4424775820102\t48.3999867820141\t51.5082654013472\n+T1vsT2_api-mir-3043-3\tT1vsT2\tapi-mir-3043-3\t-0.0973262703093035\t1.06978899689003\t0.843794553084964\tT1=T2\t0\t0.973221981180124\t57.6997552376986\t40.4424775820102\t48.3999867820141\t51.5082654013472\n+T1vsT2_api-mir-3050\tT1vsT2\tapi-mir-3050\t0.0559546373818562\t1.03954674822327\t0.89941183195061\tT1=T2\t0\t0.973221981180124\t1142501.70015826\t795661.911903157\t1028755.47253531\t850011.670784776\n+T1vsT2_api-mir-7\tT1vsT2\tapi-mir-7\t-0.105827161281639\t1.07611119606609\t0.862204791982148\tT1=T2\t0\t0.973221981180124\t181.345502480794\t189.343819213867\t207.034028814017\t173.186336148056\n+T1vsT2_api-mir-993\tT1vsT2\tapi-mir-993\t-0.0412195507768203\t1.02898328768674\t0.906486759613487\tT1=T2\t0\t0.973221981180124\t517.095986431029\t355.927103464731\t451.118742022456\t417.649465514703\n+T1vsT2_api-mir-184a\tT1vsT2\tapi-mir-184a\t-0.0390450066057793\t1.02743349090164\t0.925330905014595\tT1=T2\t0\t0.98141156592457\t48955.440785817\t35866.6670300699\t45671.9115346193\t39494.8236524716\n+T1vsT2_api-mir-3031\tT1vsT2\tapi-mir-3031\t-0.0581845126333868\t1.04115474704317\t0.920478867564632\tT1=T2\t0\t0.98141156592457\t167.696215387838\t188.245374819867\t173.378004991112\t186.623430921134\n+T1vsT2_GL349643_5190\tT1vsT2\tGL349643_5190\t-0.0426668290607514\t1.03001605785128\t0.961649132893672\tT1=T2\t0\t0.998690037981219\t2.73632941954876\t11.030329473906\t4.84406512480566\t7.56335986023563\n+T1vsT2_GL350151_32862\tT1vsT2\tGL350151_32862\t-0.0193642913017359\t1.01351278741972\t0.982148041738455\tT1=T2\t0\t0.998690037981219\t29.3696377720969\t86.6672382227376\t38.7976244676746\t68.4955728606815\n+T1vsT2_GL350151_32866\tT1vsT2\tGL350151_32866\t0.00225625053313585\t1.00156513724646\t0.998690037981219\tT1=T2\t0\t0.998690037981219\t29.8894059094906\t88.817436670779\t39.1623257237904\t69.6964707324995\n+T1vsT2_GL350151_32884\tT1vsT2\tGL350151_32884\t-0.0424226558124306\t1.02984174444643\t0.965520504767908\tT1=T2\t0\t0.998690037981219\t4.60243759106838\t24.7243951164809\t7.06858703220598\t18.050368601277\n+T1vsT2_GL350151_32898\tT1vsT2\tGL350151_32898\t-0.00976186403353511\t1.00678935239405\t0.987271238394924\tT1=T2\t0\t0.998690037981219\t4.60243759106838\t25.6087427706126\t7.06858703220598\t18.2429383304036\n+T1vsT2_GL350151_32906\tT1vsT2\tGL350151_32906\t-0.00976186403353511\t1.00678935239405\t0.987271238394924\tT1=T2\t0\t0.998690037981219\t4.60243759106838\t25.6087427706126\t7.06858703220598\t18.2429383304036\n+T1vsT2_GL351656_44862\tT1vsT2\tGL351656_44862\t-0.00976186403353511\t1.00678935239405\t0.987271238394924\tT1=T2\t0\t0.998690037981219\t4.60243759106838\t25.6087427706126\t7.06858703220598\t18.2429383304036\n+T1vsT2_api-mir-3027\tT1vsT2\tapi-mir-3027\t0.0213096232060162\t1.0148803311966\t0.965991192358469\tT1=T2\t0\t0.998690037981219\t404.312998546403\t362.527824297402\t373.591616924324\t382.300123100955\n+T1vsT2_api-mir-3033\tT1vsT2\tapi-mir-3033\t-0.00335649754218206\t1.00232925531803\t0.991314985890748\tT1=T2\t0\t0.998690037981219\t502.552807518651\t332.193472624891\t427.20126064499\t393.371130813313\n+T1vsT2_api-mir-9b\tT1vsT2\tapi-mir-9b\t-0.000782611364163497\t1.00054261202122\t0.998280719813556\tT1=T2\t0\t0.998690037981219\t436.573003510837\t335.799016629453\t398.350992944513\t364.731785016796\n' |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/Contrasts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Contrasts.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Condition T1vsT0 T1vsT2 T1AvsT1K AvsK +T0A - 0 0 + +T1A + + + + +T1K + + - - +T2A 0 - 0 + +T2K 0 - 0 - +T3A 0 0 0 + +T3K 0 0 0 - |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/Samples.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samples.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| @@ -0,0 +1,29 @@ +ID condition stage treatment +A32 T3A T3 Acetone +A34 T3A T3 Acetone +A37 T3A T3 Acetone +A39 T3A T3 Acetone +K32 T3K T3 Kinoprene +K34 T3K T3 Kinoprene +K37 T3K T3 Kinoprene +K39 T3K T3 Kinoprene +A02 T0A T0 Acetone +A06 T0A T0 Acetone +A08 T0A T0 Acetone +A09 T0A T0 Acetone +A12 T1A T1 Acetone +A16 T1A T1 Acetone +A18 T1A T1 Acetone +A19 T1A T1 Acetone +K12 T1K T1 Kinoprene +K16 T1K T1 Kinoprene +K18 T1K T1 Kinoprene +K19 T1K T1 Kinoprene +A22 T2A T2 Acetone +A24 T2A T2 Acetone +A27 T2A T2 Acetone +A29 T2A T2 Acetone +K22 T2K T2 Kinoprene +K24 T2K T2 Kinoprene +K27 T2K T2 Kinoprene +K29 T2K T2 Kinoprene |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/condition.asko.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/condition.asko.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Condition stage treatment +T3A T3 Acetone +T3K T3 Kinoprene +T0A T0 Acetone +T1A T1 Acetone +T1K T1 Kinoprene +T2A T2 Acetone +T2K T2 Kinoprene |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/context.asko.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/context.asko.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| @@ -0,0 +1,15 @@ +Context has@Condition +T1 T1A +T1 T1K +T0 T0A +T2 T2A +T2 T2K +T1A T1A +T1K T1K +A T0A +A T1A +A T2A +A T3A +K T1K +K T2K +K T3K |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/contrast.asko.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contrast.asko.txt Thu Apr 12 05:23:45 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Contrast context1_of@Context context2_of@Context +T1vsT0 T1 T0 +T1vsT2 T1 T2 +T1AvsT1K T1A T1K +AvsK A K |
| b |
| diff -r 000000000000 -r ceef9bc6bbc7 test-data/counts.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/counts.csv Thu Apr 12 05:23:45 2018 -0400 |
| b |
| b'@@ -0,0 +1,381 @@\n+#miRNA\tread_count\tprecursor\ttotal\tA32\tA34\tA37\tA39\tK32\tK34\tK37\tK39\tA02\tA06\tA08\tA09\tA12\tA16\tA18\tA19\tK12\tK16\tK18\tK19\tA22\tA24\tA27\tA29\tK22\tK24\tK27\tK29\tA32(norm)\tA34(norm)\tA37(norm)\tA39(norm)\tK32(norm)\tK34(norm)\tK37(norm)\tK39(norm)\tA02(norm)\tA06(norm)\tA08(norm)\tA09(norm)\tA12(norm)\tA16(norm)\tA18(norm)\tA19(norm)\tK12(norm)\tK16(norm)\tK18(norm)\tK19(norm)\tA22(norm)\tA24(norm)\tA27(norm)\tA29(norm)\tK22(norm)\tK24(norm)\tK27(norm)\tK29(norm)\n+GL349623_679\t346.00\tGL349623_679\t346.00\t16.00\t1.00\t11.00\t6.00\t4.00\t14.00\t4.00\t16.00\t7.00\t49.00\t1.00\t10.00\t8.00\t18.00\t23.00\t18.00\t0\t16.00\t9.00\t10.00\t22.00\t16.00\t12.00\t20.00\t10.00\t4.00\t12.00\t9.00\t7.39\t2.57\t7.74\t3.64\t2.74\t14.77\t2.56\t8.85\t1.51\t9.55\t1.39\t4.27\t2.92\t4.37\t7.78\t5.12\t0\t4.54\t4.97\t5.45\t3.64\t4.52\t2.76\t7.64\t2.85\t4.19\t4.87\t2.67\n+GL349624_956\t13.00\tGL349624_956\t13.00\t0\t0\t0\t1.00\t0\t0\t0\t0\t0\t3.00\t0\t0\t0\t1.00\t1.00\t2.00\t0\t0\t0\t0\t0\t1.00\t0\t2.00\t0\t0\t1.00\t1.00\t0\t0\t0\t0.61\t0\t0\t0\t0\t0\t0.58\t0\t0\t0\t0.24\t0.34\t0.57\t0\t0\t0\t0\t0\t0.28\t0\t0.76\t0\t0\t0.41\t0.30\n+GL349630_2419\t2618.00\tGL349630_2419\t2618.00\t10.00\t1.00\t14.00\t66.00\t18.00\t31.00\t207.00\t47.00\t32.00\t627.00\t63.00\t93.00\t20.00\t39.00\t75.00\t52.00\t5.00\t166.00\t260.00\t152.00\t14.00\t20.00\t97.00\t85.00\t19.00\t11.00\t155.00\t239.00\t4.62\t2.57\t9.85\t40.02\t12.32\t32.71\t132.53\t26.01\t6.91\t122.25\t87.69\t39.70\t7.30\t9.48\t25.36\t14.81\t9.44\t47.06\t143.62\t82.78\t2.32\t5.65\t22.31\t32.45\t5.41\t11.51\t62.88\t70.79\n+GL349630_2421\t2618.00\tGL349630_2421\t2618.00\t10.00\t1.00\t14.00\t66.00\t18.00\t31.00\t207.00\t47.00\t32.00\t627.00\t63.00\t93.00\t20.00\t39.00\t75.00\t52.00\t5.00\t166.00\t260.00\t152.00\t14.00\t20.00\t97.00\t85.00\t19.00\t11.00\t155.00\t239.00\t4.62\t2.57\t9.85\t40.02\t12.32\t32.71\t132.53\t26.01\t6.91\t122.25\t87.69\t39.70\t7.30\t9.48\t25.36\t14.81\t9.44\t47.06\t143.62\t82.78\t2.32\t5.65\t22.31\t32.45\t5.41\t11.51\t62.88\t70.79\n+GL349630_2423\t2618.00\tGL349630_2423\t2618.00\t10.00\t1.00\t14.00\t66.00\t18.00\t31.00\t207.00\t47.00\t32.00\t627.00\t63.00\t93.00\t20.00\t39.00\t75.00\t52.00\t5.00\t166.00\t260.00\t152.00\t14.00\t20.00\t97.00\t85.00\t19.00\t11.00\t155.00\t239.00\t4.62\t2.57\t9.85\t40.02\t12.32\t32.71\t132.53\t26.01\t6.91\t122.25\t87.69\t39.70\t7.30\t9.48\t25.36\t14.81\t9.44\t47.06\t143.62\t82.78\t2.32\t5.65\t22.31\t32.45\t5.41\t11.51\t62.88\t70.79\n+GL349630_2425\t2618.00\tGL349630_2425\t2618.00\t10.00\t1.00\t14.00\t66.00\t18.00\t31.00\t207.00\t47.00\t32.00\t627.00\t63.00\t93.00\t20.00\t39.00\t75.00\t52.00\t5.00\t166.00\t260.00\t152.00\t14.00\t20.00\t97.00\t85.00\t19.00\t11.00\t155.00\t239.00\t4.62\t2.57\t9.85\t40.02\t12.32\t32.71\t132.53\t26.01\t6.91\t122.25\t87.69\t39.70\t7.30\t9.48\t25.36\t14.81\t9.44\t47.06\t143.62\t82.78\t2.32\t5.65\t22.31\t32.45\t5.41\t11.51\t62.88\t70.79\n+GL349630_2427\t250.00\tGL349630_2427\t250.00\t1.00\t0\t3.00\t7.00\t2.00\t5.00\t16.00\t9.00\t0\t54.00\t15.00\t7.00\t3.00\t0\t9.00\t0\t1.00\t14.00\t36.00\t14.00\t0\t1.00\t9.00\t6.00\t0\t3.00\t14.00\t21.00\t0.46\t0\t2.11\t4.24\t1.37\t5.28\t10.24\t4.98\t0\t10.53\t20.88\t2.99\t1.09\t0\t3.04\t0\t1.89\t3.97\t19.89\t7.62\t0\t0.28\t2.07\t2.29\t0\t3.14\t5.68\t6.22\n+GL349633_2878\t13.00\tGL349633_2878\t13.00\t1.00\t0\t0\t0\t1.00\t0\t0\t1.00\t1.00\t1.00\t0\t0\t2.00\t0\t0\t0\t1.00\t0\t1.00\t0\t1.00\t2.00\t0\t0\t0\t0\t1.00\t0\t0.46\t0\t0\t0\t0.68\t0\t0\t0.55\t0.22\t0.19\t0\t0\t0.73\t0\t0\t0\t1.89\t0\t0.55\t0\t0.17\t0.56\t0\t0\t0\t0\t0.41\t0\n+GL349634_3207\t107.00\tGL349634_3207\t107.00\t4.00\t0\t0\t5.00\t1.00\t4.00\t4.00\t2.00\t8.00\t8.00\t1.00\t6.00\t1.00\t8.00\t3.00\t5.00\t0\t7.00\t5.00\t3.00\t3.00\t7.00\t3.00\t3.00\t8.00\t2.00\t1.00\t5.00\t1.85\t0\t0\t3.03\t0.68\t4.22\t2.56\t1.11\t1.73\t1.56\t1.39\t2.56\t0.36\t1.94\t1.01\t1.42\t0\t1.98\t2.76\t1.63\t0.50\t1.98\t0.69\t1.15\t2.28\t2.09\t0.41\t1.48\n+GL349634_3209\t271.00\tGL349634_3209\t271.00\t6.00\t5.00\t6.00\t19.00\t5.00\t1.00\t13.00\t7.00\t8.00\t8.00\t3.00\t13.00\t0\t13.00\t11.00\t20.00\t2.00\t16.00\t12.00\t12.00\t18.00\t8.00\t9.00\t18.00\t15.00\t2.00\t10.00\t11.00\t2.77\t12.85\t4.22\t11.52\t3.42\t1.06\t8.32\t3.87\t1.73\t1.56\t4.18\t5.55\t0\t3.16\t3.72\t5.69\t3.78\t4.54\t6.63\t6.54\t2.98\t2.26\t2.07\t6.87\t4.27\t2.09\t4.06\t3.26\n+GL349637_3676\t15.00\tGL349637_3676\t15.00\t0\t0\t1.00\t0\t0\t0\t3.00\t0\t3.00\t1.00\t0\t0\t0\t0\t0\t2.00\t0\t1.00\t2.00\t0\t0\t0\t1.00\t0\t0\t0\t0\t1.00\t0\t0\t0.70\t0\t0\t0\t1.92\t0\t0.65\t0.19\t0\t0\t0\t0\t0\t0.57\t0\t0.28\t1.10\t0\t0\t0\t0.23\t0\t0\t0\t0\t0.30\n+GL349639_4112\t92.00\tGL349639_4112\t92.00\t1.00\t1.00\t3.00\t0\t1.00\t3.00\t0\t3.00\t4.00\t17.00\t5.00\t7.00\t0\t2.00\t8.00\t1.00\t0\t8.00\t2.00\t3.00\t6.00\t3.'..b'\t73.13\t135.00\t90.87\t109.00\n+api-miR-92b\t9834.00\tapi-mir-92b-2\t9834.00\t169.00\t33.00\t162.00\t222.00\t112.00\t114.00\t178.00\t175.00\t951.00\t1372.00\t208.00\t618.00\t238.00\t459.00\t472.00\t610.00\t56.00\t571.00\t420.00\t436.00\t360.00\t274.00\t335.00\t311.00\t257.00\t129.00\t224.00\t368.00\t78.07\t84.83\t113.97\t134.61\t76.65\t120.27\t113.97\t96.84\t205.41\t267.50\t289.53\t263.80\t86.87\t111.53\t159.57\t173.68\t105.78\t161.88\t232.01\t237.45\t59.53\t77.35\t77.04\t118.73\t73.13\t135.00\t90.87\t109.00\n+api-miR-965\t268.00\tapi-mir-965\t268.00\t2.00\t4.00\t10.00\t8.00\t7.00\t12.00\t15.00\t12.00\t19.00\t10.00\t3.00\t15.00\t3.00\t21.00\t13.00\t17.00\t1.00\t11.00\t2.00\t7.00\t16.00\t7.00\t15.00\t10.00\t9.00\t8.00\t5.00\t6.00\t0.92\t10.28\t7.04\t4.85\t4.79\t12.66\t9.60\t6.64\t4.10\t1.95\t4.18\t6.40\t1.09\t5.10\t4.40\t4.84\t1.89\t3.12\t1.10\t3.81\t2.65\t1.98\t3.45\t3.82\t2.56\t8.37\t2.03\t1.78\n+api-miR-971\t334.00\tapi-mir-971\t334.00\t1.00\t13.00\t13.00\t9.00\t12.00\t18.00\t14.00\t10.00\t21.00\t4.00\t1.00\t7.00\t3.00\t20.00\t12.00\t16.00\t9.00\t5.00\t13.00\t7.00\t16.00\t29.00\t10.00\t17.00\t18.00\t11.00\t18.00\t7.00\t0.46\t33.42\t9.15\t5.46\t8.21\t18.99\t8.96\t5.53\t4.54\t0.78\t1.39\t2.99\t1.09\t4.86\t4.06\t4.56\t17.00\t1.42\t7.18\t3.81\t2.65\t8.19\t2.30\t6.49\t5.12\t11.51\t7.30\t2.07\n+api-miR-981\t517.00\tapi-mir-981\t517.00\t30.00\t9.00\t22.00\t32.00\t17.00\t15.00\t23.00\t37.00\t15.00\t6.00\t1.00\t2.00\t14.00\t17.00\t14.00\t22.00\t6.00\t19.00\t6.00\t5.00\t50.00\t21.00\t20.00\t28.00\t30.00\t13.00\t17.00\t26.00\t13.86\t23.13\t15.48\t19.40\t11.63\t15.83\t14.73\t20.48\t3.24\t1.17\t1.39\t0.85\t5.11\t4.13\t4.73\t6.26\t11.33\t5.39\t3.31\t2.72\t8.27\t5.93\t4.60\t10.69\t8.54\t13.60\t6.90\t7.70\n+api-miR-993\t11230.00\tapi-mir-993\t11230.00\t267.00\t66.00\t249.00\t276.00\t197.00\t226.00\t285.00\t329.00\t530.00\t604.00\t135.00\t392.00\t290.00\t763.00\t594.00\t766.00\t71.00\t605.00\t372.00\t335.00\t626.00\t513.00\t602.00\t443.00\t400.00\t191.00\t469.00\t634.00\t123.34\t169.65\t175.18\t167.35\t134.82\t238.43\t182.48\t182.06\t114.47\t117.76\t187.92\t167.33\t105.85\t185.40\t200.82\t218.09\t134.12\t171.52\t205.49\t182.45\t103.52\t144.83\t138.44\t169.12\t113.82\t199.89\t190.25\t187.80\n+api-miR-996\t580.00\tapi-mir-996\t580.00\t22.00\t8.00\t27.00\t12.00\t13.00\t7.00\t20.00\t12.00\t9.00\t26.00\t13.00\t30.00\t2.00\t49.00\t47.00\t67.00\t3.00\t21.00\t24.00\t20.00\t18.00\t25.00\t26.00\t18.00\t7.00\t11.00\t25.00\t18.00\t10.16\t20.56\t19.00\t7.28\t8.90\t7.39\t12.81\t6.64\t1.94\t5.07\t18.10\t12.81\t0.73\t11.91\t15.89\t19.08\t5.67\t5.95\t13.26\t10.89\t2.98\t7.06\t5.98\t6.87\t1.99\t11.51\t10.14\t5.33\n+api-miR-998\t815739.00\tapi-mir-998\t815739.00\t12482.00\t3298.00\t14188.00\t16915.00\t8609.00\t9846.00\t17132.00\t17357.00\t45277.00\t73639.00\t15634.00\t43134.00\t20820.00\t46131.00\t44572.00\t50662.00\t4943.00\t53632.00\t27863.00\t30230.00\t52123.00\t26874.00\t41591.00\t33179.00\t20736.00\t10747.00\t29075.00\t45050.00\t5766.08\t8477.58\t9981.64\t10256.25\t5891.74\t10387.73\t10969.02\t9605.15\t9779.32\t14357.36\t21762.25\t18412.20\t7599.08\t11209.49\t15069.00\t14424.41\t9337.21\t15204.49\t15391.58\t16463.70\t8619.19\t7586.92\t9564.83\t12666.17\t5900.46\t11246.95\t11794.47\t13344.14\n+api-miR-9a\t23047.00\tapi-mir-9a\t23047.00\t673.00\t229.00\t595.00\t789.00\t385.00\t687.00\t681.00\t898.00\t1326.00\t1521.00\t286.00\t811.00\t454.00\t1209.00\t876.00\t1278.00\t191.00\t1181.00\t717.00\t677.00\t1217.00\t892.00\t1258.00\t935.00\t894.00\t366.00\t844.00\t1177.00\t310.89\t588.65\t418.60\t478.40\t263.48\t724.80\t436.02\t496.94\t286.40\t296.55\t398.11\t346.18\t165.71\t293.78\t296.16\t363.87\t360.79\t334.81\t396.07\t368.70\t201.25\t251.82\t289.31\t356.94\t254.39\t383.03\t342.37\t348.64\n+api-miR-9b\t10304.00\tapi-mir-9b\t10304.00\t225.00\t84.00\t251.00\t290.00\t184.00\t235.00\t296.00\t370.00\t576.00\t642.00\t140.00\t371.00\t281.00\t617.00\t518.00\t557.00\t76.00\t478.00\t335.00\t330.00\t660.00\t350.00\t475.00\t484.00\t351.00\t168.00\t393.00\t567.00\t103.94\t215.92\t176.59\t175.84\t125.92\t247.93\t189.52\t204.75\t124.41\t125.17\t194.88\t158.37\t102.56\t149.93\t175.13\t158.59\t143.56\t135.51\t185.05\t179.72\t109.14\t98.81\t109.24\t184.77\t99.88\t175.82\t159.42\t167.95\n+api-miR-iab-4\t251.00\tapi-mir-iab-4\t251.00\t5.00\t1.00\t10.00\t4.00\t6.00\t1.00\t6.00\t6.00\t11.00\t21.00\t8.00\t18.00\t4.00\t17.00\t11.00\t21.00\t3.00\t15.00\t6.00\t10.00\t10.00\t7.00\t10.00\t11.00\t6.00\t0\t7.00\t16.00\t2.31\t2.57\t7.04\t2.43\t4.11\t1.06\t3.84\t3.32\t2.38\t4.09\t11.14\t7.68\t1.46\t4.13\t3.72\t5.98\t5.67\t4.25\t3.31\t5.45\t1.65\t1.98\t2.30\t4.20\t1.71\t0\t2.84\t4.74\n' 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